From dccaa9350a239b3a9336da3aeffaf2e2e3f3480d Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Tue, 10 Sep 2024 17:43:04 -0400
Subject: [PATCH 01/98] [BI-2304] - updated getEntryNumber

---
 src/breeding-insight/utils/GermplasmUtils.ts | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/breeding-insight/utils/GermplasmUtils.ts b/src/breeding-insight/utils/GermplasmUtils.ts
index 87f911fbd..5415fe46d 100644
--- a/src/breeding-insight/utils/GermplasmUtils.ts
+++ b/src/breeding-insight/utils/GermplasmUtils.ts
@@ -48,8 +48,7 @@ export class GermplasmUtils {
 
     static getEntryNumber(germplasm: Germplasm, referenceId: string | undefined): string | undefined {
         if (germplasm.additionalInfo) {
-            return referenceId ? germplasm.additionalInfo.listEntryNumbers[<any>referenceId] :
-                germplasm.additionalInfo.importEntryNumber;
+            return germplasm.additionalInfo.importEntryNumber;
         }
         return "";
     }

From 5d237519bb8176ac07956129d8ab6ac6ccc3e0e4 Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Wed, 11 Sep 2024 16:22:35 -0400
Subject: [PATCH 02/98] [BI-2129] - Accessibility: Germplasm Table Fixes

---
 src/components/germplasm/GermplasmLink.vue | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/components/germplasm/GermplasmLink.vue b/src/components/germplasm/GermplasmLink.vue
index 7a9e1d4e7..0e795550f 100644
--- a/src/components/germplasm/GermplasmLink.vue
+++ b/src/components/germplasm/GermplasmLink.vue
@@ -16,10 +16,10 @@
   -->
 
 <template>
-    <router-link v-if="this.germplasmUUID" v-bind:to="{name: 'germplasm-details', params: {programId: activeProgram.id, germplasmId: this.germplasmUUID}}">
+    <router-link v-if="this.germplasmUUID && this.germplasmUUID!=''" v-bind:to="{name: 'germplasm-details', params: {programId: activeProgram.id, germplasmId: this.germplasmUUID}}">
       {{ this.germplasmGID }}
     </router-link>
-    <router-link v-else v-bind:to="{name: 'germplasm-details', params: {programId: activeProgram.id, germplasmId: 'gid-'+this.germplasmGID}}">
+    <router-link v-else-if="this.germplasmGID && this.germplasmGID!=''" v-bind:to="{name: 'germplasm-details', params: {programId: activeProgram.id, germplasmId: 'gid-'+this.germplasmGID}}">
       {{ this.germplasmGID }}
     </router-link>
 </template>
@@ -43,7 +43,6 @@ export default class GermplasmLink extends Vue {
   private germplasmUUID!: String;
   @Prop()
   private germplasmGID!: String;
-
 }
 
 </script>

From 8cb792c13494c6b06cb9278178543cdf2630f800 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Wed, 18 Sep 2024 14:11:11 +0000
Subject: [PATCH 03/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index e876f7d0f..d838311d9 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v0.10.0+731",
+  "version": "v0.10.0+737",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/1a514f677b9488cec2cd0202aeb30c2a5ea9a0e3"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/048c7b4e4be0eee396c474f98645cb1697d672f5"
 }

From a93cabe85664a639f724d2a4d4d40ccebfdbcd15 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Wed, 11 Sep 2024 15:33:17 -0400
Subject: [PATCH 04/98] [BI-2255] seperated 'editable' logic (based on
 user-rights) and 'currentTraitEditable' logic (based on if trait is already
 used in an experiment).

---
 src/components/ontology/OntologyTable.vue    | 3 ++-
 src/components/trait/TraitDetailPanel.vue    | 7 +++++--
 src/components/trait/forms/BaseTraitForm.vue | 6 ++++--
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/components/ontology/OntologyTable.vue b/src/components/ontology/OntologyTable.vue
index b2b58681a..35b255f7f 100644
--- a/src/components/ontology/OntologyTable.vue
+++ b/src/components/ontology/OntologyTable.vue
@@ -154,7 +154,8 @@
             v-bind:entity-options="entityOptions"
             v-bind:attribute-options="attributeOptions"
             v-bind:edit-active="traitSidePanelState.editActive"
-            v-bind:editable="$ability.can('update', 'Trait') && currentTraitEditable"
+            v-bind:editable="$ability.can('update', 'Trait')"
+            v-bind:currentTraitEditable="currentTraitEditable"
             v-bind:loading-editable="loadingTraitEditable"
             v-bind:edit-form-state="traitSidePanelState.dataFormState"
             v-bind:client-validations="traitValidations"
diff --git a/src/components/trait/TraitDetailPanel.vue b/src/components/trait/TraitDetailPanel.vue
index eb0fe2fdf..302584eba 100644
--- a/src/components/trait/TraitDetailPanel.vue
+++ b/src/components/trait/TraitDetailPanel.vue
@@ -185,12 +185,11 @@
           </div>
         </template>
       </div>
-
       <!-- maybe break out controls for reuse eventually -->
       <div v-if="!isSubscribed" class="columns is-centered is-mobile is-variable is-multiline is-0 my-0">
         <div class="column is-half p-0 mt-5">
           <a
-              v-if="!data.isDup"
+              v-if="!data.isDup && editable"
               v-on:click="$emit('activate-edit', data)"
               v-on:keypress.enter.space="$emit('activate-edit', data)"
               tabindex="0"
@@ -212,6 +211,7 @@
         v-bind:data-form-state="editFormState"
         v-on:show-error-notification="$emit('show-error-notification', $event)"
       >
+
         <template v-slot="validations">
           <BaseTraitForm
               v-bind:trait.sync="editTrait"
@@ -229,6 +229,7 @@
               v-bind:client-validations="validations"
               v-bind:validation-handler="validationHandler"
               v-bind:editable="editable"
+              v-bind:currentTraitEditable="currentTraitEditable"
               v-bind:editable-check-loading="loadingEditable"
               v-bind:from-import-table="fromImportTable"
           ></BaseTraitForm>
@@ -280,6 +281,8 @@
     private editActive!: boolean;
     @Prop()
     private editable!: boolean | undefined;
+    @Prop()
+    private currentTraitEditable!: boolean | undefined;
     @Prop({default: true})
     private loadingEditable!: boolean;
     @Prop({default: false})
diff --git a/src/components/trait/forms/BaseTraitForm.vue b/src/components/trait/forms/BaseTraitForm.vue
index 93014318f..89e27c62a 100644
--- a/src/components/trait/forms/BaseTraitForm.vue
+++ b/src/components/trait/forms/BaseTraitForm.vue
@@ -20,7 +20,7 @@
   </div>
 
   <div class="column is-full">
-    <article v-if="!editable && !editableCheckLoading && !fromImportTable && $ability.can('update', 'Trait')" class="message is-primary mb-3">
+    <article v-if="!currentTraitEditable && !editableCheckLoading && !fromImportTable && $ability.can('update', 'Trait')" class="message is-primary mb-3">
       <div class="message-body">
         <div class="media">
           <figure class="media-left">
@@ -38,7 +38,7 @@
     </article>
 
   </div>
-  <template v-if="editable">
+  <template v-if="currentTraitEditable">
 <!-- term type -->
   <div class="column is-2">
     <span class="is-pulled-right required new-term pb-2 pr-3">Term Type</span>
@@ -379,6 +379,8 @@ export default class BaseTraitForm extends Vue {
   @Prop()
   editable!: boolean;
   @Prop()
+  currentTraitEditable!: boolean;
+  @Prop()
   editableCheckLoading!: boolean;
   @Prop({default: false})
   private fromImportTable!: boolean;

From 37e32215c4f98aa2f6992c76ba9ac805f3f1b382 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Mon, 16 Sep 2024 10:24:02 -0400
Subject: [PATCH 05/98] [BI-2255] Fixed bug - When adding new trait, got bad
 error message

---
 src/components/ontology/OntologyTable.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/components/ontology/OntologyTable.vue b/src/components/ontology/OntologyTable.vue
index 35b255f7f..2f1cbf1c0 100644
--- a/src/components/ontology/OntologyTable.vue
+++ b/src/components/ontology/OntologyTable.vue
@@ -91,6 +91,7 @@
             v-bind:validation-handler="validationHandler"
             v-bind:editable-check-loading="false"
             v-bind:editable="true"
+            v-bind:currentTraitEditable="true"
         ></BaseTraitForm>
       </template>
     </NewDataForm>

From d1dd7bfc3ed86390d15b6aaa4fbe91a2e7165a70 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Thu, 19 Sep 2024 14:16:46 +0000
Subject: [PATCH 06/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index d838311d9..de240ffa3 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v0.10.0+737",
+  "version": "v0.10.0+739",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/048c7b4e4be0eee396c474f98645cb1697d672f5"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/4874a820dad82506e92482efc509635e6c475e6c"
 }

From 926c4b018f22c6c1772c3a1a9bc42caa61e91715 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Wed, 11 Sep 2024 11:55:44 -0400
Subject: [PATCH 07/98] [BI-2224] Show 'New Observations', 'Existing
 Observatins', and 'Mutated Observations' count

---
 src/views/import/ImportExperiment.vue | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/views/import/ImportExperiment.vue b/src/views/import/ImportExperiment.vue
index e8e807dee..1eb597cca 100644
--- a/src/views/import/ImportExperiment.vue
+++ b/src/views/import/ImportExperiment.vue
@@ -72,7 +72,10 @@
             <br>Germplasm: {{ statistics.GIDs.newObjectCount }}
             <br>Environment(s): {{ statistics.Environments.newObjectCount }}
             <br>Observation Variables: {{ dynamicColumns.length }}
-            <br>Observations: {{ statistics.Observations.newObjectCount }}
+            <br>New Observations: {{ statistics.Observations.newObjectCount }}
+            <br>Existing Observations: {{ statistics.Existing_Observations.newObjectCount }}
+            <br>Mutated Observations: {{ statistics.Mutated_Observations.newObjectCount }}
+
           </div>
           </div>
         </ConfirmImportMessageBox>

From 49520537257aab79134152006e84b65bb9fbb5b4 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Mon, 16 Sep 2024 09:10:09 -0400
Subject: [PATCH 08/98] [BI-2224] WIP

---
 src/views/import/ImportExperiment.vue | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/views/import/ImportExperiment.vue b/src/views/import/ImportExperiment.vue
index 1eb597cca..47039dab8 100644
--- a/src/views/import/ImportExperiment.vue
+++ b/src/views/import/ImportExperiment.vue
@@ -72,9 +72,15 @@
             <br>Germplasm: {{ statistics.GIDs.newObjectCount }}
             <br>Environment(s): {{ statistics.Environments.newObjectCount }}
             <br>Observation Variables: {{ dynamicColumns.length }}
-            <br>New Observations: {{ statistics.Observations.newObjectCount }}
-            <br>Existing Observations: {{ statistics.Existing_Observations.newObjectCount }}
-            <br>Mutated Observations: {{ statistics.Mutated_Observations.newObjectCount }}
+            <span v-if="statistics.Existing_Observations.newObjectCount = 0" >
+              <br>Observations: {{ statistics.Observations.newObjectCount }}
+            </span>
+            <span v-else>
+              <br>NewObservations: {{ statistics.Observations.newObjectCount }}
+              <br>Existing Observations: {{ statistics.Existing_Observations.newObjectCount }}
+              <br>Mutated Observations: {{ statistics.Mutated_Observations.newObjectCount }}
+            </span>
+
 
           </div>
           </div>

From 204d647de6ced0c4566454b9add89e2b9b8837bf Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Mon, 16 Sep 2024 11:51:25 -0400
Subject: [PATCH 09/98] [BI-2224] Used the isExisting() method to determine
 workflow

---
 src/views/import/ImportExperiment.vue | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/views/import/ImportExperiment.vue b/src/views/import/ImportExperiment.vue
index 47039dab8..7521fec6f 100644
--- a/src/views/import/ImportExperiment.vue
+++ b/src/views/import/ImportExperiment.vue
@@ -72,14 +72,15 @@
             <br>Germplasm: {{ statistics.GIDs.newObjectCount }}
             <br>Environment(s): {{ statistics.Environments.newObjectCount }}
             <br>Observation Variables: {{ dynamicColumns.length }}
-            <span v-if="statistics.Existing_Observations.newObjectCount = 0" >
-              <br>Observations: {{ statistics.Observations.newObjectCount }}
-            </span>
-            <span v-else>
-              <br>NewObservations: {{ statistics.Observations.newObjectCount }}
+
+            <span v-if="isExisting(rows)" >
+              <br>New Observations: {{ statistics.Observations.newObjectCount }}
               <br>Existing Observations: {{ statistics.Existing_Observations.newObjectCount }}
               <br>Mutated Observations: {{ statistics.Mutated_Observations.newObjectCount }}
             </span>
+            <span v-else>
+              <br>Observations: {{ statistics.Observations.newObjectCount }}
+            </span>
 
 
           </div>

From 45136fbe6fcfd6f995a0eaf101e4798a51661759 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Thu, 19 Sep 2024 09:41:16 -0400
Subject: [PATCH 10/98] [BI-2224] Changed wording from 'Mutated' to
 'Overwritten'

---
 src/views/import/ImportExperiment.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/views/import/ImportExperiment.vue b/src/views/import/ImportExperiment.vue
index 7521fec6f..425752fb1 100644
--- a/src/views/import/ImportExperiment.vue
+++ b/src/views/import/ImportExperiment.vue
@@ -76,7 +76,7 @@
             <span v-if="isExisting(rows)" >
               <br>New Observations: {{ statistics.Observations.newObjectCount }}
               <br>Existing Observations: {{ statistics.Existing_Observations.newObjectCount }}
-              <br>Mutated Observations: {{ statistics.Mutated_Observations.newObjectCount }}
+              <br>Overwritten Observations: {{ statistics.Mutated_Observations.newObjectCount }}
             </span>
             <span v-else>
               <br>Observations: {{ statistics.Observations.newObjectCount }}

From c95aa42f7a81cfa595c143b30cf5b893204affda Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 23 Sep 2024 17:45:23 +0000
Subject: [PATCH 11/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index de240ffa3..30adf3c72 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v0.10.0+739",
+  "version": "v0.10.0+741",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/4874a820dad82506e92482efc509635e6c475e6c"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/2da22c470f0089ba315a861da353b8e3459b6326"
 }

From 0b642ecde79b7cbbaf648880dfa5ae80ea1948a5 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Wed, 25 Sep 2024 16:28:04 -0400
Subject: [PATCH 12/98] [BI-1933] - fixed duplicate API call

---
 src/components/germplasm/GermplasmTable.vue | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/components/germplasm/GermplasmTable.vue b/src/components/germplasm/GermplasmTable.vue
index 0d0228a3d..621f40d26 100644
--- a/src/components/germplasm/GermplasmTable.vue
+++ b/src/components/germplasm/GermplasmTable.vue
@@ -155,8 +155,6 @@ export default class GermplasmTable extends Vue {
         this.germplasmSort,
         this.paginationController
     ));
-
-    this.getGermplasm();
   }
 
   @Watch('paginationController', { deep: true})

From 22ee565d4d48aed0a68252bb07b80c644c0e6dcd Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Tue, 1 Oct 2024 14:15:07 -0400
Subject: [PATCH 13/98] [BI-1933] - reset loading flag in fetch function

---
 src/components/germplasm/GermplasmTable.vue | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/components/germplasm/GermplasmTable.vue b/src/components/germplasm/GermplasmTable.vue
index 621f40d26..d0b42a800 100644
--- a/src/components/germplasm/GermplasmTable.vue
+++ b/src/components/germplasm/GermplasmTable.vue
@@ -175,6 +175,9 @@ export default class GermplasmTable extends Vue {
 
   @Watch('filters', {deep: true})
   async getGermplasm() {
+    // Set loading = true so the table shows a loading indicator rather than an "empty" message.
+    this.germplasmLoading = true;
+
     try {
       // Only process the most recent call
       const {call, callId} = this.germplasmCallStack.makeCall(this.filters);

From c4382c09c0346a3bab48e2352dcc2413d24156ce Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Tue, 1 Oct 2024 14:37:22 -0400
Subject: [PATCH 14/98] [BI-1933] - added paginationCall to mounted()

---
 src/components/germplasm/GermplasmTable.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/components/germplasm/GermplasmTable.vue b/src/components/germplasm/GermplasmTable.vue
index d0b42a800..34438d2a5 100644
--- a/src/components/germplasm/GermplasmTable.vue
+++ b/src/components/germplasm/GermplasmTable.vue
@@ -155,6 +155,7 @@ export default class GermplasmTable extends Vue {
         this.germplasmSort,
         this.paginationController
     ));
+    this.paginationChanged();
   }
 
   @Watch('paginationController', { deep: true})

From 4598b7fada5e42034c7bea43343f4caf5c3a0263 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Wed, 2 Oct 2024 10:09:26 -0400
Subject: [PATCH 15/98] [BI-1933] - updated tables that use pagination
 controller

---
 src/components/admin/AdminProgramsTable.vue                 | 3 ++-
 src/components/admin/AdminUsersTable.vue                    | 3 ++-
 src/components/experiments/ExperimentsObservationsTable.vue | 2 ++
 src/components/germplasm/GermplasmListsTable.vue            | 3 ++-
 src/components/ontology/OntologyTable.vue                   | 3 ++-
 src/components/program/ProgramLocationsTable.vue            | 3 ++-
 src/components/program/ProgramUsersTable.vue                | 3 ++-
 src/components/tables/expandableTable/ExpandableTable.vue   | 2 +-
 src/components/trait/TraitsImportTable.vue                  | 3 ++-
 9 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/src/components/admin/AdminProgramsTable.vue b/src/components/admin/AdminProgramsTable.vue
index 48d74fece..1d5c6e46c 100644
--- a/src/components/admin/AdminProgramsTable.vue
+++ b/src/components/admin/AdminProgramsTable.vue
@@ -312,8 +312,8 @@ export default class AdminProgramsTable extends Vue {
 
   mounted() {
     this.updatePagination();
-    this.getPrograms();
     this.getSpecies();
+    this.paginationChanged();
   }
 
   setSort(field: string, order: string) {
@@ -348,6 +348,7 @@ export default class AdminProgramsTable extends Vue {
   }
 
   getPrograms() {
+    this.programsLoading = true;
     ProgramService.getAll(this.paginationController.currentCall, this.programSort).then(([programs, metadata]) => {
 
       // Check that our most recent query is this one
diff --git a/src/components/admin/AdminUsersTable.vue b/src/components/admin/AdminUsersTable.vue
index 6cc2159c4..019069a11 100644
--- a/src/components/admin/AdminUsersTable.vue
+++ b/src/components/admin/AdminUsersTable.vue
@@ -297,7 +297,7 @@ export default class AdminUsersTable extends Vue {
   mounted() {
     this.getRoles();
     this.updatePagination();
-    this.getUsers();
+    this.paginationChanged();
   }
 
     setSort(field: string, order: string) {
@@ -344,6 +344,7 @@ export default class AdminUsersTable extends Vue {
   }
 
   getUsers() {
+    this.usersLoading = true;
     UserService.getAll(this.paginationController.currentCall, this.systemUserSort).then(([users, metadata]) => {
       if (this.paginationController.matchesCurrentRequest(metadata.pagination)){
         this.users = users;
diff --git a/src/components/experiments/ExperimentsObservationsTable.vue b/src/components/experiments/ExperimentsObservationsTable.vue
index 4e8568ce6..cdf332ab9 100644
--- a/src/components/experiments/ExperimentsObservationsTable.vue
+++ b/src/components/experiments/ExperimentsObservationsTable.vue
@@ -154,6 +154,7 @@ export default class ExperimentsObservationsTable extends Vue {
     ));
 
     this.paginationController.pageSize = 20;
+    this.paginationChanged();
   }
 
   @Watch('paginationController', { deep: true})
@@ -174,6 +175,7 @@ export default class ExperimentsObservationsTable extends Vue {
 
   @Watch('filters', {deep: true})
   async getExperiments() {
+    this.experimentsLoading = true;
     try {
       const {call, callId} = this.experimentCallStack.makeCall(this.filters);
 
diff --git a/src/components/germplasm/GermplasmListsTable.vue b/src/components/germplasm/GermplasmListsTable.vue
index ab629778c..4e1a6ea63 100644
--- a/src/components/germplasm/GermplasmListsTable.vue
+++ b/src/components/germplasm/GermplasmListsTable.vue
@@ -162,7 +162,7 @@ export default class GermplasmListsTable extends Vue {
         this.germplasmListSort,
         this.paginationController
     ));
-    this.getGermplasmLists();
+    this.paginationChanged();
   }
 
   @Watch('paginationController', { deep: true})
@@ -183,6 +183,7 @@ export default class GermplasmListsTable extends Vue {
 
   @Watch('filters', {deep: true})
   async getGermplasmLists() {
+    this.germplasmListsLoading = true;
     try {
       const {call, callId} = this.germplasmListCallStack.makeCall(this.filters);
       const response = await call;
diff --git a/src/components/ontology/OntologyTable.vue b/src/components/ontology/OntologyTable.vue
index 2f1cbf1c0..0be298ce9 100644
--- a/src/components/ontology/OntologyTable.vue
+++ b/src/components/ontology/OntologyTable.vue
@@ -339,6 +339,7 @@ export default class OntologyTable extends Vue {
   ontologySort!: OntologySort;
 
   mounted() {
+    this.paginationController.pageSize = 200;
     this.getSubscribedOntology();
     this.getObservationLevels();
     this.getAttributesEntitiesDescriptions();
@@ -349,7 +350,7 @@ export default class OntologyTable extends Vue {
         this.paginationController
     ));
     this.registerSidePanelEventHandlers();
-    this.getTraits();
+    this.paginationChanged();
   }
 
   @Watch('paginationController', { deep: true})
diff --git a/src/components/program/ProgramLocationsTable.vue b/src/components/program/ProgramLocationsTable.vue
index 9e61cf2ac..8527d61bf 100644
--- a/src/components/program/ProgramLocationsTable.vue
+++ b/src/components/program/ProgramLocationsTable.vue
@@ -194,7 +194,7 @@ export default class ProgramLocationsTable extends Vue {
 
   mounted() {
     this.updatePagination();
-    this.getLocations();
+    this.paginationChanged();
   }
 
   setSort(field: string, order: string) {
@@ -222,6 +222,7 @@ export default class ProgramLocationsTable extends Vue {
   }
 
   getLocations() {
+    this.locationsLoading = true;
     ProgramLocationService.getAll(this.activeProgram!.id!, this.paginationController.currentCall, this.locationSort).then(([programLocations, metadata]) => {
       if (this.paginationController.matchesCurrentRequest(metadata.pagination)){
         this.locations = programLocations;
diff --git a/src/components/program/ProgramUsersTable.vue b/src/components/program/ProgramUsersTable.vue
index de9faa87b..9425a854a 100644
--- a/src/components/program/ProgramUsersTable.vue
+++ b/src/components/program/ProgramUsersTable.vue
@@ -253,8 +253,8 @@ export default class ProgramUsersTable extends Vue {
   mounted() {
     this.updatePagination();
     this.getRoles();
-    this.getUsers();
     this.getSystemUsers();
+    this.paginationChanged();
   }
 
   setSort(field: string, order: string) {
@@ -286,6 +286,7 @@ export default class ProgramUsersTable extends Vue {
   }
 
   getUsers() {
+    this.usersLoading = true;
     ProgramUserService.getAll(this.activeProgram!.id!, this.paginationController.currentCall, this.programUserSort).then(([programUsers, metadata]) => {
       if (this.paginationController.matchesCurrentRequest(metadata.pagination)){
         this.users = programUsers;
diff --git a/src/components/tables/expandableTable/ExpandableTable.vue b/src/components/tables/expandableTable/ExpandableTable.vue
index d517c7100..8774af218 100644
--- a/src/components/tables/expandableTable/ExpandableTable.vue
+++ b/src/components/tables/expandableTable/ExpandableTable.vue
@@ -74,7 +74,7 @@
         </a>
       </b-table-column>
 
-      <template v-slot:empty v-if="this.loading !== true">
+      <template v-slot:empty v-if="!loading">
         <slot name="emptyMessage" />
       </template>
 
diff --git a/src/components/trait/TraitsImportTable.vue b/src/components/trait/TraitsImportTable.vue
index 201009026..fab2191e5 100644
--- a/src/components/trait/TraitsImportTable.vue
+++ b/src/components/trait/TraitsImportTable.vue
@@ -250,7 +250,7 @@ export default class TraitsImportTable extends Vue {
 
   mounted() {
     this.updatePagination();
-    this.getTraitUpload();
+    this.paginationChanged();
   }
 
   @Watch('paginationController', { deep: true})
@@ -271,6 +271,7 @@ export default class TraitsImportTable extends Vue {
 
   @Watch('importPreviewOntologySort', {deep: true})
   getTraitUpload() {
+    this.loaded = false;
     TraitUploadService.getTraits(this.activeProgram!.id!, this.paginationController.currentCall, this.importPreviewOntologySort).then(([upload, metadata]) => {
       if (this.paginationController.matchesCurrentRequest(metadata.pagination)){
         this.traits = upload.data || [];

From 51aeadb98789d03e763d6496514c703c34c59958 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Wed, 2 Oct 2024 15:48:17 -0400
Subject: [PATCH 16/98] [BI-1933] - fixed pagination bug

---
 src/components/admin/AdminProgramsTable.vue      | 3 +--
 src/components/admin/AdminUsersTable.vue         | 1 -
 src/components/program/ProgramLocationsTable.vue | 1 -
 src/components/program/ProgramUsersTable.vue     | 1 -
 src/components/trait/TraitsImportTable.vue       | 1 -
 5 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/src/components/admin/AdminProgramsTable.vue b/src/components/admin/AdminProgramsTable.vue
index 1d5c6e46c..614ee0be7 100644
--- a/src/components/admin/AdminProgramsTable.vue
+++ b/src/components/admin/AdminProgramsTable.vue
@@ -311,7 +311,6 @@ export default class AdminProgramsTable extends Vue {
   }
 
   mounted() {
-    this.updatePagination();
     this.getSpecies();
     this.paginationChanged();
   }
@@ -333,7 +332,7 @@ export default class AdminProgramsTable extends Vue {
 
   @Watch('paginationController', { deep: true})
   paginationChanged() {
-    let currentCall = this.paginationController.currentCall
+    let currentCall = this.paginationController.currentCall;
     let paginationQuery = this.paginationController.getPaginationSelections();
     if(currentCall && currentCall!.page == paginationQuery.page && currentCall!.pageSize == paginationQuery.pageSize && currentCall!.showAll == paginationQuery.showAll) {
       return;
diff --git a/src/components/admin/AdminUsersTable.vue b/src/components/admin/AdminUsersTable.vue
index 019069a11..7a181ce33 100644
--- a/src/components/admin/AdminUsersTable.vue
+++ b/src/components/admin/AdminUsersTable.vue
@@ -296,7 +296,6 @@ export default class AdminUsersTable extends Vue {
 
   mounted() {
     this.getRoles();
-    this.updatePagination();
     this.paginationChanged();
   }
 
diff --git a/src/components/program/ProgramLocationsTable.vue b/src/components/program/ProgramLocationsTable.vue
index 8527d61bf..cd9c10864 100644
--- a/src/components/program/ProgramLocationsTable.vue
+++ b/src/components/program/ProgramLocationsTable.vue
@@ -193,7 +193,6 @@ export default class ProgramLocationsTable extends Vue {
   }
 
   mounted() {
-    this.updatePagination();
     this.paginationChanged();
   }
 
diff --git a/src/components/program/ProgramUsersTable.vue b/src/components/program/ProgramUsersTable.vue
index 9425a854a..ef66b26c6 100644
--- a/src/components/program/ProgramUsersTable.vue
+++ b/src/components/program/ProgramUsersTable.vue
@@ -251,7 +251,6 @@ export default class ProgramUsersTable extends Vue {
   }
 
   mounted() {
-    this.updatePagination();
     this.getRoles();
     this.getSystemUsers();
     this.paginationChanged();
diff --git a/src/components/trait/TraitsImportTable.vue b/src/components/trait/TraitsImportTable.vue
index fab2191e5..887cad27c 100644
--- a/src/components/trait/TraitsImportTable.vue
+++ b/src/components/trait/TraitsImportTable.vue
@@ -249,7 +249,6 @@ export default class TraitsImportTable extends Vue {
   private fullNameSortLabel: string = OntologySortField.FullName;
 
   mounted() {
-    this.updatePagination();
     this.paginationChanged();
   }
 

From c76a138a5d4c6bb73e924dc07c561a080dbf7ba0 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 7 Oct 2024 16:18:53 +0000
Subject: [PATCH 17/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 30adf3c72..f4e366cd8 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v0.10.0+741",
+  "version": "v0.10.0+744",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/2da22c470f0089ba315a861da353b8e3459b6326"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/823fd802379f7e4b2036bb3fbd03819ac116be06"
 }

From 4c8f14f24535268d6c1d0cf2a2b2159b0a0c2ba8 Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Mon, 7 Oct 2024 14:40:45 -0400
Subject: [PATCH 18/98] Update version

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index f4e366cd8..4f37206a6 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v0.10.0+744",
+  "version": "v1.1.0+744",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",

From 2f38392546bc5c0732b75c1b0fed7bd80dd96947 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 7 Oct 2024 18:41:00 +0000
Subject: [PATCH 19/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 4f37206a6..f9b80b65f 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.1.0+744",
+  "version": "v1.1.0+749",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/823fd802379f7e4b2036bb3fbd03819ac116be06"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/4c8f14f24535268d6c1d0cf2a2b2159b0a0c2ba8"
 }

From f465031cc6379a4b8431e34fb942c279fbbc93ca Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Tue, 8 Oct 2024 11:11:39 -0400
Subject: [PATCH 20/98] [BI-1933] - tweaked TraitsImportTable.vue

---
 src/components/trait/TraitsImportTable.vue | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/components/trait/TraitsImportTable.vue b/src/components/trait/TraitsImportTable.vue
index 887cad27c..ac7894251 100644
--- a/src/components/trait/TraitsImportTable.vue
+++ b/src/components/trait/TraitsImportTable.vue
@@ -270,7 +270,6 @@ export default class TraitsImportTable extends Vue {
 
   @Watch('importPreviewOntologySort', {deep: true})
   getTraitUpload() {
-    this.loaded = false;
     TraitUploadService.getTraits(this.activeProgram!.id!, this.paginationController.currentCall, this.importPreviewOntologySort).then(([upload, metadata]) => {
       if (this.paginationController.matchesCurrentRequest(metadata.pagination)){
         this.traits = upload.data || [];

From 5fe64acd368b7f4352201eee9f4d558ba77b2da2 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Tue, 8 Oct 2024 15:14:09 +0000
Subject: [PATCH 21/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index f9b80b65f..fb2e2fb2f 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.1.0+749",
+  "version": "v1.1.0+751",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/4c8f14f24535268d6c1d0cf2a2b2159b0a0c2ba8"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/5f4732b7513c163af9e03058fb106bfb59a25bed"
 }

From e7cd686d963360afdb01bcda4fe855bd38075523 Mon Sep 17 00:00:00 2001
From: sb2597 <62260853+sb2597@users.noreply.github.com>
Date: Mon, 4 Nov 2024 15:37:20 -0500
Subject: [PATCH 22/98] Update pull_request_template.md

(Accessibility) Added check for SiteImprove to the PR checklist
---
 .github/pull_request_template.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index 79c205060..24004a490 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -20,3 +20,4 @@ _Please include any details needed for reviewers to test this code_
 - [ ] I have commented my code, particularly in hard-to-understand areas
 - [ ] I have made corresponding changes to documentation
 - [ ] I have run TAF: _\<link to TAF run>_
+- [ ] I have run SiteImprove on pages impacted by changes 

From ab06e6a38b4b558222a9d791460ff6a010fb9c28 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 4 Nov 2024 20:37:31 +0000
Subject: [PATCH 23/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index fb2e2fb2f..26fa73e4d 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.1.0+751",
+  "version": "v1.1.0+765",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/5f4732b7513c163af9e03058fb106bfb59a25bed"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/e7cd686d963360afdb01bcda4fe855bd38075523"
 }

From c0b1aa3168cf992f65942f6c609f9d98772aa97c Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Fri, 8 Nov 2024 16:00:08 +0000
Subject: [PATCH 24/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index b4395373d..1c5bd4007 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+767",
+  "version": "v1.0.0+770",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/6e483dceae69337b62bf5589a4f07ccea9870df4"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/d0751f64faeb6b59c1aae279682aa9150c561334"
 }

From 515f202fdc94109b17f1c20aa2762cbf99e98685 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Fri, 8 Nov 2024 18:26:16 +0000
Subject: [PATCH 25/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 1c5bd4007..1e2bb8471 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+770",
+  "version": "v1.0.0+779",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/d0751f64faeb6b59c1aae279682aa9150c561334"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/0f65a87d67816c618d3ec8df12ae50c47876d03a"
 }

From 2ba9da293e98bfbaa65c5e8158918b336505541f Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Thu, 7 Nov 2024 14:59:38 -0500
Subject: [PATCH 26/98] [BI-2342] observation filter is now case insensitive

---
 src/views/import/Dataset.vue | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/views/import/Dataset.vue b/src/views/import/Dataset.vue
index ec881a4ff..6b84dac85 100644
--- a/src/views/import/Dataset.vue
+++ b/src/views/import/Dataset.vue
@@ -387,7 +387,9 @@ export default class Dataset extends ProgramsBase {
 
   filterByObservations(index: number, propsRow: any, input: string) {
     let obsValue = propsRow.data.traitValues[index];
-    obsValue = obsValue ? obsValue : "";  //convert null or undefined to an empty string
+    //Make case insensitive
+    obsValue = obsValue ? obsValue.toUpperCase() : "";  //convert null or undefined to an empty string;
+    input = input.toUpperCase();
     return obsValue.includes(input);
   }
 

From 8ac74bea863be786adaae4a0c7394593790f18d2 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 11 Nov 2024 16:52:15 +0000
Subject: [PATCH 27/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 1e2bb8471..0e437598d 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+779",
+  "version": "v1.0.0+781",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/0f65a87d67816c618d3ec8df12ae50c47876d03a"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/55e8983ad7d338e975047582ef46a3ffc45a7e4f"
 }

From ab2a53179ae71450604f65ddb173f85baea22d08 Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Fri, 15 Nov 2024 15:31:33 -0500
Subject: [PATCH 28/98] [BI-2343] - GID filtering not informative

---
 src/views/import/Dataset.vue                | 7 +++++++
 src/views/sample-mgmt/SubmissionDetails.vue | 9 ++++++++-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/views/import/Dataset.vue b/src/views/import/Dataset.vue
index 6b84dac85..bd104ec66 100644
--- a/src/views/import/Dataset.vue
+++ b/src/views/import/Dataset.vue
@@ -99,6 +99,7 @@
             sortable
             searchable
             :th-attrs="() => ({scope:'col'})"
+            :custom-search="(props, filterString) => exactSearchGID(props, filterString)"
         >
           {{ props.row.data.gid }}
         </b-table-column>
@@ -405,6 +406,12 @@ export default class Dataset extends ProgramsBase {
     }
   }
 
+  //Filter GIDs by exact match
+  exactSearchGID(props: any, input: string) {
+    let value = props.data.gid;
+    return Number(value) === (Number(input));
+  }
+
   //sort GIDs numerically
   sortGID(a: any, b: any, isAsc: boolean){
     let first :number = parseInt(a.data.gid);
diff --git a/src/views/sample-mgmt/SubmissionDetails.vue b/src/views/sample-mgmt/SubmissionDetails.vue
index aa5d6e74e..3fc24ade1 100644
--- a/src/views/sample-mgmt/SubmissionDetails.vue
+++ b/src/views/sample-mgmt/SubmissionDetails.vue
@@ -154,7 +154,8 @@
               {{ props.row.data.additionalInfo.germplasmName || props.row.data.sampleName }}
             </b-table-column>
             <b-table-column field="data.additionalInfo.gid" label="GID" v-slot="props" searchable
-                            :th-attrs="(column) => ({scope:'col'})">
+                            :th-attrs="(column) => ({scope:'col'})"
+                            :custom-search="(props, filterString) => exactSearchGID(props, filterString)">
               <GermplasmLink
                   v-bind:germplasmGID="props.row.data.additionalInfo.gid"
               />
@@ -707,5 +708,11 @@ export default class SubmissionDetails extends ProgramsBase {
       return b.data.plateName.localeCompare(a.data.plateName, undefined, {numeric: true, sensitivity: 'base'});
     }
   }
+
+  //Filter GIDs by exact match
+  exactSearchGID(props: any, input: string) {
+    let value = props.data.additionalInfo.gid;
+    return Number(value) === (Number(input));
+  }
 }
 </script>
\ No newline at end of file

From 5dcd1a9fd3e1ba9220193f2f8303e92323414389 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Wed, 27 Nov 2024 16:15:19 +0000
Subject: [PATCH 29/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 0e437598d..228ed275d 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+781",
+  "version": "v1.0.0+783",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/55e8983ad7d338e975047582ef46a3ffc45a7e4f"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/3129f1a11a2639fb56dc4036e51019b0b08bf656"
 }

From f6bc13a18f92c19d4b51e551246bc6a4e82c7269 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Thu, 21 Nov 2024 12:05:03 -0500
Subject: [PATCH 30/98] [BI-2124] default germplame lists to creation date
 order (newest on top)

---
 src/components/germplasm/GermplasmListsTable.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/germplasm/GermplasmListsTable.vue b/src/components/germplasm/GermplasmListsTable.vue
index 4e1a6ea63..c5f3f2ad2 100644
--- a/src/components/germplasm/GermplasmListsTable.vue
+++ b/src/components/germplasm/GermplasmListsTable.vue
@@ -23,7 +23,7 @@
       v-bind:pagination="paginationController"
       backend-sorting
       backend-filtering
-      v-bind:default-sort="[fieldMap['name'], 'ASC']"
+      v-bind:default-sort="[fieldMap['dateCreated'], 'Desc']"
       v-on:sort="setSort"
       v-on:search="initSearch"
       v-bind:search-debounce="400"

From cd731f172785454f0b8316ab71067a34d8931c55 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Fri, 13 Dec 2024 16:30:31 +0000
Subject: [PATCH 31/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 228ed275d..9a83e2cb1 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+783",
+  "version": "v1.0.0+785",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/3129f1a11a2639fb56dc4036e51019b0b08bf656"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/c271ee72fc039685c51ee3dbcda713a65ddb89f0"
 }

From c650f58355398c65ec996da3c254f627988a80ef Mon Sep 17 00:00:00 2001
From: dmeidlin <14339308+dmeidlin@users.noreply.github.com>
Date: Wed, 6 Nov 2024 16:19:53 -0500
Subject: [PATCH 32/98] get submission details after update

---
 src/views/sample-mgmt/SubmissionDetails.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/views/sample-mgmt/SubmissionDetails.vue b/src/views/sample-mgmt/SubmissionDetails.vue
index 3fc24ade1..851c37ea9 100644
--- a/src/views/sample-mgmt/SubmissionDetails.vue
+++ b/src/views/sample-mgmt/SubmissionDetails.vue
@@ -622,6 +622,7 @@ export default class SubmissionDetails extends ProgramsBase {
         throw response.value;
       }
       await this.getSubmission(false);
+      await this.getSubmissionDetails();
     } catch (e) {
       this.$emit('show-error-notification', 'Error while trying to update status');
     } finally {

From 92f487982deabda4e5c4957cacd163b3d8eb6e81 Mon Sep 17 00:00:00 2001
From: dmeidlin <14339308+dmeidlin@users.noreply.github.com>
Date: Thu, 7 Nov 2024 10:58:18 -0500
Subject: [PATCH 33/98] fetch sample details

---
 src/views/sample-mgmt/SubmissionDetails.vue | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/views/sample-mgmt/SubmissionDetails.vue b/src/views/sample-mgmt/SubmissionDetails.vue
index 851c37ea9..f9873bc1e 100644
--- a/src/views/sample-mgmt/SubmissionDetails.vue
+++ b/src/views/sample-mgmt/SubmissionDetails.vue
@@ -579,6 +579,7 @@ export default class SubmissionDetails extends ProgramsBase {
       // let orderResponse = response.value;
       // this.submission!.vendorOrderId = orderResponse.orderId;
       await this.getSubmission(false);
+      await this.getSubmissionDetails();
     } catch (e) {
       // this.$emit('show-error-notification', 'Error while trying to submit sample order');
       this.submissionError = e;
@@ -595,6 +596,7 @@ export default class SubmissionDetails extends ProgramsBase {
         throw response.value;
       }
       await this.getSubmission(false);
+      await this.getSubmissionDetails();
     } catch (e) {
       this.$emit('show-error-notification', 'Error while trying to check order status');
     } finally {

From a1ecca787acefc170531dde9100ef115dc54ba16 Mon Sep 17 00:00:00 2001
From: dmeidlin <14339308+dmeidlin@users.noreply.github.com>
Date: Tue, 10 Dec 2024 16:03:01 -0500
Subject: [PATCH 34/98] update package-lock.json

---
 package-lock.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index dc20b309e..e8cbddb6e 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "bi-web",
-  "version": "v0.10.0+723",
+  "version": "v1.0.0+783",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "bi-web",
-      "version": "v0.10.0+723",
+      "version": "v1.0.0+783",
       "hasInstallScript": true,
       "dependencies": {
         "@casl/ability": "~4.0.0",

From ce2cc0ec3c04fc01c42d69d58afccca9d33d422c Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Fri, 20 Dec 2024 15:34:53 +0000
Subject: [PATCH 35/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 9a83e2cb1..40c78874d 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+785",
+  "version": "v1.0.0+787",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/c271ee72fc039685c51ee3dbcda713a65ddb89f0"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/749ec7ad03b3a7d06a420b5fda4f325e79fb8b36"
 }

From 7908fc251cb1c34be5212c317bb9c973d1051062 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Thu, 2 Jan 2025 10:40:12 -0500
Subject: [PATCH 36/98] [BI-2425] - enabled sub-entity menu option

---
 src/views/experiments-and-observations/ExperimentDetails.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/views/experiments-and-observations/ExperimentDetails.vue b/src/views/experiments-and-observations/ExperimentDetails.vue
index 8b27f93c7..20457906c 100644
--- a/src/views/experiments-and-observations/ExperimentDetails.vue
+++ b/src/views/experiments-and-observations/ExperimentDetails.vue
@@ -205,7 +205,7 @@ export default class ExperimentDetails extends ProgramsBase {
       new ActionMenuItem('experiment-import-file', 'import-file', 'Import file', this.$ability.can('create', 'Import')),
       new ActionMenuItem('experiment-download-file', 'download-file', 'Download file'),
       new ActionMenuItem('experiment-add-collaborator', 'add-collaborator', 'Add Collaborator',  this.$ability.can('manage', 'Collaborator')),
-      // new ActionMenuItem('experiment-create-sub-entity-dataset', 'create-sub-entity-dataset', 'Create Sub-Entity Dataset')
+      new ActionMenuItem('experiment-create-sub-entity-dataset', 'create-sub-entity-dataset', 'Create Sub-Entity Dataset')
   ];
 
   mounted () {

From e01424a0b10af6cca211e9246db30a73f39da03e Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Thu, 2 Jan 2025 15:48:32 +0000
Subject: [PATCH 37/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 40c78874d..d8428efcd 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+787",
+  "version": "v1.0.0+789",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/749ec7ad03b3a7d06a420b5fda4f325e79fb8b36"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/c7125bfe6e28c4a5e896f0fb313b96a91dd7bda4"
 }

From 4ca8541fbd02cc15d24dc812c941bb34f38127cb Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Thu, 2 Jan 2025 10:58:53 -0500
Subject: [PATCH 38/98] [BI-2426] - disabled sub-entity menu option

sub-entity features will not be included in v1.1
---
 src/views/experiments-and-observations/ExperimentDetails.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/views/experiments-and-observations/ExperimentDetails.vue b/src/views/experiments-and-observations/ExperimentDetails.vue
index 20457906c..8b27f93c7 100644
--- a/src/views/experiments-and-observations/ExperimentDetails.vue
+++ b/src/views/experiments-and-observations/ExperimentDetails.vue
@@ -205,7 +205,7 @@ export default class ExperimentDetails extends ProgramsBase {
       new ActionMenuItem('experiment-import-file', 'import-file', 'Import file', this.$ability.can('create', 'Import')),
       new ActionMenuItem('experiment-download-file', 'download-file', 'Download file'),
       new ActionMenuItem('experiment-add-collaborator', 'add-collaborator', 'Add Collaborator',  this.$ability.can('manage', 'Collaborator')),
-      new ActionMenuItem('experiment-create-sub-entity-dataset', 'create-sub-entity-dataset', 'Create Sub-Entity Dataset')
+      // new ActionMenuItem('experiment-create-sub-entity-dataset', 'create-sub-entity-dataset', 'Create Sub-Entity Dataset')
   ];
 
   mounted () {

From 28d86bae1b27df3b427639658d62757eefc303f1 Mon Sep 17 00:00:00 2001
From: dmeidlin <14339308+dmeidlin@users.noreply.github.com>
Date: Fri, 15 Nov 2024 12:38:56 -0500
Subject: [PATCH 39/98] add delete option to germplasm list management

---
 src/breeding-insight/dao/GermplasmDAO.ts      |   2 +-
 .../{GermplasmFilter.ts => ListFilter.ts}     |  11 +-
 .../service/GermplasmService.ts               |   5 +-
 src/breeding-insight/service/ListService.ts   | 157 +++++++++++
 .../germplasm/GermplasmListDeletionlModal.vue |  89 +++++++
 src/components/germplasm/GermplasmTable.vue   |   2 +-
 src/store/filtering/getters.ts                |   2 +-
 src/store/filtering/index.ts                  |   2 +-
 src/store/filtering/mutations.ts              |   2 +-
 src/store/filtering/types.ts                  |   2 +-
 src/util/ListType.ts                          |   2 +-
 src/views/germplasm/GermplasmByList.vue       | 252 +++++++++++++-----
 src/views/germplasm/GermplasmLists.vue        |  30 +--
 13 files changed, 470 insertions(+), 88 deletions(-)
 rename src/breeding-insight/model/{GermplasmFilter.ts => ListFilter.ts} (86%)
 create mode 100644 src/breeding-insight/service/ListService.ts
 create mode 100644 src/components/germplasm/GermplasmListDeletionlModal.vue

diff --git a/src/breeding-insight/dao/GermplasmDAO.ts b/src/breeding-insight/dao/GermplasmDAO.ts
index af5eeb1f2..33072750b 100644
--- a/src/breeding-insight/dao/GermplasmDAO.ts
+++ b/src/breeding-insight/dao/GermplasmDAO.ts
@@ -30,7 +30,7 @@ export class GermplasmDAO {
         config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/lists`;
         config.method = 'get';
         config.programId = programId;
-        config.params = {listType: ListType.Germplasm};
+        config.params = {listType: ListType.GERMPLASM};
         if (paginationQuery.page) config.params.page = paginationQuery.page - 1;
         if (paginationQuery.pageSize) config.params.pageSize = paginationQuery.pageSize;
 
diff --git a/src/breeding-insight/model/GermplasmFilter.ts b/src/breeding-insight/model/ListFilter.ts
similarity index 86%
rename from src/breeding-insight/model/GermplasmFilter.ts
rename to src/breeding-insight/model/ListFilter.ts
index 0a0644472..e5bd51ffb 100644
--- a/src/breeding-insight/model/GermplasmFilter.ts
+++ b/src/breeding-insight/model/ListFilter.ts
@@ -18,14 +18,17 @@
 import {GermplasmSortField} from "@/breeding-insight/model/Sort";
 import {BaseFilter} from "@/breeding-insight/model/BaseFilter";
 
-export enum GermplasmBIField {
+export enum ListBIField {
     ListDbId = "listDbId",
     ListName = "listName",
 }
 
-export class GermplasmFilter extends BaseFilter {
-    [GermplasmBIField.ListDbId]: string;
-    [GermplasmBIField.ListName]: string;
+export class ListFilter extends BaseFilter {
+    [ListBIField.ListDbId]: string;
+    [ListBIField.ListName]: string;
+}
+
+export class GermplasmFilter extends ListFilter {
     [GermplasmSortField.AccessionNumber]: string;
     [GermplasmSortField.DefaultDisplayName]: string;
     [GermplasmSortField.BreedingMethod]: string;
diff --git a/src/breeding-insight/service/GermplasmService.ts b/src/breeding-insight/service/GermplasmService.ts
index 7049e37f2..4f943b413 100644
--- a/src/breeding-insight/service/GermplasmService.ts
+++ b/src/breeding-insight/service/GermplasmService.ts
@@ -24,7 +24,8 @@ import {Germplasm} from "@/breeding-insight/brapi/model/germplasm";
 import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
 import {SortOrder} from "@/breeding-insight/model/Sort";
 import * as api from "@/util/api";
-import {GermplasmFilter} from "@/breeding-insight/model/GermplasmFilter";
+import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
+
 
 export class GermplasmService {
 
@@ -67,7 +68,7 @@ export class GermplasmService {
             }
 
             //Get the list germplasm
-            const {data} = await api.call({
+            const {data}: any = await api.call({
                 url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/germplasm/lists/${listId}/records`,
                 method: 'get',
                 params: params
diff --git a/src/breeding-insight/service/ListService.ts b/src/breeding-insight/service/ListService.ts
new file mode 100644
index 000000000..bf3b38a7c
--- /dev/null
+++ b/src/breeding-insight/service/ListService.ts
@@ -0,0 +1,157 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import {GermplasmList} from "@/breeding-insight/model/GermplasmList";
+import {BiResponse, Metadata} from "@/breeding-insight/model/BiResponse";
+import {PaginationQuery} from "@/breeding-insight/model/PaginationQuery";
+import {PaginationUtilities} from "@/breeding-insight/model/view_models/PaginationUtilities";
+import {GermplasmDAO} from "@/breeding-insight/dao/GermplasmDAO";
+import {Germplasm} from "@/breeding-insight/brapi/model/germplasm";
+import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
+import {GermplasmListSortField, SortOrder} from "@/breeding-insight/model/Sort";
+import * as api from "@/util/api";
+import {ListType} from "@/util/ListType";
+import {ListFilter} from "@/breeding-insight/model/ListFilter";
+
+export class ListService {
+    static async deleteList(programId: string | undefined, listDbId: string) {
+        if (programId == undefined) {
+            throw new Error("Not valid program");
+        }
+        try {
+            const response = await api.call({
+                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/deltalists/${listDbId}`,
+                method: 'delete',
+                params: { hardDelete: true }
+            }) as Response;
+
+            // If we get here, it means the call was successful (likely 200 OK)
+            return new BiResponse({ success: true });
+
+        } catch (error) {
+            // Check if the error is actually a 204 No Content response
+            if (error.response && error.response.status === 204) {
+                // This is actually a successful deletion
+                return new BiResponse({ success: true });
+            }
+
+            // For other errors, log and rethrow
+            console.error('Error in deleteList:', error);
+            throw error;
+        }
+    }
+
+    static async getLists<T>(listType: ListType,
+                             programId: string,
+                             sort: { field: T, order: SortOrder },
+                             pagination: {pageSize: number, page: number},
+                             filters?: any): Promise<BiResponse> {
+        if (!programId) throw 'Program ID required';
+
+        // Set list type, sort, and pagination
+        let params: any = { listType };
+        if(filters) {
+            params = filters;
+        }
+
+        if (sort.field) {
+            params['sortField'] = sort.field;
+        }
+        if (sort.order) {
+            params['sortOrder'] = sort.order;
+        }
+        if (pagination.page || pagination.page == 0) { //have to account for 0-index pagination since 0 falsy
+            params['page'] = pagination.page;
+        }
+        if (pagination.pageSize) {
+            params['pageSize'] = pagination.pageSize;
+        }
+
+        // Make the GET call
+        try {
+            const { data }: any = await api.call({
+                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/deltalists`,
+                method: 'get',
+                params: params
+            });
+
+            return new BiResponse(data);
+
+        } catch (error) {
+            throw error;
+        }
+    }
+
+    static async getAllInList<T, U extends ListFilter>(
+        listType: ListType,
+        programId: string,
+        sort: { field: T, order: SortOrder },
+        pagination: { pageSize: number, page: number },
+        { listDbId, listName, ...brapiFilters  }: U): Promise<BiResponse> {
+        // Form the query params including list type, sorting, pagination, and filtering
+        let params: any = { listType, ...brapiFilters };
+
+        if (sort.field) {
+            params['sortField'] = sort.field;
+        }
+        if (sort.order) {
+            params['sortOrder'] = sort.order;
+        }
+        if (pagination.page || pagination.page == 0) { //have to account for 0-index pagination since 0 falsy
+            params['page'] = pagination.page;
+        }
+        if (pagination.pageSize) {
+            params['pageSize'] = pagination.pageSize;
+        }
+
+        try {
+            let listId: String = '';
+
+            if(listName && !listDbId) {
+                //Get the list db id
+                const paginationQuery = new PaginationQuery(0, 20, true);
+                //const {result: {data: lists}} = await GermplasmDAO.getAllLists(programId, paginationQuery);
+                const {result: {data: lists}} = await ListService.getLists<GermplasmListSortField>(
+                    ListType.GERMPLASM,
+                    programId,
+                    { field: GermplasmListSortField.Name, order: SortOrder.Descending },
+                    new PaginationQuery(0, 200, true));
+                const matchingLists = lists.filter((list: any) => list.listName === listName);
+                if (matchingLists.length === 0) throw Error("List name is not valid for this program");
+                if (matchingLists.length > 1) throw Error("List name must be unique");
+                listId = matchingLists[0].listDbId;
+            } else if(listDbId) {
+                listId = listDbId;
+            } else {
+                throw Error("Missing list id and name");
+            }
+
+            //Get the list germplasm
+            const { data }: any = await api.call({
+                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/deltalists/${listId}`,
+                method: 'get',
+                params: params
+            }) as Response;
+
+            return new BiResponse(data);
+
+        } catch(error) {
+            throw error;
+        }
+    }
+
+}
diff --git a/src/components/germplasm/GermplasmListDeletionlModal.vue b/src/components/germplasm/GermplasmListDeletionlModal.vue
new file mode 100644
index 000000000..4d1da73c7
--- /dev/null
+++ b/src/components/germplasm/GermplasmListDeletionlModal.vue
@@ -0,0 +1,89 @@
+<!--
+- See the NOTICE file distributed with this work for additional information
+- regarding copyright ownership.
+-
+- Licensed under the Apache License, Version 2.0 (the "License");
+- you may not use this file except in compliance with the License.
+- You may obtain a copy of the License at
+-
+-     http://www.apache.org/licenses/LICENSE-2.0
+-
+- Unless required by applicable law or agreed to in writing, software
+- distributed under the License is distributed on an "AS IS" BASIS,
+- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+- See the License for the specific language governing permissions and
+- limitations under the License.
+-->
+
+<template>
+  <ConfirmationModal
+    v-bind:unique-id="listDbId"
+    v-bind:modal-title="modalTitle"
+    v-bind:confirmedAction="deleteList"
+    v-bind:active="active"
+    modal-class="experiment-observation-remove-collaborator-button"
+    v-on:deactivate="cancelDelete"
+  >
+    <template #form>
+      <p>Are you sure you want to delete the germplasm list? Note that deleting a germplasm list will not delete the associated germplasm records.</p>
+    </template>
+    <slot />
+  </ConfirmationModal>
+</template>
+
+<script lang="ts">
+import {Component, Vue, Prop} from "vue-property-decorator";
+import {validationMixin} from "vuelidate";
+import {mapGetters} from "vuex";
+import {Program} from "@/breeding-insight/model/Program";
+import {AlertTriangleIcon} from 'vue-feather-icons';
+import {Trial} from "@/breeding-insight/model/Trial";
+import ConfirmationModal from "@/components/modals/ConfirmationModal.vue";
+import {ExperimentService} from "@/breeding-insight/service/ExperimentService";
+import { Collaborator } from '@/breeding-insight/model/Collaborator';
+import { ListService } from '@/breeding-insight/service/ListService';
+
+@Component({
+  mixins: [validationMixin],
+  components: {ConfirmationModal, AlertTriangleIcon},
+  computed: {
+    ...mapGetters([
+      'activeProgram'
+    ])
+  }
+})
+export default class ExperimentCollaboratorRemovalModal extends Vue {
+
+  @Prop()
+  active!: boolean;
+  @Prop()
+  listDbId!: string;
+  @Prop()
+  modalTitle?: string;
+
+  private activeProgram?: Program;
+
+  async deleteList(): Promise<void> {
+    if (this.activeProgram) {
+      try {
+        // Call the service method and await its completion
+        await ListService.deleteList(this.activeProgram.id, this.listDbId)
+
+        // If the above call doesn't throw an error, we assume it was successful
+        // Emit the event after the promise is resolved
+        this.$emit('list-deleted');
+
+      } catch (error) {
+        // Handle any errors that might occur during the async operation
+        console.error('Error deleting the list:', error);
+        // Optionally emit an error event or handle the error in some way
+        this.$emit('show-error-notification', `Error while trying to delete the list`);
+      }
+    }
+  }
+
+  cancelDelete(){
+    this.$emit('deactivate');
+  }
+}
+</script>
\ No newline at end of file
diff --git a/src/components/germplasm/GermplasmTable.vue b/src/components/germplasm/GermplasmTable.vue
index 974efb163..2691c40ba 100644
--- a/src/components/germplasm/GermplasmTable.vue
+++ b/src/components/germplasm/GermplasmTable.vue
@@ -94,7 +94,7 @@ import {
 } from "@/breeding-insight/model/Sort";
 import {UPDATE_GERMPLASM_SORT} from "@/store/sorting/mutation-types";
 import { PaginationQuery } from '@/breeding-insight/model/PaginationQuery';
-import {GermplasmFilter} from "@/breeding-insight/model/GermplasmFilter";
+import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
 
 @Component({
   mixins: [validationMixin],
diff --git a/src/store/filtering/getters.ts b/src/store/filtering/getters.ts
index b8d8a81a9..cfb45523a 100644
--- a/src/store/filtering/getters.ts
+++ b/src/store/filtering/getters.ts
@@ -18,7 +18,7 @@
 import {GetterTree} from 'vuex';
 import {RootState} from "@/store/types";
 import {FilterState} from "@/store/filtering/types";
-import {GermplasmFilter} from "@/breeding-insight/model/GermplasmFilter";
+import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
 
 export const getters: GetterTree<FilterState, RootState> = {
     // germplasm
diff --git a/src/store/filtering/index.ts b/src/store/filtering/index.ts
index 12cb5078b..c0b5b6dff 100644
--- a/src/store/filtering/index.ts
+++ b/src/store/filtering/index.ts
@@ -20,7 +20,7 @@ import {getters} from '@/store/filtering/getters';
 import {mutations} from '@/store/filtering/mutations';
 import {RootState} from '@/store/types';
 import {FilterState} from "@/store/filtering/types";
-import {GermplasmFilter} from "@/breeding-insight/model/GermplasmFilter";
+import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
 
 export let state: FilterState;
 state = {
diff --git a/src/store/filtering/mutations.ts b/src/store/filtering/mutations.ts
index 8a6212a69..5976d9bc1 100644
--- a/src/store/filtering/mutations.ts
+++ b/src/store/filtering/mutations.ts
@@ -17,7 +17,7 @@
 
 import {MutationTree} from 'vuex';
 import {FilterState} from "@/store/filtering/types";
-import {GermplasmFilter} from "@/breeding-insight/model/GermplasmFilter";
+import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
 import {UPDATE_GERMPLASM_FILTER} from "@/store/filtering/mutation-types";
 
 export const mutations: MutationTree<FilterState> = {
diff --git a/src/store/filtering/types.ts b/src/store/filtering/types.ts
index 3d1c7b83f..6d9dd0daa 100644
--- a/src/store/filtering/types.ts
+++ b/src/store/filtering/types.ts
@@ -1,4 +1,4 @@
-import { GermplasmFilter } from "@/breeding-insight/model/GermplasmFilter";
+import { GermplasmFilter } from "@/breeding-insight/model/ListFilter";
 
 export interface FilterState {
     // germplasm table
diff --git a/src/util/ListType.ts b/src/util/ListType.ts
index 09a2b11c6..23df7121f 100644
--- a/src/util/ListType.ts
+++ b/src/util/ListType.ts
@@ -16,5 +16,5 @@
  */
 
 export enum ListType {
-    Germplasm = "germplasm",
+    GERMPLASM = "germplasm",
 }
diff --git a/src/views/germplasm/GermplasmByList.vue b/src/views/germplasm/GermplasmByList.vue
index 821a852f0..69985c08c 100644
--- a/src/views/germplasm/GermplasmByList.vue
+++ b/src/views/germplasm/GermplasmByList.vue
@@ -18,45 +18,100 @@
 <template>
   <div class="germplasm">
     <router-link
-        v-bind:to="{name: 'germplasm-lists', params: {programId: activeProgram.id}}"
+        v-bind:to="germplasmListsRoute()"
     >
       <a>&lt; Germplasm Lists</a>
     </router-link>
     <h1 class="title">
-      {{ list ? list.listName : "" | toStartCase }}
+      {{ toStartCase(list ? list.listName : "") }}
     </h1>
-<div class="columns">
-  <div class="column is-10">
-    <div class="columns is-multiline">
-      <div class="column germplasm-list-meta-field"><b>Description:</b></div>
-      <div class="column germplasm-list-meta-data">{{ list ? list.listDescription : ""}}</div>
-      <div class="column germplasm-list-meta-field"><b>User:</b></div>
-      <div class="column germplasm-list-meta-data">{{ list ? list.listOwnerName : ""}}</div>
-      <div class="column germplasm-list-meta-field"><b>Import Date:</b></div>
-      <div class="column germplasm-list-meta-data">{{ list ? list.dateCreated : "" | toYMD }}</div>
-      <div class="column germplasm-list-meta-field"><b>Total Entries:</b></div>
-      <div class="column germplasm-list-meta-data">{{ list ? list.listSize : ""}}</div>
-    </div>
-  </div>
-  <div class="column is-2">
-    <div class="columns is-multiline">
-      <div class="column is-full"></div>
-      <div class="column is-full"></div>
-      <div class="column is-full"></div>
-      <div class="column is-full buttons">
-        <GermplasmDownloadButton
-            v-bind:modal-title="`Download ${list ? list.listName : ''}`"
-            fieldset-legend="File Format"
-            v-bind:listDbId="list ? list.listDbId : '' "
-        >
-          <button class="button is-primary has-text-weight-bold">
-            <strong>Download</strong>
-          </button>
-        </GermplasmDownloadButton>
+
+    <GermplasmListDeletionModal
+        v-bind:active="deleteModalActive"
+        v-bind:list-db-id="listDbId"
+        v-bind:modal-title="`Delete ${list.listName}`"
+        v-on:show-error-notification="$emit('show-error-notification', $event)"
+        v-on:deactivate="deleteModalActive = false"
+        v-on:list-deleted="deleteSuccess"
+    />
+    <FormModal
+        v-bind:active.sync="downloadModalActive"
+        v-bind:title="`Download ${list ? list.listName : ''}`"
+        v-on:deactivate="closeDownloadModal"
+    >
+      <template #form>
+        <fieldset>
+          <legend class="label">
+            File Formnat
+          </legend>
+          <div
+              v-for="option in fileOptions"
+              v-bind:key="option.id"
+          >
+            <label class="radio">
+              <input
+                  v-model="fileExtension"
+                  type="radio"
+                  name="fileType"
+                  v-bind:value="option.id"
+              ><span class="check" />
+              <span class="control-label"> {{ option.name }} </span>
+            </label>
+          </div>
+        </fieldset>
+      </template>
+      <template #buttons>
+        <div class="columns">
+          <div class="column is-whole has-text-centered buttons">
+            <button
+                class="button is-primary has-text-weight-bold"
+                v-on:click="invokeDownload"
+            >
+              <strong>Download</strong>
+            </button>
+            <button
+                class="button"
+                v-on:click="closeDownloadModal"
+            >
+              Cancel
+            </button>
+          </div>
+        </div>
+      </template>
+    </FormModal>
+    <div class="columns">
+      <div class="column is-10">
+        <div class="columns is-multiline">
+          <div class="column germplasm-list-meta-field"><b>Description:</b></div>
+          <div class="column germplasm-list-meta-data">{{ list ? list.listDescription : ""}}</div>
+          <div class="column germplasm-list-meta-field"><b>User:</b></div>
+          <div class="column germplasm-list-meta-data">{{ list ? list.listOwnerName : ""}}</div>
+          <div class="column germplasm-list-meta-field"><b>Import Date:</b></div>
+          <div class="column germplasm-list-meta-data">{{ toYMD(list ? list.dateCreated : "") }}</div>
+          <div class="column germplasm-list-meta-field"><b>Total Entries:</b></div>
+          <div class="column germplasm-list-meta-data">{{ list ? list.listSize : ""}}</div>
+        </div>
+      </div>
+      <div class="column is-2">
+        <div class="columns is-multiline">
+          <div class="column is-full"></div>
+          <div class="column is-full"></div>
+          <div class="column is-full"></div>
+          <div class="column is-full buttons">
+            <ActionMenu
+                class = "is-pulled-right has-text-weight-bold above-tabs-button"
+                v-bind:is-primary="true"
+                v-bind:id="'manage-germplasm-list-dropdown-button'"
+                v-bind:button-text="'Manage List'"
+                v-bind:action-menu-items=actions
+                v-on:delete-list="deleteList()"
+                v-on:download-file="openDownloadModal()"
+            >
+            </ActionMenu>
+          </div>
+        </div>
       </div>
     </div>
-  </div>
-</div>
     <GermplasmTable
         v-bind:germplasmFetch="germplasmFetch"
         entryNumberVisible="true"
@@ -67,59 +122,136 @@
 </template>
 
 <script lang="ts">
-import { Component } from 'vue-property-decorator'
+import {Component} from 'vue-property-decorator'
 import GermplasmBase from "@/components/germplasm/GermplasmBase.vue";
 import GermplasmTable from '@/components/germplasm/GermplasmTable.vue';
-import { GermplasmService } from '@/breeding-insight/service/GermplasmService';
-import { GermplasmSort } from '@/breeding-insight/model/Sort';
-import { BiResponse } from '@/breeding-insight/model/BiResponse';
-import { GermplasmDAO } from '@/breeding-insight/dao/GermplasmDAO';
-import { PaginationQuery } from '@/breeding-insight/model/PaginationQuery';
-import { mapGetters } from 'vuex';
-import { Program } from '@/breeding-insight/model/Program';
+import {GermplasmListSortField, GermplasmSort, SortOrder, GermplasmSortField} from '@/breeding-insight/model/Sort';
+import {BiResponse} from '@/breeding-insight/model/BiResponse';
+import {PaginationQuery} from '@/breeding-insight/model/PaginationQuery';
+import {mapGetters} from 'vuex';
+import {Program} from '@/breeding-insight/model/Program';
 import {StringFormatters} from "@/breeding-insight/utils/StringFormatters";
 import GermplasmDownloadButton from '@/components/germplasm/GermplasmDownloadButton.vue';
+import GermplasmListDeletionModal from '@/components/germplasm/GermplasmListDeletionlModal.vue'
 import {PaginationController} from "@/breeding-insight/model/view_models/PaginationController";
+import ActionMenu from "@/components/layouts/menus/ActionMenu.vue";
+import {ActionMenuItem} from "@/breeding-insight/model/ActionMenuItem";
+import {FileTypeOption} from '@/breeding-insight/model/FileTypeOption';
+import FormModal from "@/components/modals/FormModal.vue";
+import {ListService} from '@/breeding-insight/service/ListService';
+import {ListType} from "@/util/ListType";
+import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
 
 @Component({
-  components: { GermplasmTable, GermplasmDownloadButton },
+  components: { FormModal, GermplasmTable, GermplasmDownloadButton, GermplasmListDeletionModal, ActionMenu },
   computed: {
     ...mapGetters([
       'activeProgram'
     ])
-  },
-  filters: {
-    toStartCase: StringFormatters.toStartCase,
-    toYMD: (date) => date.split('T')[0]
   }
 })
 export default class GermplasmByList extends GermplasmBase {
 
   private activeProgram?: Program;
-  private list: any = null;
+  private downloadModalActive: boolean = false;
+  private deleteModalActive: boolean = false;
+  private fileOptions: FileTypeOption[] = Object.values(FileTypeOption);
+  private fileExtension: string = this.fileOptions[0].id;
+  private list: any = {};
   private referenceId?: string = '';
+  private actions: ActionMenuItem[] = [
+    new ActionMenuItem('germplasm-list-delete', 'delete-list', 'Delete', this.$ability.can('create', 'Import')),
+    new ActionMenuItem('germplasm-list-download-file', 'download-file', 'Download',  true)
+  ];
+
+  // Formatting filters
+  private toYMD(date: string | null | undefined): string {
+    if (!date) return ''; // Return an empty string if date is null, undefined, or empty
+    return date.split('T')[0];
+  }
+  private toStartCase(data: string): string | undefined {
+    return StringFormatters.toStartCase(data);
+  }
+
+  // Breadcrumb route
+  private germplasmListsRoute() {
+    if (this.activeProgram && this.activeProgram.id) {
+      return {name: 'germplasm-lists', params: {programId: this.activeProgram.id}};
+    } else {
+      return {name: 'germplasm-lists'};
+    }
+  }
+
 
   // Set the method used to populate the germplasm table
-  private germplasmFetch: (programId: string, sort: GermplasmSort, paginationController: PaginationController) => ((filters: any) => Promise<BiResponse>) =
-      function (programId: string, sort: GermplasmSort, paginationController: PaginationController) {
-        let id: string = this.$route.params.listId;
-        return function (filters: any) {
-          return GermplasmService.getAllInList(
-              programId,
-              sort,
-              {pageSize: paginationController.pageSize, page: paginationController.currentPage - 1},
-              {listDbId: `${id}`, ...filters})
-        };
-      };
+  private germplasmFetch = (
+      programId: string,
+      sort: GermplasmSort,
+      { pageSize, currentPage }: PaginationController
+  ) => (filters: any): Promise<BiResponse> =>
+      ListService.getAllInList<GermplasmSortField, GermplasmFilter>(
+          ListType.GERMPLASM,
+          programId,
+          sort,
+          { pageSize, page: currentPage - 1 },
+          { listDbId: this.$route.params.listId, ...filters }
+      );
+
 
   mounted() {
     this.getList();
   }
 
+  get listDbId(): string {
+    return this.$route.params.listId;
+  }
+
+  private deleteSuccess() {
+    // Navigate to the lists table since this list no longer exists
+    this.$router.push({ name: "germplasm-lists" });
+  }
+
+  async deleteList() {
+    this.deleteModalActive = true;
+  }
+
+  async openDownloadModal() {
+    this.downloadModalActive = true;
+  }
+
+  private closeDownloadModal() {
+    // Close the modal
+    this.downloadModalActive = false;
+
+    // Reset fileExtension.
+    this.fileExtension = this.fileOptions[0].id;
+
+  }
+
+  private downloadList(): boolean {
+    if (this.activeProgram) {
+      window.open(process.env.VUE_APP_BI_API_ROOT + '/v1/programs/' + this.activeProgram.id + '/deltalists/' + this.listDbId + '/export?fileExtension=' + this.fileExtension, '_blank');
+      return true;
+    }
+    return false;
+  }
+
+  private invokeDownload(){
+    // Invoke the download prop, which returns true if download succeeded.
+    if (this.downloadList())
+    {
+      // Close and deactivate modal.
+      this.closeDownloadModal();
+    }
+  }
+
   async getList() {
-    const paginationQuery = new PaginationQuery(0, 200, true);
-    const {result: {data: lists}} = await GermplasmDAO.getAllLists(this.activeProgram!.id!, paginationQuery);
-    const matchingLists: any[] = lists.filter(list => list.listDbId === this.$route.params.listId);
+    const {result: {data: lists}} = await ListService.getLists<GermplasmListSortField>(
+        ListType.GERMPLASM,
+        this.activeProgram!.id!,
+        { field: GermplasmListSortField.Name, order: SortOrder.Descending },
+        new PaginationQuery(0, 200, true));
+    const matchingLists: any[] = lists.filter((list: any) => list.listDbId === this.$route.params.listId);
     this.list = matchingLists[0];
 
     // Find the key used, if any, for this list in the list entry numbers map
diff --git a/src/views/germplasm/GermplasmLists.vue b/src/views/germplasm/GermplasmLists.vue
index 8f3e702d8..61dd713c4 100644
--- a/src/views/germplasm/GermplasmLists.vue
+++ b/src/views/germplasm/GermplasmLists.vue
@@ -27,33 +27,33 @@
 </template>
 
 <script lang="ts">
-import { Component } from 'vue-property-decorator'
+import {Component} from 'vue-property-decorator'
 import ProgramsBase from "@/components/program/ProgramsBase.vue";
 import GermplasmListsTable from "@/components/germplasm/GermplasmListsTable.vue";
 import {GermplasmListSort, GermplasmListSortField} from "@/breeding-insight/model/Sort";
 import {PaginationController} from "@/breeding-insight/model/view_models/PaginationController";
 import {BiResponse} from "@/breeding-insight/model/BiResponse";
-import {BrAPIService, BrAPIType} from "@/breeding-insight/service/BrAPIService";
 import {ListType} from "@/util/ListType";
+import {ListService} from "@/breeding-insight/service/ListService";
+
 @Component({
   components: {
     GermplasmListsTable
   }
 })
 export default class GermplasmLists extends ProgramsBase {
-
-  private germplasmListFetch: (programId: string, sort: GermplasmListSort, paginationController: PaginationController) => ((filters: any) => Promise<BiResponse>) =
-      function (programId: string, sort: GermplasmListSort, paginationController: PaginationController) {
-        return function (filters: any) {
-          filters.listType=ListType.Germplasm;
-          return BrAPIService.get<GermplasmListSortField>(
-              BrAPIType.LIST,
-              programId,
-              sort,
-              { pageSize: paginationController.pageSize, page: paginationController.currentPage - 1 },
-              filters)
-        };
-      };
+  private germplasmListFetch = (
+      programId: string,
+      sort: GermplasmListSort,
+      { pageSize, currentPage }: PaginationController
+  ) => (filters: any): Promise<BiResponse> =>
+      ListService.getLists<GermplasmListSortField>(
+          ListType.GERMPLASM,
+          programId,
+          sort,
+          { pageSize, page: currentPage - 1 },
+          filters
+      );
 }
 
 </script>
\ No newline at end of file

From a18760e2c3af05b30fb8cab86eeb102baaa8f3de Mon Sep 17 00:00:00 2001
From: dmeidlin <14339308+dmeidlin@users.noreply.github.com>
Date: Fri, 15 Nov 2024 16:39:20 -0500
Subject: [PATCH 40/98] add access control for list delete menu option

---
 src/breeding-insight/service/ListService.ts | 6 +++---
 src/config/AppAbility.ts                    | 3 ++-
 src/config/ability.ts                       | 2 ++
 src/views/germplasm/GermplasmByList.vue     | 4 ++--
 4 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/breeding-insight/service/ListService.ts b/src/breeding-insight/service/ListService.ts
index bf3b38a7c..14b98261a 100644
--- a/src/breeding-insight/service/ListService.ts
+++ b/src/breeding-insight/service/ListService.ts
@@ -34,7 +34,7 @@ export class ListService {
         }
         try {
             const response = await api.call({
-                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/deltalists/${listDbId}`,
+                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/lists/${listDbId}`,
                 method: 'delete',
                 params: { hardDelete: true }
             }) as Response;
@@ -84,7 +84,7 @@ export class ListService {
         // Make the GET call
         try {
             const { data }: any = await api.call({
-                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/deltalists`,
+                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/lists`,
                 method: 'get',
                 params: params
             });
@@ -142,7 +142,7 @@ export class ListService {
 
             //Get the list germplasm
             const { data }: any = await api.call({
-                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/deltalists/${listId}`,
+                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/lists/${listId}`,
                 method: 'get',
                 params: params
             }) as Response;
diff --git a/src/config/AppAbility.ts b/src/config/AppAbility.ts
index f3cb76e4c..590f043af 100644
--- a/src/config/AppAbility.ts
+++ b/src/config/AppAbility.ts
@@ -19,7 +19,8 @@ import {Ability, AbilityClass} from '@casl/ability';
 
 type Actions = 'manage' | 'create' | 'read' | 'update' | 'delete' | 'archive' | 'access' | 'submit';
 type Subjects = 'ProgramUser' | 'Location' | 'User' | 'AdminSection' | 'Trait' | 'Import' | 'ProgramConfiguration' | 'Submission'
-    | 'Experiment' | 'Germplasm' | 'Ontology' | 'SampleManagement' | 'ProgramAdministration' | 'JobManagement' | 'Collaborator' | 'BrAPI' ;
+    | 'Experiment' | 'Germplasm' | 'Ontology' | 'SampleManagement' | 'ProgramAdministration' | 'JobManagement' | 'Collaborator' | 'BrAPI'
+    | 'List';
 
 export type AppAbility = Ability<[Actions, Subjects]>;
 export const AppAbility = Ability as AbilityClass<AppAbility>;
\ No newline at end of file
diff --git a/src/config/ability.ts b/src/config/ability.ts
index b91c01900..afb865d69 100644
--- a/src/config/ability.ts
+++ b/src/config/ability.ts
@@ -59,6 +59,7 @@ const rolePermissions: Record<string, DefinePermissions> = {
     can('access', 'BrAPI');
     can('access', 'JobManagement');
     can('manage', 'Collaborator');
+    can('delete', 'List');
 
   },
   systemadministrator(user, { can }) {
@@ -79,6 +80,7 @@ const rolePermissions: Record<string, DefinePermissions> = {
     can('access', 'BrAPI');
     can('access', 'JobManagement');
     can('manage', 'Collaborator');
+    can('delete', 'List');
 
   }
 };
diff --git a/src/views/germplasm/GermplasmByList.vue b/src/views/germplasm/GermplasmByList.vue
index 69985c08c..ca321fbd8 100644
--- a/src/views/germplasm/GermplasmByList.vue
+++ b/src/views/germplasm/GermplasmByList.vue
@@ -160,7 +160,7 @@ export default class GermplasmByList extends GermplasmBase {
   private list: any = {};
   private referenceId?: string = '';
   private actions: ActionMenuItem[] = [
-    new ActionMenuItem('germplasm-list-delete', 'delete-list', 'Delete', this.$ability.can('create', 'Import')),
+    new ActionMenuItem('germplasm-list-delete', 'delete-list', 'Delete', this.$ability.can('delete', 'List')),
     new ActionMenuItem('germplasm-list-download-file', 'download-file', 'Download',  true)
   ];
 
@@ -230,7 +230,7 @@ export default class GermplasmByList extends GermplasmBase {
 
   private downloadList(): boolean {
     if (this.activeProgram) {
-      window.open(process.env.VUE_APP_BI_API_ROOT + '/v1/programs/' + this.activeProgram.id + '/deltalists/' + this.listDbId + '/export?fileExtension=' + this.fileExtension, '_blank');
+      window.open(process.env.VUE_APP_BI_API_ROOT + '/v1/programs/' + this.activeProgram.id + '/brapi/v2/lists/' + this.listDbId + '/export?fileExtension=' + this.fileExtension, '_blank');
       return true;
     }
     return false;

From 2a6d70feba14e23063171ce7f4542993e560e23c Mon Sep 17 00:00:00 2001
From: dmeidlin <14339308+dmeidlin@users.noreply.github.com>
Date: Mon, 18 Nov 2024 12:26:00 -0500
Subject: [PATCH 41/98] get germplasm list records via germplasm endpoints

---
 src/breeding-insight/service/GermplasmService.ts | 4 ++--
 src/breeding-insight/service/ListService.ts      | 2 --
 src/views/germplasm/GermplasmByList.vue          | 4 ++--
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/breeding-insight/service/GermplasmService.ts b/src/breeding-insight/service/GermplasmService.ts
index 4f943b413..bd6c421ac 100644
--- a/src/breeding-insight/service/GermplasmService.ts
+++ b/src/breeding-insight/service/GermplasmService.ts
@@ -35,7 +35,7 @@ export class GermplasmService {
                          { listDbId, listName, ...brapiFilters  }: GermplasmFilter):
         Promise<BiResponse> {
         //Form the query params including sorting, pagination, and filtering
-        let params: any = { ...brapiFilters };
+        let params: any = {list: listDbId, ...brapiFilters };
 
         if (sort.field) {
             params['sortField'] = sort.field;
@@ -69,7 +69,7 @@ export class GermplasmService {
 
             //Get the list germplasm
             const {data}: any = await api.call({
-                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/germplasm/lists/${listId}/records`,
+                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/germplasm`,
                 method: 'get',
                 params: params
             }) as Response;
diff --git a/src/breeding-insight/service/ListService.ts b/src/breeding-insight/service/ListService.ts
index 14b98261a..33996ed7b 100644
--- a/src/breeding-insight/service/ListService.ts
+++ b/src/breeding-insight/service/ListService.ts
@@ -123,8 +123,6 @@ export class ListService {
 
             if(listName && !listDbId) {
                 //Get the list db id
-                const paginationQuery = new PaginationQuery(0, 20, true);
-                //const {result: {data: lists}} = await GermplasmDAO.getAllLists(programId, paginationQuery);
                 const {result: {data: lists}} = await ListService.getLists<GermplasmListSortField>(
                     ListType.GERMPLASM,
                     programId,
diff --git a/src/views/germplasm/GermplasmByList.vue b/src/views/germplasm/GermplasmByList.vue
index ca321fbd8..1fc17751e 100644
--- a/src/views/germplasm/GermplasmByList.vue
+++ b/src/views/germplasm/GermplasmByList.vue
@@ -141,6 +141,7 @@ import FormModal from "@/components/modals/FormModal.vue";
 import {ListService} from '@/breeding-insight/service/ListService';
 import {ListType} from "@/util/ListType";
 import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
+import {GermplasmService} from "@/breeding-insight/service/GermplasmService";
 
 @Component({
   components: { FormModal, GermplasmTable, GermplasmDownloadButton, GermplasmListDeletionModal, ActionMenu },
@@ -189,8 +190,7 @@ export default class GermplasmByList extends GermplasmBase {
       sort: GermplasmSort,
       { pageSize, currentPage }: PaginationController
   ) => (filters: any): Promise<BiResponse> =>
-      ListService.getAllInList<GermplasmSortField, GermplasmFilter>(
-          ListType.GERMPLASM,
+      GermplasmService.getAllInList<GermplasmSortField>(
           programId,
           sort,
           { pageSize, page: currentPage - 1 },

From c49c3d81fc571a7f09c256892e701c5f53250a2f Mon Sep 17 00:00:00 2001
From: dmeidlin <14339308+dmeidlin@users.noreply.github.com>
Date: Wed, 20 Nov 2024 09:59:16 -0500
Subject: [PATCH 42/98] revert to germplasm endpoints

---
 src/breeding-insight/service/ListService.ts | 68 +--------------------
 src/views/germplasm/GermplasmByList.vue     |  2 +-
 2 files changed, 3 insertions(+), 67 deletions(-)

diff --git a/src/breeding-insight/service/ListService.ts b/src/breeding-insight/service/ListService.ts
index 33996ed7b..087923396 100644
--- a/src/breeding-insight/service/ListService.ts
+++ b/src/breeding-insight/service/ListService.ts
@@ -15,17 +15,10 @@
  * limitations under the License.
  */
 
-import {GermplasmList} from "@/breeding-insight/model/GermplasmList";
-import {BiResponse, Metadata} from "@/breeding-insight/model/BiResponse";
-import {PaginationQuery} from "@/breeding-insight/model/PaginationQuery";
-import {PaginationUtilities} from "@/breeding-insight/model/view_models/PaginationUtilities";
-import {GermplasmDAO} from "@/breeding-insight/dao/GermplasmDAO";
-import {Germplasm} from "@/breeding-insight/brapi/model/germplasm";
-import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
-import {GermplasmListSortField, SortOrder} from "@/breeding-insight/model/Sort";
+import {BiResponse} from "@/breeding-insight/model/BiResponse";
+import {SortOrder} from "@/breeding-insight/model/Sort";
 import * as api from "@/util/api";
 import {ListType} from "@/util/ListType";
-import {ListFilter} from "@/breeding-insight/model/ListFilter";
 
 export class ListService {
     static async deleteList(programId: string | undefined, listDbId: string) {
@@ -95,61 +88,4 @@ export class ListService {
             throw error;
         }
     }
-
-    static async getAllInList<T, U extends ListFilter>(
-        listType: ListType,
-        programId: string,
-        sort: { field: T, order: SortOrder },
-        pagination: { pageSize: number, page: number },
-        { listDbId, listName, ...brapiFilters  }: U): Promise<BiResponse> {
-        // Form the query params including list type, sorting, pagination, and filtering
-        let params: any = { listType, ...brapiFilters };
-
-        if (sort.field) {
-            params['sortField'] = sort.field;
-        }
-        if (sort.order) {
-            params['sortOrder'] = sort.order;
-        }
-        if (pagination.page || pagination.page == 0) { //have to account for 0-index pagination since 0 falsy
-            params['page'] = pagination.page;
-        }
-        if (pagination.pageSize) {
-            params['pageSize'] = pagination.pageSize;
-        }
-
-        try {
-            let listId: String = '';
-
-            if(listName && !listDbId) {
-                //Get the list db id
-                const {result: {data: lists}} = await ListService.getLists<GermplasmListSortField>(
-                    ListType.GERMPLASM,
-                    programId,
-                    { field: GermplasmListSortField.Name, order: SortOrder.Descending },
-                    new PaginationQuery(0, 200, true));
-                const matchingLists = lists.filter((list: any) => list.listName === listName);
-                if (matchingLists.length === 0) throw Error("List name is not valid for this program");
-                if (matchingLists.length > 1) throw Error("List name must be unique");
-                listId = matchingLists[0].listDbId;
-            } else if(listDbId) {
-                listId = listDbId;
-            } else {
-                throw Error("Missing list id and name");
-            }
-
-            //Get the list germplasm
-            const { data }: any = await api.call({
-                url: `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/lists/${listId}`,
-                method: 'get',
-                params: params
-            }) as Response;
-
-            return new BiResponse(data);
-
-        } catch(error) {
-            throw error;
-        }
-    }
-
 }
diff --git a/src/views/germplasm/GermplasmByList.vue b/src/views/germplasm/GermplasmByList.vue
index 1fc17751e..d1a0569bb 100644
--- a/src/views/germplasm/GermplasmByList.vue
+++ b/src/views/germplasm/GermplasmByList.vue
@@ -230,7 +230,7 @@ export default class GermplasmByList extends GermplasmBase {
 
   private downloadList(): boolean {
     if (this.activeProgram) {
-      window.open(process.env.VUE_APP_BI_API_ROOT + '/v1/programs/' + this.activeProgram.id + '/brapi/v2/lists/' + this.listDbId + '/export?fileExtension=' + this.fileExtension, '_blank');
+      window.open(process.env.VUE_APP_BI_API_ROOT + '/v1/programs/' + this.activeProgram.id + '/germplasm/export?fileExtension=' + this.fileExtension + '&list=' + this.listDbId, '_blank');
       return true;
     }
     return false;

From a3297b8a3d0c064f93eae016531720a050324c81 Mon Sep 17 00:00:00 2001
From: dmeidlin <14339308+dmeidlin@users.noreply.github.com>
Date: Wed, 18 Dec 2024 11:02:55 -0500
Subject: [PATCH 43/98] fix listType query param for lists call

---
 package-lock.json                             | 42 ++++++++++++-------
 src/assets/scss/main.scss                     |  2 +-
 src/breeding-insight/service/ListService.ts   |  3 +-
 .../germplasm/GermplasmListDeletionlModal.vue |  4 +-
 4 files changed, 32 insertions(+), 19 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index e8cbddb6e..760481dde 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -8581,13 +8581,20 @@
       }
     },
     "node_modules/debug": {
-      "version": "4.1.1",
-      "resolved": "https://registry.npmjs.org/debug/-/debug-4.1.1.tgz",
-      "integrity": "sha512-pYAIzeRo8J6KPEaJ0VWOh5Pzkbw/RetuzehGM7QRRX5he4fPHx2rdKMB256ehJCkX+XRQm16eZLqLNS8RSZXZw==",
-      "deprecated": "Debug versions >=3.2.0 <3.2.7 || >=4 <4.3.1 have a low-severity ReDos regression when used in a Node.js environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (https://github.com/visionmedia/debug/issues/797)",
+      "version": "4.3.1",
+      "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.1.tgz",
+      "integrity": "sha512-doEwdvm4PCeK4K3RQN2ZC2BYUBaxwLARCqZmMjtF8a51J2Rb0xpVloFRnCODwqjpwnAoao4pelN8l3RJdv3gRQ==",
       "dev": true,
       "dependencies": {
-        "ms": "^2.1.1"
+        "ms": "2.1.2"
+      },
+      "engines": {
+        "node": ">=6.0"
+      },
+      "peerDependenciesMeta": {
+        "supports-color": {
+          "optional": true
+        }
       }
     },
     "node_modules/decamelize": {
@@ -10960,9 +10967,9 @@
       }
     },
     "node_modules/follow-redirects": {
-      "version": "1.13.0",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.13.0.tgz",
-      "integrity": "sha512-aq6gF1BEKje4a9i9+5jimNFIpq4Q1WiwBToeRK5NvZBd/TRsmW8BsJfOEGkr76TbOyPVD3OVDN910EcUNtRYEA==",
+      "version": "1.15.9",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.9.tgz",
+      "integrity": "sha512-gew4GsXizNgdoRyqmyfMHyAmXsZDk6mHkSxZFCzW9gwlbtOW44CDtYavM+y+72qD/Vq2l550kMF52DT8fOLJqQ==",
       "dev": true,
       "funding": [
         {
@@ -10972,6 +10979,11 @@
       ],
       "engines": {
         "node": ">=4.0"
+      },
+      "peerDependenciesMeta": {
+        "debug": {
+          "optional": true
+        }
       }
     },
     "node_modules/for-in": {
@@ -31923,12 +31935,12 @@
       }
     },
     "debug": {
-      "version": "4.1.1",
-      "resolved": "https://registry.npmjs.org/debug/-/debug-4.1.1.tgz",
-      "integrity": "sha512-pYAIzeRo8J6KPEaJ0VWOh5Pzkbw/RetuzehGM7QRRX5he4fPHx2rdKMB256ehJCkX+XRQm16eZLqLNS8RSZXZw==",
+      "version": "4.3.1",
+      "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.1.tgz",
+      "integrity": "sha512-doEwdvm4PCeK4K3RQN2ZC2BYUBaxwLARCqZmMjtF8a51J2Rb0xpVloFRnCODwqjpwnAoao4pelN8l3RJdv3gRQ==",
       "dev": true,
       "requires": {
-        "ms": "^2.1.1"
+        "ms": "2.1.2"
       }
     },
     "decamelize": {
@@ -33867,9 +33879,9 @@
       "requires": {}
     },
     "follow-redirects": {
-      "version": "1.13.0",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.13.0.tgz",
-      "integrity": "sha512-aq6gF1BEKje4a9i9+5jimNFIpq4Q1WiwBToeRK5NvZBd/TRsmW8BsJfOEGkr76TbOyPVD3OVDN910EcUNtRYEA==",
+      "version": "1.15.9",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.9.tgz",
+      "integrity": "sha512-gew4GsXizNgdoRyqmyfMHyAmXsZDk6mHkSxZFCzW9gwlbtOW44CDtYavM+y+72qD/Vq2l550kMF52DT8fOLJqQ==",
       "dev": true
     },
     "for-in": {
diff --git a/src/assets/scss/main.scss b/src/assets/scss/main.scss
index fedd7dd2d..66397d521 100644
--- a/src/assets/scss/main.scss
+++ b/src/assets/scss/main.scss
@@ -945,7 +945,7 @@ tr:nth-child(odd) td.db-filled {
   margin-right: 10px;
 }
 
-.sub-entity-dataset-modal, .experiment-observations-download-button, .experiment-observation-add-collaborator-button, .experiment-observation-remove-collaborator-button {
+.sub-entity-dataset-modal, .experiment-observations-download-button, .experiment-observation-add-collaborator-button, .experiment-observation-remove-collaborator-button, .germplasm-list-deletion-button {
   .modal {
     .modal-card {
       width: $medium-modal-content-width;
diff --git a/src/breeding-insight/service/ListService.ts b/src/breeding-insight/service/ListService.ts
index 087923396..f7c0301bf 100644
--- a/src/breeding-insight/service/ListService.ts
+++ b/src/breeding-insight/service/ListService.ts
@@ -57,8 +57,9 @@ export class ListService {
 
         // Set list type, sort, and pagination
         let params: any = { listType };
+
         if(filters) {
-            params = filters;
+            params = { listType, ...filters };
         }
 
         if (sort.field) {
diff --git a/src/components/germplasm/GermplasmListDeletionlModal.vue b/src/components/germplasm/GermplasmListDeletionlModal.vue
index 4d1da73c7..b24ec3ee5 100644
--- a/src/components/germplasm/GermplasmListDeletionlModal.vue
+++ b/src/components/germplasm/GermplasmListDeletionlModal.vue
@@ -21,7 +21,7 @@
     v-bind:modal-title="modalTitle"
     v-bind:confirmedAction="deleteList"
     v-bind:active="active"
-    modal-class="experiment-observation-remove-collaborator-button"
+    modal-class="germplasm-list-deletion-button"
     v-on:deactivate="cancelDelete"
   >
     <template #form>
@@ -52,7 +52,7 @@ import { ListService } from '@/breeding-insight/service/ListService';
     ])
   }
 })
-export default class ExperimentCollaboratorRemovalModal extends Vue {
+export default class GermplasmListDeletionlModal extends Vue {
 
   @Prop()
   active!: boolean;

From 05605115dcc1acd5bf7a57b93db728bf101befbe Mon Sep 17 00:00:00 2001
From: dmeidlin <14339308+dmeidlin@users.noreply.github.com>
Date: Fri, 20 Dec 2024 10:32:27 -0500
Subject: [PATCH 44/98] incorporate PR feedback

---
 src/breeding-insight/service/GermplasmService.ts | 2 +-
 src/breeding-insight/service/ListService.ts      | 3 ++-
 src/views/germplasm/GermplasmByList.vue          | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/breeding-insight/service/GermplasmService.ts b/src/breeding-insight/service/GermplasmService.ts
index bd6c421ac..0c6903b4f 100644
--- a/src/breeding-insight/service/GermplasmService.ts
+++ b/src/breeding-insight/service/GermplasmService.ts
@@ -35,7 +35,7 @@ export class GermplasmService {
                          { listDbId, listName, ...brapiFilters  }: GermplasmFilter):
         Promise<BiResponse> {
         //Form the query params including sorting, pagination, and filtering
-        let params: any = {list: listDbId, ...brapiFilters };
+        let params: any = {listDbId: listDbId, ...brapiFilters };
 
         if (sort.field) {
             params['sortField'] = sort.field;
diff --git a/src/breeding-insight/service/ListService.ts b/src/breeding-insight/service/ListService.ts
index f7c0301bf..8b5b97d29 100644
--- a/src/breeding-insight/service/ListService.ts
+++ b/src/breeding-insight/service/ListService.ts
@@ -36,7 +36,8 @@ export class ListService {
             return new BiResponse({ success: true });
 
         } catch (error) {
-            // Check if the error is actually a 204 No Content response
+            // Check if the error is actually a 204 No Content response since http clients can be configured to
+            // automatically throw an error if the response has no content
             if (error.response && error.response.status === 204) {
                 // This is actually a successful deletion
                 return new BiResponse({ success: true });
diff --git a/src/views/germplasm/GermplasmByList.vue b/src/views/germplasm/GermplasmByList.vue
index d1a0569bb..8db93ead0 100644
--- a/src/views/germplasm/GermplasmByList.vue
+++ b/src/views/germplasm/GermplasmByList.vue
@@ -23,7 +23,7 @@
       <a>&lt; Germplasm Lists</a>
     </router-link>
     <h1 class="title">
-      {{ toStartCase(list ? list.listName : "") }}
+      {{ list ? list.listName : "" }}
     </h1>
 
     <GermplasmListDeletionModal

From 2bd27e7b70bacbb0de91ebde5a3671291c3c84cb Mon Sep 17 00:00:00 2001
From: dmeidlin <14339308+dmeidlin@users.noreply.github.com>
Date: Fri, 10 Jan 2025 15:55:22 -0500
Subject: [PATCH 45/98] upadte package-lock.json

---
 package-lock.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 760481dde..494aa6ebf 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+783",
+  "version": "v1.0.0+789",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "bi-web",
-      "version": "v1.0.0+783",
+      "version": "v1.0.0+789",
       "hasInstallScript": true,
       "dependencies": {
         "@casl/ability": "~4.0.0",

From aa61e4b6dd6f84132ae72088f3bbb892a746a0c9 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Fri, 10 Jan 2025 20:57:56 +0000
Subject: [PATCH 46/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index d8428efcd..ddc9686bd 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+789",
+  "version": "v1.0.0+791",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/c7125bfe6e28c4a5e896f0fb313b96a91dd7bda4"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/79e1aa9f3743af3594d6feba349f85f99f247ded"
 }

From 89865d9a0606d4f7e9ca841998cded05d883a259 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Wed, 15 Jan 2025 16:23:59 -0500
Subject: [PATCH 47/98] [BI-2437]fixed bug

---
 src/components/layouts/UserSideBarLayout.vue | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/components/layouts/UserSideBarLayout.vue b/src/components/layouts/UserSideBarLayout.vue
index 6cc19db6e..2498cf42c 100644
--- a/src/components/layouts/UserSideBarLayout.vue
+++ b/src/components/layouts/UserSideBarLayout.vue
@@ -294,7 +294,8 @@
     }
 
     filterPrograms($event: any) {
-      let filter = $event.target.value.toLowerCase();
+      this.programFilterValue = $event.target.value;
+      let filter = this.programFilterValue.toLowerCase();
       if(filter.trim().length > 0) {
         this.filteredPrograms = this.programs.filter(value => value.name!.toLowerCase().includes(filter));
       } else {

From b2083d063baf9a0ab339f040b890bec5b725fb23 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Fri, 17 Jan 2025 15:43:35 +0000
Subject: [PATCH 48/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index ddc9686bd..439adaf32 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+791",
+  "version": "v1.0.0+793",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/79e1aa9f3743af3594d6feba349f85f99f247ded"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/5b679f5b7efdc7ce04d5dcbeb93d155c4648dff0"
 }

From dc0bd3a59b0cec52cc2f78749183870e92b8fa8c Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Fri, 13 Dec 2024 09:06:17 -0800
Subject: [PATCH 49/98] WIP

---
 src/breeding-insight/dao/ExperimentDAO.ts     |  21 ++
 .../service/ExperimentService.ts              |   7 +
 .../experiments/ExperimentDeleteModal.vue     | 192 ++++++++++++++++++
 .../ExperimentObservationsDownloadModal.vue   |   2 +-
 src/components/modals/DeleteModal.vue         |  93 +++++++++
 src/config/AppAbility.ts                      |   2 +-
 src/config/ability.ts                         |   1 +
 .../ExperimentDetails.vue                     |  21 ++
 8 files changed, 337 insertions(+), 2 deletions(-)
 create mode 100644 src/components/experiments/ExperimentDeleteModal.vue
 create mode 100644 src/components/modals/DeleteModal.vue

diff --git a/src/breeding-insight/dao/ExperimentDAO.ts b/src/breeding-insight/dao/ExperimentDAO.ts
index 7c2f4759d..f0474ea56 100644
--- a/src/breeding-insight/dao/ExperimentDAO.ts
+++ b/src/breeding-insight/dao/ExperimentDAO.ts
@@ -108,6 +108,27 @@ export class ExperimentDAO {
         }
     }
 
+    static async observationUnitCount(programId: string, experimentId: string, id: string): Promise<Result<Error, number>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators/${id}`;
+        config.method = 'get';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        config.responseType = 'text';
+        // config.validateStatus = (status: number) => status >= 200 && status < 300;
+        try {
+            const response = await api.call(config);
+            // Check if the status code indicates success
+            if (response.status >= 200 && response.status < 300) {
+                return ResultGenerator.success(true);
+            } else {
+                throw new Error(`Unexpected status code: ${response.status}`);
+            }
+        } catch (error) {
+            return ResultGenerator.err(error);
+        }
+    }
+
     static async getDatasetMetadata(programId: string, experimentId: string): Promise<Result<Error, DatasetMetadata[]>> {
         const config: any = {};
         config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/datasets`;
diff --git a/src/breeding-insight/service/ExperimentService.ts b/src/breeding-insight/service/ExperimentService.ts
index 7464c0b6d..7a6707ba0 100644
--- a/src/breeding-insight/service/ExperimentService.ts
+++ b/src/breeding-insight/service/ExperimentService.ts
@@ -100,4 +100,11 @@ export class ExperimentService {
         }
         return await ExperimentDAO.deleteCollaborator(programId, experimentId, id);
     }
+
+    static async observationUnitCount(programId: string | undefined, experimentId: string, id: string): Promise<Result<Error, number>> {
+        if (!programId) {
+            return ResultGenerator.err(new Error('Missing or invalid program id'));
+        }
+        return await ExperimentDAO.deleteCollaborator(programId, experimentId, id);
+    }
 }
diff --git a/src/components/experiments/ExperimentDeleteModal.vue b/src/components/experiments/ExperimentDeleteModal.vue
new file mode 100644
index 000000000..a1a7101a1
--- /dev/null
+++ b/src/components/experiments/ExperimentDeleteModal.vue
@@ -0,0 +1,192 @@
+<!--
+- See the NOTICE file distributed with this work for additional information
+- regarding copyright ownership.
+-
+- Licensed under the Apache License, Version 2.0 (the "License");
+- you may not use this file except in compliance with the License.
+- You may obtain a copy of the License at
+-
+-     http://www.apache.org/licenses/LICENSE-2.0
+-
+- Unless required by applicable law or agreed to in writing, software
+- distributed under the License is distributed on an "AS IS" BASIS,
+- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+- See the License for the specific language governing permissions and
+- limitations under the License.
+-->
+
+<template>
+  <DeleteModal
+    v-bind:unique-id="trialId"
+    v-bind:modal-title="modalTitle"
+    v-bind:deleteAction ="deleteaAction"
+    v-bind:active="active && loadingStudyOptionsComplete && loadingDatasetOptionsComplete"
+    modal-class="experiment-observations-download-button"
+    v-on:deactivate="resetExportOptions"
+  >
+    <template #form>
+      <p>{{obsCount}} observations will be deleted. All records will be lost. Are you sure you want to delete the experimental data?</p>
+    </template>
+    <slot />
+  </DeleteModal>
+</template>
+
+
+<script lang="ts">
+import {Component, Vue, Prop, Watch} from "vue-property-decorator";
+import {validationMixin} from "vuelidate";
+import {mapGetters} from "vuex";
+import {Program} from "@/breeding-insight/model/Program";
+import {ExperimentExportOptions} from "@/breeding-insight/model/ExperimentExportOptions";
+import {FileTypeOption} from "@/breeding-insight/model/FileTypeOption";
+import {AlertTriangleIcon} from 'vue-feather-icons';
+import {Trial} from "@/breeding-insight/model/Trial";
+import {Metadata} from "@/breeding-insight/model/BiResponse";
+import {Study} from "@/breeding-insight/model/Study";
+import {StudyService} from "@/breeding-insight/service/StudyService";
+import {Result} from "@/breeding-insight/model/Result";
+import {BrAPIUtils} from "@/breeding-insight/utils/BrAPIUtils";
+import DeleteModal from "@/components/modals/DeleteModal.vue";
+import {DatasetMetadata} from "@/breeding-insight/model/DatasetMetadata";
+import {ExperimentService} from "@/breeding-insight/service/ExperimentService";
+
+@Component({
+  mixins: [validationMixin],
+  components: {DeleteModal, AlertTriangleIcon},
+  computed: {
+    ...mapGetters([
+      'activeProgram'
+    ])
+  }
+})
+export default class ExperimentDeleteModal extends Vue {
+
+  @Prop()
+  active!: boolean;
+  @Prop()
+  trialId!: string;
+  @Prop()
+  experiment!: Trial;
+  @Prop()
+  modalTitle?: string;
+  @Prop()
+  defaultDatasetId?: string; // TODO do I need this?
+
+  private activeProgram?: Program;
+  private fileOptions: ExperimentExportOptions = new ExperimentExportOptions();
+  private obsCount: number = 5;
+  //private showEnvironmentsValidationError: boolean = false;
+  private fileExtensionOptions: object[] = Object.values(FileTypeOption);
+  private datasetOptions: DatasetMetadata[] = [];
+  private environmentOptions: object[] = [];
+  private loadingStudyOptionsComplete: boolean = false;
+  private loadingDatasetOptionsComplete: boolean = false;
+
+  //TODO remove?
+  @Watch('experiment', {immediate: true})
+  onExperimentChanged() {
+    // Reset loading flags.
+    console.info("......hi Delete Modal........");
+    this.loadingStudyOptionsComplete = false;
+    this.loadingDatasetOptionsComplete = false;
+    this.getObsservationUnitCount();
+    this.getDatasetOptions();
+  }
+
+  async getObsservationUnitCount() {
+    // Fetch all environments (studies) for this experiment.
+    try {
+      // console.info("..............");
+      // console.info(this.experiment);
+      const response: Result<Error, [Study[], Metadata]> = await StudyService.getAll(this.activeProgram!.id!, this.experiment);
+      if(response.isErr()) throw response.value;
+      let [studies, metadata] = response.value;
+      // Set environment options.
+      this.environmentOptions = studies.map((s) => ({id: BrAPIUtils.getBreedingInsightId(s.externalReferences!, '/studies'), name: s.name}));
+      // console.info(":<><><><><><><>><>");
+      // console.info(this.environmentOptions);
+      this.loadingStudyOptionsComplete = true;
+    } catch (error) {
+      // Display error that studies cannot be loaded
+      this.$emit('show-error-notification', 'Error while trying to load studies');
+    }
+  }
+
+  async getDatasetOptions() {
+    // Fetch all datasets available for this experiment.
+    try {
+      const response: Result<Error, DatasetMetadata[]> = await ExperimentService.getDatasetMetadataByTrial(this.activeProgram!.id!, this.experiment!);
+      if (response.isErr()) {
+        throw response.value;
+      }
+      this.datasetOptions = response.value;
+      console.info("########");
+      console.info(this.datasetOptions);
+      this.setDefaultDatasetOption();
+
+      this.loadingDatasetOptionsComplete = true;
+    } catch (err) {
+      // Display error that datasets cannot be loaded
+      this.$emit('show-error-notification', 'Error while trying to load datasets');
+      throw err;
+    }
+  }
+
+  setDefaultDatasetOption() {
+    // Set default selected dataset to property if provided, fall back to first in list of options.
+    if (this.defaultDatasetId !== undefined) {
+      this.fileOptions.datasetId = this.defaultDatasetId;
+    } else if (this.datasetOptions.length > 0){
+      this.fileOptions.datasetId = this.datasetOptions[0].id;
+    }
+  }
+
+  async deleteaAction(): Promise<void> {
+    if (this.activeProgram) {
+      try {
+        // Call the service method and await its completion
+        //TODO add deleteExperiment to ExperimentService
+        await ExperimentService.removeCollaboratorFromExperiment(
+            this.activeProgram.id,
+            this.trialId,
+            this.collaborator.collaboratorId
+        );
+
+        // If the above call doesn't throw an error, we assume it was successful
+        // Emit the event after the promise is resolved
+        this.$emit('remove-collaborator');
+
+      } catch (error) {
+        // Handle any errors that might occur during the async operation
+        console.error('Error removing collaborator:', error);
+        // Optionally emit an error event or handle the error in some way
+        this.$emit('show-error-notification', `Error while trying to remove a collaborator`);
+      }
+    }
+  }
+
+  resetExportOptions(){
+    // Notify parent when deactivated to close modal
+    this.$emit('deactivate');
+    // Reset file export options.
+    this.fileOptions = new ExperimentExportOptions();
+    // Make sure default dataset option is selected.
+    this.setDefaultDatasetOption();
+    // Reset validation state.
+    // this.showEnvironmentsValidationError = false;
+  }
+
+  validateOptions(): boolean {
+    // Either "All environments" or one or more specific environments must be selected.
+    if (this.fileOptions.environments.length === 0 && !this.fileOptions.allEnvironments){
+      this.$emit('show-error-notification', 'One or more environments must be selected.');
+       // this.showEnvironmentsValidationError = true;
+      return false;
+    }
+    return true;
+  }
+  mounted() {
+    this.obsCount = 77;
+  }
+}
+</script>
\ No newline at end of file
diff --git a/src/components/experiments/ExperimentObservationsDownloadModal.vue b/src/components/experiments/ExperimentObservationsDownloadModal.vue
index 653204d8d..9592c5aa4 100644
--- a/src/components/experiments/ExperimentObservationsDownloadModal.vue
+++ b/src/components/experiments/ExperimentObservationsDownloadModal.vue
@@ -55,7 +55,7 @@
         <div class="column control">
           <fieldset>
             <legend class="label required">
-              <span class="required">Environment(s)</span>
+              <span class="required">Environment(s)!</span>
             </legend>
             <div class="control">
               <label
diff --git a/src/components/modals/DeleteModal.vue b/src/components/modals/DeleteModal.vue
new file mode 100644
index 000000000..2522b3c25
--- /dev/null
+++ b/src/components/modals/DeleteModal.vue
@@ -0,0 +1,93 @@
+<!--
+- See the NOTICE file distributed with this work for additional information
+- regarding copyright ownership.
+-
+- Licensed under the Apache License, Version 2.0 (the "License");
+- you may not use this file except in compliance with the License.
+- You may obtain a copy of the License at
+-
+-     http://www.apache.org/licenses/LICENSE-2.0
+-
+- Unless required by applicable law or agreed to in writing, software
+- distributed under the License is distributed on an "AS IS" BASIS,
+- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+- See the License for the specific language governing permissions and
+- limitations under the License.
+-->
+
+<template>
+  <section
+    v-bind:id="'deleteModal-' + uniqueId"
+    v-bind:class="modalClass"
+  >
+    <FormModal
+      v-bind:active.sync="active"
+      v-bind:title="modalTitle"
+      v-on:deactivate="closeDeleteModal"
+    >
+      <template #form>
+        <slot name="form" />
+      </template>
+      <template #buttons>
+        <div class="columns">
+          <div class="column is-whole has-text-centered buttons">
+            <button
+              class="button is-primary has-text-weight-bold"
+              v-on:click="invokeDeleteAction"
+            >
+              <strong>Yes</strong>
+            </button>
+            <button
+              class="button"
+              v-on:click="closeDeleteModal"
+            >
+              Cancel
+            </button>
+          </div>
+        </div>
+      </template>
+    </FormModal>
+  </section>
+</template>
+
+
+<script lang="ts">
+import {Component, Vue, Prop} from "vue-property-decorator";
+import {validationMixin} from "vuelidate";
+import FormModal from "@/components/modals/FormModal.vue";
+
+@Component({
+  mixins: [validationMixin],
+  components: {FormModal}
+})
+export default class DeleteModal extends Vue {
+
+  @Prop()
+  uniqueId!: string;
+  @Prop()
+  modalTitle?: string;
+  @Prop()
+  obsCount: number;
+  @Prop()
+  modalClass?: string;
+  @Prop()
+  deleteAction!: () => boolean;
+  @Prop()
+  active!: boolean;
+
+  closeDeleteModal(){
+    // Emit deactivate event, allows parent to reset form state, for example.
+    this.$emit('deactivate');
+  }
+
+  invokeDeleteAction(){
+    // Invoke the deleteAction prop, which returns true if action was confirmed.
+    if (this.deleteAction())
+    {
+      // Close and deactivate modal.
+      this.closeDeleteModal();
+    }
+  }
+
+}
+</script>
\ No newline at end of file
diff --git a/src/config/AppAbility.ts b/src/config/AppAbility.ts
index 590f043af..cd2eb53aa 100644
--- a/src/config/AppAbility.ts
+++ b/src/config/AppAbility.ts
@@ -17,7 +17,7 @@
 
 import {Ability, AbilityClass} from '@casl/ability';
 
-type Actions = 'manage' | 'create' | 'read' | 'update' | 'delete' | 'archive' | 'access' | 'submit';
+type Actions = 'manage' | 'delete' |'create' | 'read' | 'update' | 'delete' | 'archive' | 'access' | 'submit';
 type Subjects = 'ProgramUser' | 'Location' | 'User' | 'AdminSection' | 'Trait' | 'Import' | 'ProgramConfiguration' | 'Submission'
     | 'Experiment' | 'Germplasm' | 'Ontology' | 'SampleManagement' | 'ProgramAdministration' | 'JobManagement' | 'Collaborator' | 'BrAPI'
     | 'List';
diff --git a/src/config/ability.ts b/src/config/ability.ts
index afb865d69..2094733ef 100644
--- a/src/config/ability.ts
+++ b/src/config/ability.ts
@@ -48,6 +48,7 @@ const rolePermissions: Record<string, DefinePermissions> = {
     can('update', 'Trait');
     can('archive', 'Trait');
     can('create', 'Import');
+    can('delete', 'Experiment');
     can('access', 'ProgramConfiguration');
     can('create', 'ProgramConfiguration');
     can('update', 'ProgramConfiguration');
diff --git a/src/views/experiments-and-observations/ExperimentDetails.vue b/src/views/experiments-and-observations/ExperimentDetails.vue
index 20457906c..05291c56b 100644
--- a/src/views/experiments-and-observations/ExperimentDetails.vue
+++ b/src/views/experiments-and-observations/ExperimentDetails.vue
@@ -33,6 +33,15 @@
         v-on:deactivate="downloadModalActive = false"
     />
 
+    <ExperimentDeleteModal
+        v-bind:experiment="experiment"
+        v-bind:modal-title="`Delete ${experiment.trialName}`"
+        v-bind:trial-id="experimentUUID"
+        v-bind:active="deleteModalActive"
+        v-on:show-error-notification="$emit('show-error-notification', $event)"
+        v-on:deactivate="deleteModalActive = false"
+    />
+
     <SubEntityDatasetModal
         v-bind:experiment="experiment"
         v-bind:default-observation-level="experimentObservationUnit"
@@ -120,6 +129,7 @@
                       v-on:download-file="downloadFile()"
                       v-on:create-sub-entity-dataset="openSubEntityModal()"
                       v-on:add-collaborator="addCollaborator()"
+                      v-on:delete-experiment="deleteExperiment()"
           />
         </article>
       </div>
@@ -164,6 +174,7 @@ import ProgramsBase from "@/components/program/ProgramsBase.vue";
 import ActionMenu from "@/components/layouts/menus/ActionMenu.vue";
 import {ActionMenuItem} from "@/breeding-insight/model/ActionMenuItem";
 import ExperimentObservationsDownloadModal from "@/components/experiments/ExperimentObservationsDownloadModal.vue";
+import ExperimentDeleteModal from "@/components/experiments/ExperimentDeleteModal.vue";
 import SubEntityDatasetModal from "@/components/modals/SubEntityDatasetModal.vue";
 import {DatasetMetadata} from "@/breeding-insight/model/DatasetMetadata";
 import {SubEntityDatasetNewRequest} from "@/breeding-insight/model/SubEntityDatasetNewRequest";
@@ -176,6 +187,7 @@ import ExperimentCollaboratorRemovalModal from "@/components/experiments/Experim
     SubEntityDatasetModal,
     PlusCircleIcon,
     ExperimentObservationsDownloadModal,
+    ExperimentDeleteModal,
     ExperimentAddCollaboratorModal,
     ExperimentCollaboratorRemovalModal,
     ActionMenu
@@ -195,6 +207,8 @@ export default class ExperimentDetails extends ProgramsBase {
   private experimentLoading: boolean = true;
   private addCollaboratorActive: boolean = false;
   private downloadModalActive: boolean = false;
+  private deleteModalActive: boolean = false;
+  private obsCount
   private subEntityModalActive: boolean = false;
   private removeCollaboratorActive: boolean = false;
   private selectedForRemoval?: Collaborator = new Collaborator();
@@ -206,6 +220,7 @@ export default class ExperimentDetails extends ProgramsBase {
       new ActionMenuItem('experiment-download-file', 'download-file', 'Download file'),
       new ActionMenuItem('experiment-add-collaborator', 'add-collaborator', 'Add Collaborator',  this.$ability.can('manage', 'Collaborator')),
       new ActionMenuItem('experiment-create-sub-entity-dataset', 'create-sub-entity-dataset', 'Create Sub-Entity Dataset')
+      new ActionMenuItem('experiment-delete', 'delete-experiment', 'Delete experiment', this.$ability.can('delete', 'Experiment'))
   ];
 
   mounted () {
@@ -226,6 +241,10 @@ export default class ExperimentDetails extends ProgramsBase {
     this.downloadModalActive = true;
   }
 
+  private deleteExperiment() {
+    this.deleteModalActive = true;
+  }
+
   private addCollaborator() {
     this.addCollaboratorActive = true;
   }
@@ -300,6 +319,8 @@ export default class ExperimentDetails extends ProgramsBase {
 
   @Watch('$route')
   async getExperiment () {
+    console.info(".....route.....");
+    console.info(this.$route);
     this.experimentLoading = true;
     try {
       const response: Result<Error, Trial> = await ExperimentService.getSingleExperiment(this.activeProgram!.id!, this.experimentUUID, true);

From c109ce60a10046359bf076d8840d3859d39d60ca Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Fri, 13 Dec 2024 13:23:51 -0800
Subject: [PATCH 50/98] WIP

---
 .../service/ExperimentService.ts              | 13 ++---
 .../ExperimentDetails.vue                     | 51 +++++++++++++++++++
 2 files changed, 58 insertions(+), 6 deletions(-)

diff --git a/src/breeding-insight/service/ExperimentService.ts b/src/breeding-insight/service/ExperimentService.ts
index 7a6707ba0..fedf1c1ad 100644
--- a/src/breeding-insight/service/ExperimentService.ts
+++ b/src/breeding-insight/service/ExperimentService.ts
@@ -101,10 +101,11 @@ export class ExperimentService {
         return await ExperimentDAO.deleteCollaborator(programId, experimentId, id);
     }
 
-    static async observationUnitCount(programId: string | undefined, experimentId: string, id: string): Promise<Result<Error, number>> {
-        if (!programId) {
-            return ResultGenerator.err(new Error('Missing or invalid program id'));
-        }
-        return await ExperimentDAO.deleteCollaborator(programId, experimentId, id);
-    }
+    // static async hasObservationUnit(programId: string | undefined, experimentId: string, id: string): Promise<Result<Error, boolean>> {
+    //     if (!programId) {
+    //         return ResultGenerator.err(new Error('Missing or invalid program id'));
+    //     }
+    //     const response: Result<Error, DatasetMetadata[]> =
+    //     return await ExperimentDAO.deleteCollaborator(programId, experimentId, id);
+    // }
 }
diff --git a/src/views/experiments-and-observations/ExperimentDetails.vue b/src/views/experiments-and-observations/ExperimentDetails.vue
index 05291c56b..cb9f14483 100644
--- a/src/views/experiments-and-observations/ExperimentDetails.vue
+++ b/src/views/experiments-and-observations/ExperimentDetails.vue
@@ -213,6 +213,7 @@ export default class ExperimentDetails extends ProgramsBase {
   private removeCollaboratorActive: boolean = false;
   private selectedForRemoval?: Collaborator = new Collaborator();
   private datasetMetadata: DatasetMetadata[] = [];
+  private hasObsUnits: boolean = false;
   private collaborators: Collaborator[] = [];
 
   private actions: ActionMenuItem[] = [
@@ -360,6 +361,7 @@ async getAssignedCollaborators(): Promise<void> {
       if (response.isErr()) {
         throw response.value;
       }
+      console.info(".....Setting datsetMetadata");
       this.datasetMetadata = response.value;
     } catch (err) {
       // Display error that experiment cannot be loaded
@@ -367,5 +369,54 @@ async getAssignedCollaborators(): Promise<void> {
       throw err;
     }
   }
+
+  @Watch( 'datasetMetadata')
+  //TODO could this be an anonymous function?
+  async getHasObservationUnits():  Promise<void> {
+    console.info("()()()()(()dataset watch");
+    for (const dsm of this.datasetMetadata) {
+      let datasetId = dsm.id;
+      // console.info(datasetId);
+      try {
+        const response: Result<Error, DatasetModel> = await ExperimentService.getDatasetModel(this.activeProgram!.id!, this.experimentUUID, datasetId);
+        if (response.isErr()) {
+          throw response.value;
+        }
+        let dataset = response.value;
+        console.info("././././/./././../././.");
+        if(dataset && dataset.data && dataset.data.length>0){
+          this.hasObsUnits = true;
+          console.info("You got it");
+          break;
+        }
+      } catch (err) {
+        // Display error that dataset cannot be loaded
+        this.$emit('show-error-notification', 'Error while trying to load dataset');
+        throw err;
+      }
+    }
+  }
+
+  // async fetchDataSet(): Promise<Result<Error, DatasetModel>> {
+  //   try {
+  //     const response: Result<Error, DatasetModel> = await ExperimentService.getDatasetModel(this.activeProgram!.id!, this.experimentUUID, datasetId);
+  //     if (response.isErr()) {
+  //       throw response.value;
+  //     }
+  //     // let dataset = response.value;
+  //     // console.info(dataset);
+  //   } catch (err) {
+  //     // Display error that dataset cannot be loaded
+  //     this.$emit('show-error-notification', 'Error while trying to load dataset');
+  //     throw err;
+  //   }
+  //   return response.value;
+  // }
+
+
+
+  // async hasObservationUnits(): Promise<boolean> {
+  //
+  // }
 }
 </script>
\ No newline at end of file

From cf3bff89dcebd5216d45a95f8c4dc62f035c4dce Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Thu, 19 Dec 2024 13:04:43 -0800
Subject: [PATCH 51/98] [BI-2377] WIP

---
 ExperimentDAO.ts                              | 218 ++++++++++++++++++
 src/breeding-insight/dao/ExperimentDAO.ts     |  47 +++-
 src/breeding-insight/model/DatasetModel.ts    |   6 +-
 .../service/ExperimentService.ts              |  11 +
 .../experiments/ExperimentDeleteModal.vue     |  33 ++-
 .../ExperimentDetails.vue                     | 112 ++++++---
 6 files changed, 369 insertions(+), 58 deletions(-)
 create mode 100644 ExperimentDAO.ts

diff --git a/ExperimentDAO.ts b/ExperimentDAO.ts
new file mode 100644
index 000000000..39bf4d900
--- /dev/null
+++ b/ExperimentDAO.ts
@@ -0,0 +1,218 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import {BiResponse, Response} from "@/breeding-insight/model/BiResponse";
+import * as api from "@/util/api";
+import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
+import {Trial} from "@/breeding-insight/model/Trial.ts";
+import {DatasetModel} from "@/breeding-insight/model/DatasetModel";
+import {DatasetMetadata} from "@/breeding-insight/model/DatasetMetadata";
+import {Collaborator} from "@/breeding-insight/model/Collaborator";
+
+export class ExperimentDAO {
+
+      static async getSingleExperiment(programId: string, experimentId: string, stats: boolean): Promise<Result<Error, Trial>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/trials/${experimentId}`;
+        config.method = 'get';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        config.params = {stats: stats};
+        try {
+            const res = await api.call(config) as Response;
+            let { result } = res.data;
+            return ResultGenerator.success(result);
+        } catch (error) {
+            return ResultGenerator.err(error);
+        }
+    }
+
+    static async getUnassignedCollaborators(programId: string, experimentId: string): Promise<Result<Error, Collaborator[]>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators?active=false`;
+        config.method = 'get';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        try {
+            const res = await api.call(config) as Response;
+            let { result } = res.data;
+            return ResultGenerator.success(result);
+        } catch (error) {
+            return ResultGenerator.err(error);
+        }
+    }
+
+    static async addCollaborator(programId: string, experimentId: string, userId: string): Promise<Result<Error, Collaborator>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators`;
+        config.method = 'post';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        config.data = {userId: userId};
+        try {
+            const res = await api.call(config) as Response;
+            let { result } = res.data;
+            return ResultGenerator.success(result);
+        } catch (error) {
+            return ResultGenerator.err(error);
+        }
+    }
+
+    static async deleteCollaborator(programId: string, experimentId: string, id: string): Promise<Result<Error, boolean>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators/${id}`;
+        config.method = 'delete';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        config.responseType = 'text';
+        config.validateStatus = (status: number) => status >= 200 && status < 300;
+        try {
+            const response = await api.call(config);
+            // Check if the status code indicates success
+            if (response.status >= 200 && response.status < 300) {
+                return ResultGenerator.success(true);
+            } else {
+                throw new Error(`Unexpected status code: ${response.status}`);
+            }
+        } catch (error) {
+            return ResultGenerator.err(error);
+        }
+    }
+
+    static async getAssignedCollaborators(programId: string, experimentId: string): Promise<Result<Error, Collaborator[]>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators?active=true`;
+        config.method = 'get';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        try {
+            const res = await api.call(config) as Response;
+            let { result } = res.data;
+            return ResultGenerator.success(result);
+        } catch (error) {
+            return ResultGenerator.err(error);
+        }
+    }
+
+
+    static async deleteExperiment(programId: string, experimentId: string, softDelete: boolean): Promise<Result<Error, boolean>> {
+          console.info("ExperimentDAO....in deleteExperiment");
+          console.info(softDelete ? "soft delete": "hard delete");
+        console.info("A");
+        const config: any = {};
+        console.info("B");
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}`;
+        config.method = 'delete';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        config.params = {
+            hard : ! softDelete,
+        };
+        console.info("C");
+        try {
+            console.info("D");
+            console.info(config);
+            const response = await api.call(config);
+            console.info("E");
+            // Check if the status code indicates success
+            if (response.status >= 200 && response.status < 300) {
+                return ResultGenerator.success(true);
+            } else {
+                throw new Error(`Unexpected status code: ${response.status}`);
+            }
+        } catch (error) {
+            console.info("F");
+            return ResultGenerator.err(error);
+        }
+    }
+    // static async observationUnitCount(programId: string, experimentId: string, id: string): Promise<Result<Error, number>> {
+    //     const config: any = {};
+    //     config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators/${id}`;
+    //     config.method = 'get';
+    //     config.programId = programId;
+    //     config.experimentId = experimentId;
+    //     config.responseType = 'text';
+    //     // config.validateStatus = (status: number) => status >= 200 && status < 300;
+    //     try {
+    //         const response = await api.call(config);
+    //         // Check if the status code indicates success
+    //         if (response.status >= 200 && response.status < 300) {
+    //             return ResultGenerator.success(true);
+    //         } else {
+    //             throw new Error(`Unexpected status code: ${response.status}`);
+    //         }
+    //     } catch (error) {
+    //         return ResultGenerator.err(error);
+    //     }
+    // }
+
+    static async getDatasetMetadata(programId: string, experimentId: string): Promise<Result<Error, DatasetMetadata[]>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/datasets`;
+        config.method = 'get';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        try {
+            const res = await api.call(config) as Response;
+            let { result } = res.data;
+            return ResultGenerator.success(result);
+        } catch (error) {
+            return ResultGenerator.err(error);
+        }
+    }
+
+    static async getDatasetById(programId: string, experimentId: string, datasetId: string, stats: boolean): Promise<Result<Error, DatasetModel>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/dataset/${datasetId}`;
+        config.method = 'get';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        config.datasetId = datasetId;
+        config.params = {
+            stats : stats,
+        };
+        console.info(">>>>config:");
+        console.info(config);
+        try {
+            console.info("....before..");
+            const res = await api.call(config) as Response;
+            console.info("....after..");
+
+            let { result } = res.data;
+            return ResultGenerator.success(result);
+        } catch (error) {
+            console.info("....error..");ß
+            return ResultGenerator.err(error);
+        }
+    }
+
+    static async createSubEntityDataset(programId: string, experimentId: string, name: string, repeatedMeasures: number): Promise<Result<Error, DatasetModel>> {
+        const config: any = {};
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/dataset`;
+        config.method = 'post';
+        config.programId = programId;
+        config.experimentId = experimentId;
+        config.data = {name: name, repeatedMeasures: repeatedMeasures}  // Corresponds to SubEntityDatasetRequest in bi-api.
+        try {
+            const res = await api.call(config) as Response;
+            let { result } = res.data;
+            return ResultGenerator.success(result);
+        } catch (error) {
+            return ResultGenerator.err(error);
+        }
+    }
+}
diff --git a/src/breeding-insight/dao/ExperimentDAO.ts b/src/breeding-insight/dao/ExperimentDAO.ts
index f0474ea56..220bcc424 100644
--- a/src/breeding-insight/dao/ExperimentDAO.ts
+++ b/src/breeding-insight/dao/ExperimentDAO.ts
@@ -108,16 +108,26 @@ export class ExperimentDAO {
         }
     }
 
-    static async observationUnitCount(programId: string, experimentId: string, id: string): Promise<Result<Error, number>> {
+
+    static async deleteExperiment(programId: string, experimentId: string, softDelete: boolean): Promise<Result<Error, boolean>> {
+          console.info("ExperimentDAO....in deleteExperiment");
+          console.info(softDelete ? "soft delete": "hard delete");
+        console.info("A");
         const config: any = {};
-        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators/${id}`;
-        config.method = 'get';
+        console.info("B");
+        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}`;
+        config.method = 'delete';
         config.programId = programId;
         config.experimentId = experimentId;
-        config.responseType = 'text';
-        // config.validateStatus = (status: number) => status >= 200 && status < 300;
+        config.params = {
+            hard : ! softDelete,
+        };
+        console.info("C");
         try {
+            console.info("D");
+            console.info(config);
             const response = await api.call(config);
+            console.info("E");
             // Check if the status code indicates success
             if (response.status >= 200 && response.status < 300) {
                 return ResultGenerator.success(true);
@@ -125,9 +135,30 @@ export class ExperimentDAO {
                 throw new Error(`Unexpected status code: ${response.status}`);
             }
         } catch (error) {
+            console.info("F");
             return ResultGenerator.err(error);
         }
     }
+    // static async observationUnitCount(programId: string, experimentId: string, id: string): Promise<Result<Error, number>> {
+    //     const config: any = {};
+    //     config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators/${id}`;
+    //     config.method = 'get';
+    //     config.programId = programId;
+    //     config.experimentId = experimentId;
+    //     config.responseType = 'text';
+    //     // config.validateStatus = (status: number) => status >= 200 && status < 300;
+    //     try {
+    //         const response = await api.call(config);
+    //         // Check if the status code indicates success
+    //         if (response.status >= 200 && response.status < 300) {
+    //             return ResultGenerator.success(true);
+    //         } else {
+    //             throw new Error(`Unexpected status code: ${response.status}`);
+    //         }
+    //     } catch (error) {
+    //         return ResultGenerator.err(error);
+    //     }
+    // }
 
     static async getDatasetMetadata(programId: string, experimentId: string): Promise<Result<Error, DatasetMetadata[]>> {
         const config: any = {};
@@ -154,11 +185,17 @@ export class ExperimentDAO {
         config.params = {
             stats : stats,
         };
+        console.info(">>>>config:");
+        console.info(config);
         try {
+            console.info("....before..");
             const res = await api.call(config) as Response;
+            console.info("....after..");
+
             let { result } = res.data;
             return ResultGenerator.success(result);
         } catch (error) {
+            console.info("....error..");
             return ResultGenerator.err(error);
         }
     }
diff --git a/src/breeding-insight/model/DatasetModel.ts b/src/breeding-insight/model/DatasetModel.ts
index 37d5abe82..39094fe6a 100644
--- a/src/breeding-insight/model/DatasetModel.ts
+++ b/src/breeding-insight/model/DatasetModel.ts
@@ -30,9 +30,9 @@ export class DatasetModel {
 
   constructor(id: string,
               experimentId: string,
-              data: Observation[],
-              observationUnits: ObservationUnit[],
-              observationVariables: ObservationVariable[],
+              data?: Observation[],
+              observationUnits?: ObservationUnit[],
+              observationVariables?: ObservationVariable[],
               additionalInfo?: any
   ) {
     this.id = id;
diff --git a/src/breeding-insight/service/ExperimentService.ts b/src/breeding-insight/service/ExperimentService.ts
index fedf1c1ad..bab531ea0 100644
--- a/src/breeding-insight/service/ExperimentService.ts
+++ b/src/breeding-insight/service/ExperimentService.ts
@@ -101,6 +101,17 @@ export class ExperimentService {
         return await ExperimentDAO.deleteCollaborator(programId, experimentId, id);
     }
 
+    static async deleteExperiment(programId: string | undefined, experimentId: string, hasObsUnits: boolean): Promise<Result<Error, boolean>> {
+
+            console.info("-----has unit obj");
+            console.info(hasObsUnits);
+
+        if (!programId) {
+            return ResultGenerator.err(new Error('Missing or invalid program id'));
+        }
+        return await ExperimentDAO.deleteExperiment(programId, experimentId, hasObsUnits);
+    }
+
     // static async hasObservationUnit(programId: string | undefined, experimentId: string, id: string): Promise<Result<Error, boolean>> {
     //     if (!programId) {
     //         return ResultGenerator.err(new Error('Missing or invalid program id'));
diff --git a/src/components/experiments/ExperimentDeleteModal.vue b/src/components/experiments/ExperimentDeleteModal.vue
index a1a7101a1..6c7bb6057 100644
--- a/src/components/experiments/ExperimentDeleteModal.vue
+++ b/src/components/experiments/ExperimentDeleteModal.vue
@@ -19,7 +19,7 @@
   <DeleteModal
     v-bind:unique-id="trialId"
     v-bind:modal-title="modalTitle"
-    v-bind:deleteAction ="deleteaAction"
+    v-bind:deleteAction ="deleteAction"
     v-bind:active="active && loadingStudyOptionsComplete && loadingDatasetOptionsComplete"
     modal-class="experiment-observations-download-button"
     v-on:deactivate="resetExportOptions"
@@ -66,6 +66,8 @@ export default class ExperimentDeleteModal extends Vue {
   @Prop()
   trialId!: string;
   @Prop()
+  obsCount!: number;
+  @Prop()
   experiment!: Trial;
   @Prop()
   modalTitle?: string;
@@ -74,7 +76,7 @@ export default class ExperimentDeleteModal extends Vue {
 
   private activeProgram?: Program;
   private fileOptions: ExperimentExportOptions = new ExperimentExportOptions();
-  private obsCount: number = 5;
+  // private obsCount: number = 5;
   //private showEnvironmentsValidationError: boolean = false;
   private fileExtensionOptions: object[] = Object.values(FileTypeOption);
   private datasetOptions: DatasetMetadata[] = [];
@@ -141,26 +143,33 @@ export default class ExperimentDeleteModal extends Vue {
     }
   }
 
-  async deleteaAction(): Promise<void> {
+  async deleteAction(): Promise<void> {
     if (this.activeProgram) {
       try {
         // Call the service method and await its completion
-        //TODO add deleteExperiment to ExperimentService
-        await ExperimentService.removeCollaboratorFromExperiment(
+        console.debug("obs count...");
+        console.debug(this.obsCount);
+        let hasObsUnits: boolean = this.obsCount > 0;
+        await ExperimentService.deleteExperiment(
             this.activeProgram.id,
             this.trialId,
-            this.collaborator.collaboratorId
+            hasObsUnits
         );
-
+        this.$router.push({
+          name: 'experiments-observations',
+          params: {
+            programId: this.activeProgram!.id!
+          },
+        });
         // If the above call doesn't throw an error, we assume it was successful
         // Emit the event after the promise is resolved
         this.$emit('remove-collaborator');
 
       } catch (error) {
         // Handle any errors that might occur during the async operation
-        console.error('Error removing collaborator:', error);
+        console.error('Error while trying to delete experiment:', error);
         // Optionally emit an error event or handle the error in some way
-        this.$emit('show-error-notification', `Error while trying to remove a collaborator`);
+        this.$emit('show-error-notification', `Error while trying to delete experiment`);
       }
     }
   }
@@ -185,8 +194,8 @@ export default class ExperimentDeleteModal extends Vue {
     }
     return true;
   }
-  mounted() {
-    this.obsCount = 77;
-  }
+  // mounted() {
+  //   this.obsCount = 77;
+  // }
 }
 </script>
\ No newline at end of file
diff --git a/src/views/experiments-and-observations/ExperimentDetails.vue b/src/views/experiments-and-observations/ExperimentDetails.vue
index cb9f14483..68760ad1a 100644
--- a/src/views/experiments-and-observations/ExperimentDetails.vue
+++ b/src/views/experiments-and-observations/ExperimentDetails.vue
@@ -38,6 +38,7 @@
         v-bind:modal-title="`Delete ${experiment.trialName}`"
         v-bind:trial-id="experimentUUID"
         v-bind:active="deleteModalActive"
+        v-bind:obs-count="fetchObsCount()"
         v-on:show-error-notification="$emit('show-error-notification', $event)"
         v-on:deactivate="deleteModalActive = false"
     />
@@ -208,12 +209,13 @@ export default class ExperimentDetails extends ProgramsBase {
   private addCollaboratorActive: boolean = false;
   private downloadModalActive: boolean = false;
   private deleteModalActive: boolean = false;
-  private obsCount
+  // private obsCount
   private subEntityModalActive: boolean = false;
   private removeCollaboratorActive: boolean = false;
   private selectedForRemoval?: Collaborator = new Collaborator();
   private datasetMetadata: DatasetMetadata[] = [];
   private hasObsUnits: boolean = false;
+  private dataset: DatasetModel = new DatasetModel("", "");
   private collaborators: Collaborator[] = [];
 
   private actions: ActionMenuItem[] = [
@@ -222,9 +224,10 @@ export default class ExperimentDetails extends ProgramsBase {
       new ActionMenuItem('experiment-add-collaborator', 'add-collaborator', 'Add Collaborator',  this.$ability.can('manage', 'Collaborator')),
       new ActionMenuItem('experiment-create-sub-entity-dataset', 'create-sub-entity-dataset', 'Create Sub-Entity Dataset')
       new ActionMenuItem('experiment-delete', 'delete-experiment', 'Delete experiment', this.$ability.can('delete', 'Experiment'))
+
   ];
 
-  mounted () {
+  mounted() {
     this.getExperiment();
     this.getDatasetMetadata();
   }
@@ -250,7 +253,7 @@ export default class ExperimentDetails extends ProgramsBase {
     this.addCollaboratorActive = true;
   }
 
-  private removeCollaborator(collaborator:Collaborator) {
+  private removeCollaborator(collaborator: Collaborator) {
     this.selectedForRemoval = collaborator;
     this.removeCollaboratorActive = true;
   }
@@ -278,27 +281,45 @@ export default class ExperimentDetails extends ProgramsBase {
   get experimentUUID(): string {
     return this.$route.params.experimentId;
   }
+
   get userName(): string {
-    if( !this.experiment.additionalInfo ){return '';}
-    if( !this.experiment.additionalInfo.createdBy){return '';}
+    if (!this.experiment.additionalInfo) {
+      return '';
+    }
+    if (!this.experiment.additionalInfo.createdBy) {
+      return '';
+    }
     return this.experiment.additionalInfo.createdBy.userName;
   }
+
   get experimentalUnit(): string {
-    if( !this.experiment.additionalInfo ){return '';}
+    if (!this.experiment.additionalInfo) {
+      return '';
+    }
     return this.experiment.additionalInfo.defaultObservationLevel;
   }
+
   get experimentType(): string {
-    if( !this.experiment.additionalInfo ){return '';}
+    if (!this.experiment.additionalInfo) {
+      return '';
+    }
     return this.experiment.additionalInfo.experimentType;
   }
+
   get createdDate(): string {
-    if( !this.experiment.additionalInfo ){return '';}
+    if (!this.experiment.additionalInfo) {
+      return '';
+    }
     return this.experiment.additionalInfo.createdDate;
   }
+
   get germplasmCount(): string {
-    if( !this.experiment.additionalInfo ){return '';}
+    if (!this.experiment.additionalInfo) {
+      return '';
+    }
     return this.experiment.additionalInfo.germplasmCount;
   }
+
   // This is not being used.  But may be used later.
   // get environmentsCount(): string {
   //   if( !this.experiment.additionalInfo ){return '';}
@@ -319,7 +340,7 @@ export default class ExperimentDetails extends ProgramsBase {
   }
 
   @Watch('$route')
-  async getExperiment () {
+  async getExperiment() {
     console.info(".....route.....");
     console.info(this.$route);
     this.experimentLoading = true;
@@ -338,20 +359,20 @@ export default class ExperimentDetails extends ProgramsBase {
     }
   }
 
-@Watch('$route', { immediate: true })
-async getAssignedCollaborators(): Promise<void> {
-  try {
-    const response: Result<Error, Collaborator[]> = await ExperimentService.getAssignedCollaborators(this.activeProgram!.id!, this.experimentUUID);
-    if (response.isErr()) {
-      throw response.value;
+  @Watch('$route', {immediate: true})
+  async getAssignedCollaborators(): Promise<void> {
+    try {
+      const response: Result<Error, Collaborator[]> = await ExperimentService.getAssignedCollaborators(this.activeProgram!.id!, this.experimentUUID);
+      if (response.isErr()) {
+        throw response.value;
+      }
+      this.collaborators = response.value.data;
+    } catch (err) {
+      // Display error that experiment cannot be loaded
+      this.$emit('show-error-notification', 'Error while trying to load collaborators');
+      throw err;
     }
-    this.collaborators = response.value.data;
-  } catch (err) {
-    // Display error that experiment cannot be loaded
-    this.$emit('show-error-notification', 'Error while trying to load collaborators');
-    throw err;
   }
-}
 
   // Get metadata for all datasets available in this experiment.
   @Watch('$route')
@@ -370,33 +391,50 @@ async getAssignedCollaborators(): Promise<void> {
     }
   }
 
-  @Watch( 'datasetMetadata')
+  @Watch('datasetMetadata')
   //TODO could this be an anonymous function?
-  async getHasObservationUnits():  Promise<void> {
-    console.info("()()()()(()dataset watch");
-    for (const dsm of this.datasetMetadata) {
-      let datasetId = dsm.id;
-      // console.info(datasetId);
+  async getHasObservationUnits(): Promise<void> {
+    console.info("()()()()()))())()");
+      let dms = this.datasetMetadata[0];
+    console.info("..getting dms");
+    console.info(dms);
+      let datasetId = dms.id;
+    console.info("..got dms ID");
       try {
+        console.info("..getting dataset");
         const response: Result<Error, DatasetModel> = await ExperimentService.getDatasetModel(this.activeProgram!.id!, this.experimentUUID, datasetId);
         if (response.isErr()) {
+          console.info("..error");
           throw response.value;
         }
-        let dataset = response.value;
-        console.info("././././/./././../././.");
-        if(dataset && dataset.data && dataset.data.length>0){
-          this.hasObsUnits = true;
-          console.info("You got it");
-          break;
-        }
+        this.dataset = response.value;
+        console.info("has dataset");
+        // if (dataset && dataset.data && dataset.data.length > 0) {
+        //   this.hasObsUnits = true;
+        //   console.info("You got it");
+        // }
       } catch (err) {
         // Display error that dataset cannot be loaded
         this.$emit('show-error-notification', 'Error while trying to load dataset');
         throw err;
       }
+  }
+  fetchObsCount(): number{
+    let count = 1;
+    console.info(".....1");
+    if(this.dataset){
+      console.info(".....2");
+      console.info(this.dataset);
+    }
+    if(this.dataset && this.dataset.additionalInfo){
+      console.info(".....3");
+      count = this.dataset.additionalInfo.observations;
     }
+    console.info("Count = " + count);
+    return count;
   }
-
+}
+</script>
   // async fetchDataSet(): Promise<Result<Error, DatasetModel>> {
   //   try {
   //     const response: Result<Error, DatasetModel> = await ExperimentService.getDatasetModel(this.activeProgram!.id!, this.experimentUUID, datasetId);
@@ -418,5 +456,3 @@ async getAssignedCollaborators(): Promise<void> {
   // async hasObservationUnits(): Promise<boolean> {
   //
   // }
-}
-</script>
\ No newline at end of file

From b7b655b663f3804937b6c2336501901a6283607d Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Thu, 19 Dec 2024 14:07:31 -0800
Subject: [PATCH 52/98] [BI-2377] WIP

---
 ExperimentDAO.ts                              | 218 ------------------
 src/breeding-insight/dao/ExperimentDAO.ts     |  34 ---
 .../service/ExperimentService.ts              |  12 -
 .../experiments/ExperimentDeleteModal.vue     |  48 +---
 .../ExperimentObservationsDownloadModal.vue   |   2 +-
 .../ExperimentDetails.vue                     |  45 +---
 6 files changed, 13 insertions(+), 346 deletions(-)
 delete mode 100644 ExperimentDAO.ts

diff --git a/ExperimentDAO.ts b/ExperimentDAO.ts
deleted file mode 100644
index 39bf4d900..000000000
--- a/ExperimentDAO.ts
+++ /dev/null
@@ -1,218 +0,0 @@
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-import {BiResponse, Response} from "@/breeding-insight/model/BiResponse";
-import * as api from "@/util/api";
-import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
-import {Trial} from "@/breeding-insight/model/Trial.ts";
-import {DatasetModel} from "@/breeding-insight/model/DatasetModel";
-import {DatasetMetadata} from "@/breeding-insight/model/DatasetMetadata";
-import {Collaborator} from "@/breeding-insight/model/Collaborator";
-
-export class ExperimentDAO {
-
-      static async getSingleExperiment(programId: string, experimentId: string, stats: boolean): Promise<Result<Error, Trial>> {
-        const config: any = {};
-        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/brapi/v2/trials/${experimentId}`;
-        config.method = 'get';
-        config.programId = programId;
-        config.experimentId = experimentId;
-        config.params = {stats: stats};
-        try {
-            const res = await api.call(config) as Response;
-            let { result } = res.data;
-            return ResultGenerator.success(result);
-        } catch (error) {
-            return ResultGenerator.err(error);
-        }
-    }
-
-    static async getUnassignedCollaborators(programId: string, experimentId: string): Promise<Result<Error, Collaborator[]>> {
-        const config: any = {};
-        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators?active=false`;
-        config.method = 'get';
-        config.programId = programId;
-        config.experimentId = experimentId;
-        try {
-            const res = await api.call(config) as Response;
-            let { result } = res.data;
-            return ResultGenerator.success(result);
-        } catch (error) {
-            return ResultGenerator.err(error);
-        }
-    }
-
-    static async addCollaborator(programId: string, experimentId: string, userId: string): Promise<Result<Error, Collaborator>> {
-        const config: any = {};
-        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators`;
-        config.method = 'post';
-        config.programId = programId;
-        config.experimentId = experimentId;
-        config.data = {userId: userId};
-        try {
-            const res = await api.call(config) as Response;
-            let { result } = res.data;
-            return ResultGenerator.success(result);
-        } catch (error) {
-            return ResultGenerator.err(error);
-        }
-    }
-
-    static async deleteCollaborator(programId: string, experimentId: string, id: string): Promise<Result<Error, boolean>> {
-        const config: any = {};
-        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators/${id}`;
-        config.method = 'delete';
-        config.programId = programId;
-        config.experimentId = experimentId;
-        config.responseType = 'text';
-        config.validateStatus = (status: number) => status >= 200 && status < 300;
-        try {
-            const response = await api.call(config);
-            // Check if the status code indicates success
-            if (response.status >= 200 && response.status < 300) {
-                return ResultGenerator.success(true);
-            } else {
-                throw new Error(`Unexpected status code: ${response.status}`);
-            }
-        } catch (error) {
-            return ResultGenerator.err(error);
-        }
-    }
-
-    static async getAssignedCollaborators(programId: string, experimentId: string): Promise<Result<Error, Collaborator[]>> {
-        const config: any = {};
-        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators?active=true`;
-        config.method = 'get';
-        config.programId = programId;
-        config.experimentId = experimentId;
-        try {
-            const res = await api.call(config) as Response;
-            let { result } = res.data;
-            return ResultGenerator.success(result);
-        } catch (error) {
-            return ResultGenerator.err(error);
-        }
-    }
-
-
-    static async deleteExperiment(programId: string, experimentId: string, softDelete: boolean): Promise<Result<Error, boolean>> {
-          console.info("ExperimentDAO....in deleteExperiment");
-          console.info(softDelete ? "soft delete": "hard delete");
-        console.info("A");
-        const config: any = {};
-        console.info("B");
-        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}`;
-        config.method = 'delete';
-        config.programId = programId;
-        config.experimentId = experimentId;
-        config.params = {
-            hard : ! softDelete,
-        };
-        console.info("C");
-        try {
-            console.info("D");
-            console.info(config);
-            const response = await api.call(config);
-            console.info("E");
-            // Check if the status code indicates success
-            if (response.status >= 200 && response.status < 300) {
-                return ResultGenerator.success(true);
-            } else {
-                throw new Error(`Unexpected status code: ${response.status}`);
-            }
-        } catch (error) {
-            console.info("F");
-            return ResultGenerator.err(error);
-        }
-    }
-    // static async observationUnitCount(programId: string, experimentId: string, id: string): Promise<Result<Error, number>> {
-    //     const config: any = {};
-    //     config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators/${id}`;
-    //     config.method = 'get';
-    //     config.programId = programId;
-    //     config.experimentId = experimentId;
-    //     config.responseType = 'text';
-    //     // config.validateStatus = (status: number) => status >= 200 && status < 300;
-    //     try {
-    //         const response = await api.call(config);
-    //         // Check if the status code indicates success
-    //         if (response.status >= 200 && response.status < 300) {
-    //             return ResultGenerator.success(true);
-    //         } else {
-    //             throw new Error(`Unexpected status code: ${response.status}`);
-    //         }
-    //     } catch (error) {
-    //         return ResultGenerator.err(error);
-    //     }
-    // }
-
-    static async getDatasetMetadata(programId: string, experimentId: string): Promise<Result<Error, DatasetMetadata[]>> {
-        const config: any = {};
-        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/datasets`;
-        config.method = 'get';
-        config.programId = programId;
-        config.experimentId = experimentId;
-        try {
-            const res = await api.call(config) as Response;
-            let { result } = res.data;
-            return ResultGenerator.success(result);
-        } catch (error) {
-            return ResultGenerator.err(error);
-        }
-    }
-
-    static async getDatasetById(programId: string, experimentId: string, datasetId: string, stats: boolean): Promise<Result<Error, DatasetModel>> {
-        const config: any = {};
-        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/dataset/${datasetId}`;
-        config.method = 'get';
-        config.programId = programId;
-        config.experimentId = experimentId;
-        config.datasetId = datasetId;
-        config.params = {
-            stats : stats,
-        };
-        console.info(">>>>config:");
-        console.info(config);
-        try {
-            console.info("....before..");
-            const res = await api.call(config) as Response;
-            console.info("....after..");
-
-            let { result } = res.data;
-            return ResultGenerator.success(result);
-        } catch (error) {
-            console.info("....error..");ß
-            return ResultGenerator.err(error);
-        }
-    }
-
-    static async createSubEntityDataset(programId: string, experimentId: string, name: string, repeatedMeasures: number): Promise<Result<Error, DatasetModel>> {
-        const config: any = {};
-        config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/dataset`;
-        config.method = 'post';
-        config.programId = programId;
-        config.experimentId = experimentId;
-        config.data = {name: name, repeatedMeasures: repeatedMeasures}  // Corresponds to SubEntityDatasetRequest in bi-api.
-        try {
-            const res = await api.call(config) as Response;
-            let { result } = res.data;
-            return ResultGenerator.success(result);
-        } catch (error) {
-            return ResultGenerator.err(error);
-        }
-    }
-}
diff --git a/src/breeding-insight/dao/ExperimentDAO.ts b/src/breeding-insight/dao/ExperimentDAO.ts
index 220bcc424..9e1f77c0c 100644
--- a/src/breeding-insight/dao/ExperimentDAO.ts
+++ b/src/breeding-insight/dao/ExperimentDAO.ts
@@ -110,11 +110,7 @@ export class ExperimentDAO {
 
 
     static async deleteExperiment(programId: string, experimentId: string, softDelete: boolean): Promise<Result<Error, boolean>> {
-          console.info("ExperimentDAO....in deleteExperiment");
-          console.info(softDelete ? "soft delete": "hard delete");
-        console.info("A");
         const config: any = {};
-        console.info("B");
         config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}`;
         config.method = 'delete';
         config.programId = programId;
@@ -122,12 +118,8 @@ export class ExperimentDAO {
         config.params = {
             hard : ! softDelete,
         };
-        console.info("C");
         try {
-            console.info("D");
-            console.info(config);
             const response = await api.call(config);
-            console.info("E");
             // Check if the status code indicates success
             if (response.status >= 200 && response.status < 300) {
                 return ResultGenerator.success(true);
@@ -139,26 +131,6 @@ export class ExperimentDAO {
             return ResultGenerator.err(error);
         }
     }
-    // static async observationUnitCount(programId: string, experimentId: string, id: string): Promise<Result<Error, number>> {
-    //     const config: any = {};
-    //     config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}/collaborators/${id}`;
-    //     config.method = 'get';
-    //     config.programId = programId;
-    //     config.experimentId = experimentId;
-    //     config.responseType = 'text';
-    //     // config.validateStatus = (status: number) => status >= 200 && status < 300;
-    //     try {
-    //         const response = await api.call(config);
-    //         // Check if the status code indicates success
-    //         if (response.status >= 200 && response.status < 300) {
-    //             return ResultGenerator.success(true);
-    //         } else {
-    //             throw new Error(`Unexpected status code: ${response.status}`);
-    //         }
-    //     } catch (error) {
-    //         return ResultGenerator.err(error);
-    //     }
-    // }
 
     static async getDatasetMetadata(programId: string, experimentId: string): Promise<Result<Error, DatasetMetadata[]>> {
         const config: any = {};
@@ -185,17 +157,11 @@ export class ExperimentDAO {
         config.params = {
             stats : stats,
         };
-        console.info(">>>>config:");
-        console.info(config);
         try {
-            console.info("....before..");
             const res = await api.call(config) as Response;
-            console.info("....after..");
-
             let { result } = res.data;
             return ResultGenerator.success(result);
         } catch (error) {
-            console.info("....error..");
             return ResultGenerator.err(error);
         }
     }
diff --git a/src/breeding-insight/service/ExperimentService.ts b/src/breeding-insight/service/ExperimentService.ts
index bab531ea0..3a2c3b84e 100644
--- a/src/breeding-insight/service/ExperimentService.ts
+++ b/src/breeding-insight/service/ExperimentService.ts
@@ -102,21 +102,9 @@ export class ExperimentService {
     }
 
     static async deleteExperiment(programId: string | undefined, experimentId: string, hasObsUnits: boolean): Promise<Result<Error, boolean>> {
-
-            console.info("-----has unit obj");
-            console.info(hasObsUnits);
-
         if (!programId) {
             return ResultGenerator.err(new Error('Missing or invalid program id'));
         }
         return await ExperimentDAO.deleteExperiment(programId, experimentId, hasObsUnits);
     }
-
-    // static async hasObservationUnit(programId: string | undefined, experimentId: string, id: string): Promise<Result<Error, boolean>> {
-    //     if (!programId) {
-    //         return ResultGenerator.err(new Error('Missing or invalid program id'));
-    //     }
-    //     const response: Result<Error, DatasetMetadata[]> =
-    //     return await ExperimentDAO.deleteCollaborator(programId, experimentId, id);
-    // }
 }
diff --git a/src/components/experiments/ExperimentDeleteModal.vue b/src/components/experiments/ExperimentDeleteModal.vue
index 6c7bb6057..e7eaea4d4 100644
--- a/src/components/experiments/ExperimentDeleteModal.vue
+++ b/src/components/experiments/ExperimentDeleteModal.vue
@@ -20,7 +20,7 @@
     v-bind:unique-id="trialId"
     v-bind:modal-title="modalTitle"
     v-bind:deleteAction ="deleteAction"
-    v-bind:active="active && loadingStudyOptionsComplete && loadingDatasetOptionsComplete"
+    v-bind:active="active && loadingDatasetOptionsComplete"
     modal-class="experiment-observations-download-button"
     v-on:deactivate="resetExportOptions"
   >
@@ -81,38 +81,16 @@ export default class ExperimentDeleteModal extends Vue {
   private fileExtensionOptions: object[] = Object.values(FileTypeOption);
   private datasetOptions: DatasetMetadata[] = [];
   private environmentOptions: object[] = [];
-  private loadingStudyOptionsComplete: boolean = false;
-  private loadingDatasetOptionsComplete: boolean = false;
+  // private loadingStudyOptionsComplete: boolean = false;
+  private loadingDatasetOptionsComplete: boolean = true;
 
-  //TODO remove?
-  @Watch('experiment', {immediate: true})
-  onExperimentChanged() {
-    // Reset loading flags.
-    console.info("......hi Delete Modal........");
-    this.loadingStudyOptionsComplete = false;
-    this.loadingDatasetOptionsComplete = false;
-    this.getObsservationUnitCount();
-    this.getDatasetOptions();
-  }
-
-  async getObsservationUnitCount() {
-    // Fetch all environments (studies) for this experiment.
-    try {
-      // console.info("..............");
-      // console.info(this.experiment);
-      const response: Result<Error, [Study[], Metadata]> = await StudyService.getAll(this.activeProgram!.id!, this.experiment);
-      if(response.isErr()) throw response.value;
-      let [studies, metadata] = response.value;
-      // Set environment options.
-      this.environmentOptions = studies.map((s) => ({id: BrAPIUtils.getBreedingInsightId(s.externalReferences!, '/studies'), name: s.name}));
-      // console.info(":<><><><><><><>><>");
-      // console.info(this.environmentOptions);
-      this.loadingStudyOptionsComplete = true;
-    } catch (error) {
-      // Display error that studies cannot be loaded
-      this.$emit('show-error-notification', 'Error while trying to load studies');
-    }
-  }
+  // //TODO remove?
+  // @Watch('experiment', {immediate: true})
+  // onExperimentChanged() {
+  //   // Reset loading flag.
+  //   this.loadingDatasetOptionsComplete = false;
+  //   this.getDatasetOptions();
+  // }
 
   async getDatasetOptions() {
     // Fetch all datasets available for this experiment.
@@ -122,8 +100,6 @@ export default class ExperimentDeleteModal extends Vue {
         throw response.value;
       }
       this.datasetOptions = response.value;
-      console.info("########");
-      console.info(this.datasetOptions);
       this.setDefaultDatasetOption();
 
       this.loadingDatasetOptionsComplete = true;
@@ -147,13 +123,11 @@ export default class ExperimentDeleteModal extends Vue {
     if (this.activeProgram) {
       try {
         // Call the service method and await its completion
-        console.debug("obs count...");
-        console.debug(this.obsCount);
         let hasObsUnits: boolean = this.obsCount > 0;
         await ExperimentService.deleteExperiment(
             this.activeProgram.id,
             this.trialId,
-            hasObsUnits
+            hasObsUnits,
         );
         this.$router.push({
           name: 'experiments-observations',
diff --git a/src/components/experiments/ExperimentObservationsDownloadModal.vue b/src/components/experiments/ExperimentObservationsDownloadModal.vue
index 9592c5aa4..653204d8d 100644
--- a/src/components/experiments/ExperimentObservationsDownloadModal.vue
+++ b/src/components/experiments/ExperimentObservationsDownloadModal.vue
@@ -55,7 +55,7 @@
         <div class="column control">
           <fieldset>
             <legend class="label required">
-              <span class="required">Environment(s)!</span>
+              <span class="required">Environment(s)</span>
             </legend>
             <div class="control">
               <label
diff --git a/src/views/experiments-and-observations/ExperimentDetails.vue b/src/views/experiments-and-observations/ExperimentDetails.vue
index 68760ad1a..5a6a579c0 100644
--- a/src/views/experiments-and-observations/ExperimentDetails.vue
+++ b/src/views/experiments-and-observations/ExperimentDetails.vue
@@ -209,7 +209,6 @@ export default class ExperimentDetails extends ProgramsBase {
   private addCollaboratorActive: boolean = false;
   private downloadModalActive: boolean = false;
   private deleteModalActive: boolean = false;
-  // private obsCount
   private subEntityModalActive: boolean = false;
   private removeCollaboratorActive: boolean = false;
   private selectedForRemoval?: Collaborator = new Collaborator();
@@ -341,8 +340,6 @@ export default class ExperimentDetails extends ProgramsBase {
 
   @Watch('$route')
   async getExperiment() {
-    console.info(".....route.....");
-    console.info(this.$route);
     this.experimentLoading = true;
     try {
       const response: Result<Error, Trial> = await ExperimentService.getSingleExperiment(this.activeProgram!.id!, this.experimentUUID, true);
@@ -382,7 +379,6 @@ export default class ExperimentDetails extends ProgramsBase {
       if (response.isErr()) {
         throw response.value;
       }
-      console.info(".....Setting datsetMetadata");
       this.datasetMetadata = response.value;
     } catch (err) {
       // Display error that experiment cannot be loaded
@@ -392,27 +388,16 @@ export default class ExperimentDetails extends ProgramsBase {
   }
 
   @Watch('datasetMetadata')
-  //TODO could this be an anonymous function?
   async getHasObservationUnits(): Promise<void> {
-    console.info("()()()()()))())()");
       let dms = this.datasetMetadata[0];
-    console.info("..getting dms");
-    console.info(dms);
       let datasetId = dms.id;
-    console.info("..got dms ID");
       try {
-        console.info("..getting dataset");
         const response: Result<Error, DatasetModel> = await ExperimentService.getDatasetModel(this.activeProgram!.id!, this.experimentUUID, datasetId);
         if (response.isErr()) {
-          console.info("..error");
           throw response.value;
         }
         this.dataset = response.value;
-        console.info("has dataset");
-        // if (dataset && dataset.data && dataset.data.length > 0) {
-        //   this.hasObsUnits = true;
-        //   console.info("You got it");
-        // }
+
       } catch (err) {
         // Display error that dataset cannot be loaded
         this.$emit('show-error-notification', 'Error while trying to load dataset');
@@ -421,38 +406,10 @@ export default class ExperimentDetails extends ProgramsBase {
   }
   fetchObsCount(): number{
     let count = 1;
-    console.info(".....1");
-    if(this.dataset){
-      console.info(".....2");
-      console.info(this.dataset);
-    }
     if(this.dataset && this.dataset.additionalInfo){
-      console.info(".....3");
       count = this.dataset.additionalInfo.observations;
     }
-    console.info("Count = " + count);
     return count;
   }
 }
 </script>
-  // async fetchDataSet(): Promise<Result<Error, DatasetModel>> {
-  //   try {
-  //     const response: Result<Error, DatasetModel> = await ExperimentService.getDatasetModel(this.activeProgram!.id!, this.experimentUUID, datasetId);
-  //     if (response.isErr()) {
-  //       throw response.value;
-  //     }
-  //     // let dataset = response.value;
-  //     // console.info(dataset);
-  //   } catch (err) {
-  //     // Display error that dataset cannot be loaded
-  //     this.$emit('show-error-notification', 'Error while trying to load dataset');
-  //     throw err;
-  //   }
-  //   return response.value;
-  // }
-
-
-
-  // async hasObservationUnits(): Promise<boolean> {
-  //
-  // }

From c6c09759456abcf14dd1bdebf7116fb3bc7eec72 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Thu, 9 Jan 2025 10:05:15 -0500
Subject: [PATCH 53/98] [BI-2377] clean up code

---
 .../experiments/ExperimentDeleteModal.vue     | 83 ++-----------------
 src/components/modals/DeleteModal.vue         |  2 +-
 .../ExperimentDetails.vue                     | 21 ++---
 3 files changed, 16 insertions(+), 90 deletions(-)

diff --git a/src/components/experiments/ExperimentDeleteModal.vue b/src/components/experiments/ExperimentDeleteModal.vue
index e7eaea4d4..0148e46a8 100644
--- a/src/components/experiments/ExperimentDeleteModal.vue
+++ b/src/components/experiments/ExperimentDeleteModal.vue
@@ -20,14 +20,13 @@
     v-bind:unique-id="trialId"
     v-bind:modal-title="modalTitle"
     v-bind:deleteAction ="deleteAction"
-    v-bind:active="active && loadingDatasetOptionsComplete"
+    v-bind:active="active"
     modal-class="experiment-observations-download-button"
     v-on:deactivate="resetExportOptions"
   >
     <template #form>
       <p>{{obsCount}} observations will be deleted. All records will be lost. Are you sure you want to delete the experimental data?</p>
     </template>
-    <slot />
   </DeleteModal>
 </template>
 
@@ -38,16 +37,9 @@ import {validationMixin} from "vuelidate";
 import {mapGetters} from "vuex";
 import {Program} from "@/breeding-insight/model/Program";
 import {ExperimentExportOptions} from "@/breeding-insight/model/ExperimentExportOptions";
-import {FileTypeOption} from "@/breeding-insight/model/FileTypeOption";
 import {AlertTriangleIcon} from 'vue-feather-icons';
 import {Trial} from "@/breeding-insight/model/Trial";
-import {Metadata} from "@/breeding-insight/model/BiResponse";
-import {Study} from "@/breeding-insight/model/Study";
-import {StudyService} from "@/breeding-insight/service/StudyService";
-import {Result} from "@/breeding-insight/model/Result";
-import {BrAPIUtils} from "@/breeding-insight/utils/BrAPIUtils";
 import DeleteModal from "@/components/modals/DeleteModal.vue";
-import {DatasetMetadata} from "@/breeding-insight/model/DatasetMetadata";
 import {ExperimentService} from "@/breeding-insight/service/ExperimentService";
 
 @Component({
@@ -71,73 +63,29 @@ export default class ExperimentDeleteModal extends Vue {
   experiment!: Trial;
   @Prop()
   modalTitle?: string;
-  @Prop()
-  defaultDatasetId?: string; // TODO do I need this?
+
 
   private activeProgram?: Program;
   private fileOptions: ExperimentExportOptions = new ExperimentExportOptions();
-  // private obsCount: number = 5;
-  //private showEnvironmentsValidationError: boolean = false;
-  private fileExtensionOptions: object[] = Object.values(FileTypeOption);
-  private datasetOptions: DatasetMetadata[] = [];
-  private environmentOptions: object[] = [];
-  // private loadingStudyOptionsComplete: boolean = false;
-  private loadingDatasetOptionsComplete: boolean = true;
-
-  // //TODO remove?
-  // @Watch('experiment', {immediate: true})
-  // onExperimentChanged() {
-  //   // Reset loading flag.
-  //   this.loadingDatasetOptionsComplete = false;
-  //   this.getDatasetOptions();
-  // }
-
-  async getDatasetOptions() {
-    // Fetch all datasets available for this experiment.
-    try {
-      const response: Result<Error, DatasetMetadata[]> = await ExperimentService.getDatasetMetadataByTrial(this.activeProgram!.id!, this.experiment!);
-      if (response.isErr()) {
-        throw response.value;
-      }
-      this.datasetOptions = response.value;
-      this.setDefaultDatasetOption();
-
-      this.loadingDatasetOptionsComplete = true;
-    } catch (err) {
-      // Display error that datasets cannot be loaded
-      this.$emit('show-error-notification', 'Error while trying to load datasets');
-      throw err;
-    }
-  }
-
-  setDefaultDatasetOption() {
-    // Set default selected dataset to property if provided, fall back to first in list of options.
-    if (this.defaultDatasetId !== undefined) {
-      this.fileOptions.datasetId = this.defaultDatasetId;
-    } else if (this.datasetOptions.length > 0){
-      this.fileOptions.datasetId = this.datasetOptions[0].id;
-    }
-  }
 
   async deleteAction(): Promise<void> {
     if (this.activeProgram) {
       try {
-        // Call the service method and await its completion
         let hasObsUnits: boolean = this.obsCount > 0;
+        // Call the service method and await its completion
         await ExperimentService.deleteExperiment(
             this.activeProgram.id,
             this.trialId,
             hasObsUnits,
         );
+        // now switch screen to the list of remaining experiments
         this.$router.push({
           name: 'experiments-observations',
           params: {
             programId: this.activeProgram!.id!
           },
         });
-        // If the above call doesn't throw an error, we assume it was successful
-        // Emit the event after the promise is resolved
-        this.$emit('remove-collaborator');
+
 
       } catch (error) {
         // Handle any errors that might occur during the async operation
@@ -151,25 +99,6 @@ export default class ExperimentDeleteModal extends Vue {
   resetExportOptions(){
     // Notify parent when deactivated to close modal
     this.$emit('deactivate');
-    // Reset file export options.
-    this.fileOptions = new ExperimentExportOptions();
-    // Make sure default dataset option is selected.
-    this.setDefaultDatasetOption();
-    // Reset validation state.
-    // this.showEnvironmentsValidationError = false;
-  }
-
-  validateOptions(): boolean {
-    // Either "All environments" or one or more specific environments must be selected.
-    if (this.fileOptions.environments.length === 0 && !this.fileOptions.allEnvironments){
-      this.$emit('show-error-notification', 'One or more environments must be selected.');
-       // this.showEnvironmentsValidationError = true;
-      return false;
-    }
-    return true;
   }
-  // mounted() {
-  //   this.obsCount = 77;
-  // }
 }
-</script>
\ No newline at end of file
+</script>
diff --git a/src/components/modals/DeleteModal.vue b/src/components/modals/DeleteModal.vue
index 2522b3c25..af4e44ad3 100644
--- a/src/components/modals/DeleteModal.vue
+++ b/src/components/modals/DeleteModal.vue
@@ -71,7 +71,7 @@ export default class DeleteModal extends Vue {
   @Prop()
   modalClass?: string;
   @Prop()
-  deleteAction!: () => boolean;
+  deleteAction!: () => Promise<void>;
   @Prop()
   active!: boolean;
 
diff --git a/src/views/experiments-and-observations/ExperimentDetails.vue b/src/views/experiments-and-observations/ExperimentDetails.vue
index 5a6a579c0..e7c864000 100644
--- a/src/views/experiments-and-observations/ExperimentDetails.vue
+++ b/src/views/experiments-and-observations/ExperimentDetails.vue
@@ -38,7 +38,7 @@
         v-bind:modal-title="`Delete ${experiment.trialName}`"
         v-bind:trial-id="experimentUUID"
         v-bind:active="deleteModalActive"
-        v-bind:obs-count="fetchObsCount()"
+        v-bind:obs-count="obsCount"
         v-on:show-error-notification="$emit('show-error-notification', $event)"
         v-on:deactivate="deleteModalActive = false"
     />
@@ -214,7 +214,7 @@ export default class ExperimentDetails extends ProgramsBase {
   private selectedForRemoval?: Collaborator = new Collaborator();
   private datasetMetadata: DatasetMetadata[] = [];
   private hasObsUnits: boolean = false;
-  private dataset: DatasetModel = new DatasetModel("", "");
+  private obsCount: number = 0;
   private collaborators: Collaborator[] = [];
 
   private actions: ActionMenuItem[] = [
@@ -388,28 +388,25 @@ export default class ExperimentDetails extends ProgramsBase {
   }
 
   @Watch('datasetMetadata')
-  async getHasObservationUnits(): Promise<void> {
+  async getObsUnitCount(): Promise<void> {
       let dms = this.datasetMetadata[0];
       let datasetId = dms.id;
       try {
         const response: Result<Error, DatasetModel> = await ExperimentService.getDatasetModel(this.activeProgram!.id!, this.experimentUUID, datasetId);
+
         if (response.isErr()) {
           throw response.value;
         }
-        this.dataset = response.value;
-
+        let dataset = response.value;
+        if(dataset && dataset.additionalInfo){
+          this.obsCount = dataset.additionalInfo.observations;
+        }
       } catch (err) {
         // Display error that dataset cannot be loaded
         this.$emit('show-error-notification', 'Error while trying to load dataset');
         throw err;
       }
   }
-  fetchObsCount(): number{
-    let count = 1;
-    if(this.dataset && this.dataset.additionalInfo){
-      count = this.dataset.additionalInfo.observations;
-    }
-    return count;
-  }
+
 }
 </script>

From 99f5093169d6d04da7bd126b9549b1f875a4105b Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Thu, 9 Jan 2025 12:01:29 -0500
Subject: [PATCH 54/98] [BI-2377] fixed bug introduced by merge.

---
 src/views/experiments-and-observations/ExperimentDetails.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/views/experiments-and-observations/ExperimentDetails.vue b/src/views/experiments-and-observations/ExperimentDetails.vue
index e7c864000..3a17aa567 100644
--- a/src/views/experiments-and-observations/ExperimentDetails.vue
+++ b/src/views/experiments-and-observations/ExperimentDetails.vue
@@ -221,7 +221,7 @@ export default class ExperimentDetails extends ProgramsBase {
       new ActionMenuItem('experiment-import-file', 'import-file', 'Import file', this.$ability.can('create', 'Import')),
       new ActionMenuItem('experiment-download-file', 'download-file', 'Download file'),
       new ActionMenuItem('experiment-add-collaborator', 'add-collaborator', 'Add Collaborator',  this.$ability.can('manage', 'Collaborator')),
-      new ActionMenuItem('experiment-create-sub-entity-dataset', 'create-sub-entity-dataset', 'Create Sub-Entity Dataset')
+      new ActionMenuItem('experiment-create-sub-entity-dataset', 'create-sub-entity-dataset', 'Create Sub-Entity Dataset'),
       new ActionMenuItem('experiment-delete', 'delete-experiment', 'Delete experiment', this.$ability.can('delete', 'Experiment'))
 
   ];

From 8ef642c80e8652e063809dc853b364317193b9ee Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Mon, 13 Jan 2025 16:15:23 -0500
Subject: [PATCH 55/98] [BI-2277] Clean-up code.  Respond to PR coments

---
 src/breeding-insight/model/DatasetModel.ts    |  6 +-
 .../experiments/ExperimentDeleteModal.vue     | 10 +-
 src/components/modals/DeleteModal.vue         | 93 -------------------
 src/config/AppAbility.ts                      |  2 +-
 4 files changed, 9 insertions(+), 102 deletions(-)
 delete mode 100644 src/components/modals/DeleteModal.vue

diff --git a/src/breeding-insight/model/DatasetModel.ts b/src/breeding-insight/model/DatasetModel.ts
index 39094fe6a..37d5abe82 100644
--- a/src/breeding-insight/model/DatasetModel.ts
+++ b/src/breeding-insight/model/DatasetModel.ts
@@ -30,9 +30,9 @@ export class DatasetModel {
 
   constructor(id: string,
               experimentId: string,
-              data?: Observation[],
-              observationUnits?: ObservationUnit[],
-              observationVariables?: ObservationVariable[],
+              data: Observation[],
+              observationUnits: ObservationUnit[],
+              observationVariables: ObservationVariable[],
               additionalInfo?: any
   ) {
     this.id = id;
diff --git a/src/components/experiments/ExperimentDeleteModal.vue b/src/components/experiments/ExperimentDeleteModal.vue
index 0148e46a8..99e3c92fc 100644
--- a/src/components/experiments/ExperimentDeleteModal.vue
+++ b/src/components/experiments/ExperimentDeleteModal.vue
@@ -16,10 +16,10 @@
 -->
 
 <template>
-  <DeleteModal
+  <ConfirmationModal
     v-bind:unique-id="trialId"
     v-bind:modal-title="modalTitle"
-    v-bind:deleteAction ="deleteAction"
+    v-bind:confirmedAction ="deleteAction"
     v-bind:active="active"
     modal-class="experiment-observations-download-button"
     v-on:deactivate="resetExportOptions"
@@ -27,7 +27,7 @@
     <template #form>
       <p>{{obsCount}} observations will be deleted. All records will be lost. Are you sure you want to delete the experimental data?</p>
     </template>
-  </DeleteModal>
+  </ConfirmationModal>
 </template>
 
 
@@ -39,12 +39,12 @@ import {Program} from "@/breeding-insight/model/Program";
 import {ExperimentExportOptions} from "@/breeding-insight/model/ExperimentExportOptions";
 import {AlertTriangleIcon} from 'vue-feather-icons';
 import {Trial} from "@/breeding-insight/model/Trial";
-import DeleteModal from "@/components/modals/DeleteModal.vue";
+import ConfirmationModal from "@/components/modals/ConfirmationModal.vue";
 import {ExperimentService} from "@/breeding-insight/service/ExperimentService";
 
 @Component({
   mixins: [validationMixin],
-  components: {DeleteModal, AlertTriangleIcon},
+  components: {ConfirmationModal, AlertTriangleIcon},
   computed: {
     ...mapGetters([
       'activeProgram'
diff --git a/src/components/modals/DeleteModal.vue b/src/components/modals/DeleteModal.vue
deleted file mode 100644
index af4e44ad3..000000000
--- a/src/components/modals/DeleteModal.vue
+++ /dev/null
@@ -1,93 +0,0 @@
-<!--
-- See the NOTICE file distributed with this work for additional information
-- regarding copyright ownership.
--
-- Licensed under the Apache License, Version 2.0 (the "License");
-- you may not use this file except in compliance with the License.
-- You may obtain a copy of the License at
--
--     http://www.apache.org/licenses/LICENSE-2.0
--
-- Unless required by applicable law or agreed to in writing, software
-- distributed under the License is distributed on an "AS IS" BASIS,
-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-- See the License for the specific language governing permissions and
-- limitations under the License.
--->
-
-<template>
-  <section
-    v-bind:id="'deleteModal-' + uniqueId"
-    v-bind:class="modalClass"
-  >
-    <FormModal
-      v-bind:active.sync="active"
-      v-bind:title="modalTitle"
-      v-on:deactivate="closeDeleteModal"
-    >
-      <template #form>
-        <slot name="form" />
-      </template>
-      <template #buttons>
-        <div class="columns">
-          <div class="column is-whole has-text-centered buttons">
-            <button
-              class="button is-primary has-text-weight-bold"
-              v-on:click="invokeDeleteAction"
-            >
-              <strong>Yes</strong>
-            </button>
-            <button
-              class="button"
-              v-on:click="closeDeleteModal"
-            >
-              Cancel
-            </button>
-          </div>
-        </div>
-      </template>
-    </FormModal>
-  </section>
-</template>
-
-
-<script lang="ts">
-import {Component, Vue, Prop} from "vue-property-decorator";
-import {validationMixin} from "vuelidate";
-import FormModal from "@/components/modals/FormModal.vue";
-
-@Component({
-  mixins: [validationMixin],
-  components: {FormModal}
-})
-export default class DeleteModal extends Vue {
-
-  @Prop()
-  uniqueId!: string;
-  @Prop()
-  modalTitle?: string;
-  @Prop()
-  obsCount: number;
-  @Prop()
-  modalClass?: string;
-  @Prop()
-  deleteAction!: () => Promise<void>;
-  @Prop()
-  active!: boolean;
-
-  closeDeleteModal(){
-    // Emit deactivate event, allows parent to reset form state, for example.
-    this.$emit('deactivate');
-  }
-
-  invokeDeleteAction(){
-    // Invoke the deleteAction prop, which returns true if action was confirmed.
-    if (this.deleteAction())
-    {
-      // Close and deactivate modal.
-      this.closeDeleteModal();
-    }
-  }
-
-}
-</script>
\ No newline at end of file
diff --git a/src/config/AppAbility.ts b/src/config/AppAbility.ts
index cd2eb53aa..590f043af 100644
--- a/src/config/AppAbility.ts
+++ b/src/config/AppAbility.ts
@@ -17,7 +17,7 @@
 
 import {Ability, AbilityClass} from '@casl/ability';
 
-type Actions = 'manage' | 'delete' |'create' | 'read' | 'update' | 'delete' | 'archive' | 'access' | 'submit';
+type Actions = 'manage' | 'create' | 'read' | 'update' | 'delete' | 'archive' | 'access' | 'submit';
 type Subjects = 'ProgramUser' | 'Location' | 'User' | 'AdminSection' | 'Trait' | 'Import' | 'ProgramConfiguration' | 'Submission'
     | 'Experiment' | 'Germplasm' | 'Ontology' | 'SampleManagement' | 'ProgramAdministration' | 'JobManagement' | 'Collaborator' | 'BrAPI'
     | 'List';

From 510d50ec58575199aa9f1d968fcc4b3d6cae831c Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Wed, 15 Jan 2025 09:35:38 -0500
Subject: [PATCH 56/98] [BI-2377] fix accessibility issue

---
 src/components/layouts/menus/ActionMenu.vue | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/components/layouts/menus/ActionMenu.vue b/src/components/layouts/menus/ActionMenu.vue
index e19c09fb6..5fa93dad4 100644
--- a/src/components/layouts/menus/ActionMenu.vue
+++ b/src/components/layouts/menus/ActionMenu.vue
@@ -16,9 +16,11 @@
 
 <template>
   <b-dropdown
-              position="is-bottom-left"
-              append-to-body
-              aria-role="menu">
+      <!--   aria-label Fixes accessibility issue https://www.w3.org/WAI/ARIA/apg/practices/landmark-regions/ -->
+      :aria-label="buttonText"
+      position="is-bottom-left"
+      append-to-body
+      aria-role="menu">
     <template #trigger>
       <button
           class="button has-text-weight-bold"

From a3d888409dbb2272a2d87df0f1bcf23f98e2dc53 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Wed, 15 Jan 2025 09:54:25 -0500
Subject: [PATCH 57/98] [BI-2377] fix bug

---
 src/components/layouts/menus/ActionMenu.vue | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/components/layouts/menus/ActionMenu.vue b/src/components/layouts/menus/ActionMenu.vue
index 5fa93dad4..9da802475 100644
--- a/src/components/layouts/menus/ActionMenu.vue
+++ b/src/components/layouts/menus/ActionMenu.vue
@@ -16,7 +16,6 @@
 
 <template>
   <b-dropdown
-      <!--   aria-label Fixes accessibility issue https://www.w3.org/WAI/ARIA/apg/practices/landmark-regions/ -->
       :aria-label="buttonText"
       position="is-bottom-left"
       append-to-body

From a4fdc6968959d83646ae9e1b338b798a9afaa492 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Thu, 16 Jan 2025 11:12:23 -0500
Subject: [PATCH 58/98] [BI-2377] shows success notification

---
 src/components/experiments/ExperimentDeleteModal.vue         | 3 ++-
 src/views/experiments-and-observations/ExperimentDetails.vue | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/components/experiments/ExperimentDeleteModal.vue b/src/components/experiments/ExperimentDeleteModal.vue
index 99e3c92fc..ff782035f 100644
--- a/src/components/experiments/ExperimentDeleteModal.vue
+++ b/src/components/experiments/ExperimentDeleteModal.vue
@@ -85,7 +85,7 @@ export default class ExperimentDeleteModal extends Vue {
             programId: this.activeProgram!.id!
           },
         });
-
+        this.$emit('show-success-notification', `Success! The experiment has been deleted.`);
 
       } catch (error) {
         // Handle any errors that might occur during the async operation
@@ -96,6 +96,7 @@ export default class ExperimentDeleteModal extends Vue {
     }
   }
 
+
   resetExportOptions(){
     // Notify parent when deactivated to close modal
     this.$emit('deactivate');
diff --git a/src/views/experiments-and-observations/ExperimentDetails.vue b/src/views/experiments-and-observations/ExperimentDetails.vue
index 3a17aa567..d595531f0 100644
--- a/src/views/experiments-and-observations/ExperimentDetails.vue
+++ b/src/views/experiments-and-observations/ExperimentDetails.vue
@@ -40,6 +40,7 @@
         v-bind:active="deleteModalActive"
         v-bind:obs-count="obsCount"
         v-on:show-error-notification="$emit('show-error-notification', $event)"
+        v-on:show-success-notification="$emit('show-success-notification', $event)"
         v-on:deactivate="deleteModalActive = false"
     />
 

From 15d4780b24afa31e223c1f65b54ce6eb5fbc61ec Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Wed, 22 Jan 2025 19:35:54 +0000
Subject: [PATCH 59/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 439adaf32..7861ab719 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+793",
+  "version": "v1.0.0+795",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/5b679f5b7efdc7ce04d5dcbeb93d155c4648dff0"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/1e9d449f2f0572481b85a62187d94cd2c414720e"
 }

From 321b82e5fc24f6cc956de9c7433cab1735ef80a4 Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Fri, 31 Jan 2025 17:21:14 -0500
Subject: [PATCH 60/98] Work in progress

---
 .../dao/SampleSubmissionDAO.ts                | 14 ++++
 .../service/SampleSubmissionService.ts        | 37 +++++----
 .../modals/SampleSubmissionDeleteModal.vue    | 79 +++++++++++++++++++
 src/config/ability.ts                         |  1 +
 src/views/sample-mgmt/SampleManagement.vue    |  3 +
 src/views/sample-mgmt/SubmissionDetails.vue   | 32 +++++++-
 6 files changed, 150 insertions(+), 16 deletions(-)
 create mode 100644 src/components/modals/SampleSubmissionDeleteModal.vue

diff --git a/src/breeding-insight/dao/SampleSubmissionDAO.ts b/src/breeding-insight/dao/SampleSubmissionDAO.ts
index 9c8e1a3fc..5f99f31b6 100644
--- a/src/breeding-insight/dao/SampleSubmissionDAO.ts
+++ b/src/breeding-insight/dao/SampleSubmissionDAO.ts
@@ -48,6 +48,20 @@ export class SampleSubmissionDAO {
     }
   }
 
+  static async deleteSubmission(programId: string, submissionId: string): Promise<Result<Error, Void>> {
+    const config: any = {};
+    config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/submissions/${submissionId}`;
+    config.method = 'delete';
+    config.programId = programId;
+    config.submissionId = submissionId;
+    try {
+      await api.call(config);
+      return ResultGenerator.success();
+    } catch (error) {
+      return ResultGenerator.err(error);
+    }
+  }
+
     static async submitToDArT(programId: string, submissionId: string): Promise<Result<Error, VendorOrderSubmission>> {
       const config: any = {};
       config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/submissions/${submissionId}/submit?vendor=dart`;
diff --git a/src/breeding-insight/service/SampleSubmissionService.ts b/src/breeding-insight/service/SampleSubmissionService.ts
index abf8d08f5..1c9042a3e 100644
--- a/src/breeding-insight/service/SampleSubmissionService.ts
+++ b/src/breeding-insight/service/SampleSubmissionService.ts
@@ -20,6 +20,7 @@ import {SampleSubmission} from "@/breeding-insight/model/SampleSubmission";
 import {SampleSubmissionDAO} from "@/breeding-insight/dao/SampleSubmissionDAO";
 import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
 import {VendorOrderSubmission} from "@/breeding-insight/brapi/model/geno/vendorOrderSubmission";
+import {programManagement} from "@/store/program-management";
 
 export class SampleSubmissionService {
   private static getSampleSubmissionUnknown: string = 'An unknown error occurred while retrieving sample submissions';
@@ -61,24 +62,30 @@ export class SampleSubmissionService {
     return await SampleSubmissionDAO.getSubmissionById(programId, submissionId, true);
   }
 
-    static async submitToDArT(programId: string, submissionId: string): Promise<Result<Error, VendorOrderSubmission>> {
-      if (!programId) {
-        return ResultGenerator.err(new Error('Missing or invalid program id'));
-      }
-      return await SampleSubmissionDAO.submitToDArT(programId, submissionId);
+  static async submitToDArT(programId: string, submissionId: string): Promise<Result<Error, VendorOrderSubmission>> {
+    if (!programId) {
+      return ResultGenerator.err(new Error('Missing or invalid program id'));
     }
+    return await SampleSubmissionDAO.submitToDArT(programId, submissionId);
+  }
 
-    static async checkVendorStatus(programId: string, submissionId: string): Promise<Result<Error, SampleSubmission>> {
-      if (!programId) {
-        return ResultGenerator.err(new Error('Missing or invalid program id'));
-      }
-      return await SampleSubmissionDAO.checkVendorStatus(programId, submissionId);
+  static async checkVendorStatus(programId: string, submissionId: string): Promise<Result<Error, SampleSubmission>> {
+    if (!programId) {
+      return ResultGenerator.err(new Error('Missing or invalid program id'));
     }
+    return await SampleSubmissionDAO.checkVendorStatus(programId, submissionId);
+  }
 
-    static async updateSubmissionStatus(programId: string, submissionId: string, status: string): Promise<Result<Error, SampleSubmission>> {
-      if (!programId) {
-        return ResultGenerator.err(new Error('Missing or invalid program id'));
-      }
-      return await SampleSubmissionDAO.updateSubmissionStatus(programId, submissionId, status);
+  static async updateSubmissionStatus(programId: string, submissionId: string, status: string): Promise<Result<Error, SampleSubmission>> {
+    if (!programId) {
+      return ResultGenerator.err(new Error('Missing or invalid program id'));
     }
+    return await SampleSubmissionDAO.updateSubmissionStatus(programId, submissionId, status);
+  }
+
+  static async deleteSubmission(programId: string, submissionId: string) : Promise<Result<Error, Void>> {
+    return await SampleSubmissionDAO.deleteSubmission(programId, submissionId);
+  }
+
+
 }
\ No newline at end of file
diff --git a/src/components/modals/SampleSubmissionDeleteModal.vue b/src/components/modals/SampleSubmissionDeleteModal.vue
new file mode 100644
index 000000000..af31d6c27
--- /dev/null
+++ b/src/components/modals/SampleSubmissionDeleteModal.vue
@@ -0,0 +1,79 @@
+<!--
+- See the NOTICE file distributed with this work for additional information
+- regarding copyright ownership.
+-
+- Licensed under the Apache License, Version 2.0 (the "License");
+- you may not use this file except in compliance with the License.
+- You may obtain a copy of the License at
+-
+-     http://www.apache.org/licenses/LICENSE-2.0
+-
+- Unless required by applicable law or agreed to in writing, software
+- distributed under the License is distributed on an "AS IS" BASIS,
+- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+- See the License for the specific language governing permissions and
+- limitations under the License.
+-->
+
+<template>
+  <ConfirmationModal
+      v-bind:unique-id="submissionId"
+      v-bind:modal-title="modalTitle"
+      v-bind:confirmedAction="deleteSampleSubmission"
+      v-bind:active="active"
+      modal-class="germplasm-list-deletion-button"
+      v-on:deactivate="cancelDelete"
+  >
+    <template #form>
+      <p>Are you sure you want to delete the sample submission?</p>
+    </template>
+    <slot />
+  </ConfirmationModal>
+</template>
+
+<script lang="ts">
+import {Component, Vue, Prop} from "vue-property-decorator";
+import {validationMixin} from "vuelidate";
+import {mapGetters} from "vuex";
+import {Program} from "@/breeding-insight/model/Program";
+import {AlertTriangleIcon} from 'vue-feather-icons';
+import ConfirmationModal from "@/components/modals/ConfirmationModal.vue";
+import {SampleSubmissionService} from "@/breeding-insight/service/SampleSubmissionService";
+
+@Component({
+  mixins: [validationMixin],
+  components: {ConfirmationModal, AlertTriangleIcon},
+  computed: {
+    ...mapGetters([
+      'activeProgram'
+    ])
+  }
+})
+export default class SampleSubmissionDeleteModal extends Vue {
+
+  @Prop()
+  active!: boolean;
+  @Prop()
+  submissionId!: string;
+  @Prop()
+  modalTitle?: string;
+
+  private activeProgram?: Program;
+
+  async deleteSampleSubmission(): Promise<void> {
+    if (this.activeProgram) {
+      try {
+        await SampleSubmissionService.deleteSubmission(this.activeProgram.id, this.submissionId);
+        this.$emit('submission-deleted');
+
+      } catch (error) {
+        this.$emit('show-error-notification', `Error while trying to delete the sample submission`);
+      }
+    }
+  }
+
+  cancelDelete(){
+    this.$emit('deactivate');
+  }
+}
+</script>
\ No newline at end of file
diff --git a/src/config/ability.ts b/src/config/ability.ts
index 2094733ef..f26ee2578 100644
--- a/src/config/ability.ts
+++ b/src/config/ability.ts
@@ -73,6 +73,7 @@ const rolePermissions: Record<string, DefinePermissions> = {
     can('manage', 'User');
     can('access', 'AdminSection');
     can('submit', 'Submission');
+    can('delete', 'Submission');
     can('access', 'Experiment');
     can('access', 'Ontology');
     can('access', 'Germplasm');
diff --git a/src/views/sample-mgmt/SampleManagement.vue b/src/views/sample-mgmt/SampleManagement.vue
index 3da5fbc77..c81277e27 100644
--- a/src/views/sample-mgmt/SampleManagement.vue
+++ b/src/views/sample-mgmt/SampleManagement.vue
@@ -99,6 +99,8 @@
         </ExpandableTable>
       </div>
     </div>
+    <!-- The following seems to be some old dead code so commented out for now, was causing console errors -->
+    <!--
     <GenericModal
         v-bind:active.sync="showGenerateFileModal"
         v-bind:msg-title="'Generate Sample Management File'"
@@ -111,6 +113,7 @@
         <button class="button" v-on:click="closeModal()">Cancel</button>
       </template>
     </GenericModal>
+    -->
   </div>
 </template>
 
diff --git a/src/views/sample-mgmt/SubmissionDetails.vue b/src/views/sample-mgmt/SubmissionDetails.vue
index f9873bc1e..f493412d3 100644
--- a/src/views/sample-mgmt/SubmissionDetails.vue
+++ b/src/views/sample-mgmt/SubmissionDetails.vue
@@ -19,6 +19,17 @@
     <router-link v-bind:to="{name: 'sample-management', params: {programId: activeProgram.id}}">
       &lt; Sample Management
     </router-link>
+
+    <SampleSubmissionDeleteModal
+      v-bind:active="deleteModalActive"
+      v-bind:submission-id="submissionId"
+      v-bind:modal-title="`Delete Submission`"
+      v-on:show-error-notification="$emit('show-error-notification', $event)"
+      v-on:deactivate="deleteModalActive = false"
+      v-on:list-deleted="deleteSuccess"
+    />
+    <!-- ${submission.name} -->
+
     <div class="mb-4"/>
     <template v-if="submissionLoading">
       <div class="loading-indicator"></div>
@@ -62,6 +73,7 @@
                       v-on:submit="startOrderSubmission()"
                       v-on:manual-update-status="startManualUpdate()"
                       v-on:check-status="checkVendorStatus()"
+                      v-on:delete="deleteSubmission()"
           />
         </article>
       </div>
@@ -358,15 +370,19 @@ import StatusEnum = VendorOrderStatusResponseResult.StatusEnum;
 import {Plate} from "@/breeding-insight/brapi/model/geno/plate";
 import * as XLSX from "xlsx";
 import {WorkBook} from "xlsx";
+import SampleSubmissionDeleteModal from "@/components/modals/SampleSubmissionDeleteModal.vue";
+import GermplasmListDeletionModal from "@/components/germplasm/GermplasmListDeletionlModal.vue";
 
 @Component({
   components: {
+    GermplasmListDeletionModal,
     GenericModal,
     ExpandableTable,
     GermplasmLink,
     PlusCircleIcon,
     ExperimentObservationsDownloadModal,
-    ActionMenu
+    ActionMenu,
+    SampleSubmissionDeleteModal
   },
   computed: {
     ...mapGetters([
@@ -392,6 +408,7 @@ export default class SubmissionDetails extends ProgramsBase {
   private showUpdateModal = false;
   private updateStarted = false;
   private statusEdit?: string = 'NOT SUBMITTED';
+  private deleteModalActive: boolean = false;
 
   private collator = new Intl.Collator('en', {numeric: true, sensitivity: 'base'});
 
@@ -406,6 +423,11 @@ export default class SubmissionDetails extends ProgramsBase {
     return this.$route.params.submissionId;
   }
 
+  private deleteSuccess() {
+    // Navigate to the submissions table since this submission no longer exists
+    this.$router.push({ name: "sample-management" });
+  }
+
   async getSubmission(showLoading: boolean = true) {
     this.submissionLoading = showLoading;
 
@@ -447,6 +469,10 @@ export default class SubmissionDetails extends ProgramsBase {
       }
     }
 
+    if (this.$ability.can('delete', 'Submission')) {
+      actionsMenuItems.push(new ActionMenuItem('submission-delete', 'delete', 'Delete'));
+    }
+
     this.actions = actionsMenuItems;
   }
 
@@ -717,5 +743,9 @@ export default class SubmissionDetails extends ProgramsBase {
     let value = props.data.additionalInfo.gid;
     return Number(value) === (Number(input));
   }
+
+  deleteSubmission() {
+    this.deleteModalActive = true;
+  }
 }
 </script>
\ No newline at end of file

From 7360fb768f236165c0cc88ca2361a2a2794c2ffc Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Mon, 3 Feb 2025 16:47:32 -0500
Subject: [PATCH 61/98] Added error handling

---
 .../modals/SampleSubmissionDeleteModal.vue          | 13 ++++++++++++-
 src/views/sample-mgmt/SubmissionDetails.vue         |  6 ++++--
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/src/components/modals/SampleSubmissionDeleteModal.vue b/src/components/modals/SampleSubmissionDeleteModal.vue
index af31d6c27..1200eafea 100644
--- a/src/components/modals/SampleSubmissionDeleteModal.vue
+++ b/src/components/modals/SampleSubmissionDeleteModal.vue
@@ -39,6 +39,8 @@ import {Program} from "@/breeding-insight/model/Program";
 import {AlertTriangleIcon} from 'vue-feather-icons';
 import ConfirmationModal from "@/components/modals/ConfirmationModal.vue";
 import {SampleSubmissionService} from "@/breeding-insight/service/SampleSubmissionService";
+import {Result} from "@/breeding-insight/model/Result";
+import {SampleSubmission} from "@/breeding-insight/model/SampleSubmission";
 
 @Component({
   mixins: [validationMixin],
@@ -60,10 +62,19 @@ export default class SampleSubmissionDeleteModal extends Vue {
 
   private activeProgram?: Program;
 
+  // TODO: move this to parent and get rid of this modal component
   async deleteSampleSubmission(): Promise<void> {
     if (this.activeProgram) {
       try {
-        await SampleSubmissionService.deleteSubmission(this.activeProgram.id, this.submissionId);
+        const result: Result<Error, Void> = await SampleSubmissionService.deleteSubmission(this.activeProgram.id, this.submissionId);
+        if (result.isErr()) {
+          const response = result.value.response;
+
+          if (response && response.status === 405) {
+            this.$emit('show-error-notification', `Cannot delete a submission with submitted or completed status`);
+            return;
+          }
+        }
         this.$emit('submission-deleted');
 
       } catch (error) {
diff --git a/src/views/sample-mgmt/SubmissionDetails.vue b/src/views/sample-mgmt/SubmissionDetails.vue
index f493412d3..33ce9b960 100644
--- a/src/views/sample-mgmt/SubmissionDetails.vue
+++ b/src/views/sample-mgmt/SubmissionDetails.vue
@@ -26,7 +26,7 @@
       v-bind:modal-title="`Delete Submission`"
       v-on:show-error-notification="$emit('show-error-notification', $event)"
       v-on:deactivate="deleteModalActive = false"
-      v-on:list-deleted="deleteSuccess"
+      v-on:submission-deleted="deleteSuccess"
     />
     <!-- ${submission.name} -->
 
@@ -470,7 +470,9 @@ export default class SubmissionDetails extends ProgramsBase {
     }
 
     if (this.$ability.can('delete', 'Submission')) {
-      actionsMenuItems.push(new ActionMenuItem('submission-delete', 'delete', 'Delete'));
+      const enabled = !this.submission!.submitted && this.submission!.vendorStatus !== StatusEnum.Completed.toUpperCase();
+
+      actionsMenuItems.push(new ActionMenuItem('submission-delete', 'delete', 'Delete', enabled));
     }
 
     this.actions = actionsMenuItems;

From e9583a3bea9e70b7e28352e5bd50d90d18738dd8 Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Tue, 4 Feb 2025 08:27:10 -0500
Subject: [PATCH 62/98] [BI-2449] - Correct Exp Preview Summary Stats

---
 src/views/import/Dataset.vue | 26 +-------------------------
 1 file changed, 1 insertion(+), 25 deletions(-)

diff --git a/src/views/import/Dataset.vue b/src/views/import/Dataset.vue
index bd104ec66..626392b8c 100644
--- a/src/views/import/Dataset.vue
+++ b/src/views/import/Dataset.vue
@@ -29,17 +29,9 @@
         <div class="message-body has-text-dark">
           <div class="columns">
             <div class="column">
-              <div class="columns mb-0">
-                <div class="column has-text-right pr-0 pb-0">
-                  <b>Observation unit:</b>
-                </div>
-                <div class="column pl-1 is-three-quarters pb-0">
-                  {{ observationUnit }}
-                </div>
-              </div>
               <div class="columns mb-0 pb-0 pt-0">
                 <div class="column has-text-right pr-0 pb-0">
-                  <b>Phenotypes:</b>
+                  <b>Observation Variables:</b>
                 </div>
                 <div class="column pl-1 is-three-quarters pb-0">
                   {{ phenotypesCount }}
@@ -53,22 +45,6 @@
                   {{ totalObservationsCount }}
                 </div>
               </div>
-              <div class="columns mb-0 pb-0 pt-0">
-                <div class="column has-text-right pr-0 pb-0">
-                  <b>Observations with data:</b>
-                </div>
-                <div class="column pl-1 is-three-quarters pb-0">
-                  {{ observationsWithData }}
-                </div>
-              </div>
-              <div class="columns mb-0 pb-0 pt-0">
-                <div class="column has-text-right pr-0 pb-0">
-                  <b>Observations without data:</b>
-                </div>
-                <div class="column pl-1 is-three-quarters pb-0">
-                  {{ observationsWithoutData }}
-                </div>
-              </div>
             </div>
           </div>
         </div>

From 7a6766a1f7edce8f298c2ee1c0cbc1ca3154c5af Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Wed, 5 Feb 2025 14:50:49 -0500
Subject: [PATCH 63/98] Updated delete menu item based on demo feedback

---
 src/views/sample-mgmt/SubmissionDetails.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/views/sample-mgmt/SubmissionDetails.vue b/src/views/sample-mgmt/SubmissionDetails.vue
index 33ce9b960..0c993923f 100644
--- a/src/views/sample-mgmt/SubmissionDetails.vue
+++ b/src/views/sample-mgmt/SubmissionDetails.vue
@@ -472,7 +472,7 @@ export default class SubmissionDetails extends ProgramsBase {
     if (this.$ability.can('delete', 'Submission')) {
       const enabled = !this.submission!.submitted && this.submission!.vendorStatus !== StatusEnum.Completed.toUpperCase();
 
-      actionsMenuItems.push(new ActionMenuItem('submission-delete', 'delete', 'Delete', enabled));
+      actionsMenuItems.push(new ActionMenuItem('submission-delete', 'delete', 'Delete submission', enabled));
     }
 
     this.actions = actionsMenuItems;

From 44c31b145836890831e2cc926394bf043e816300 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 10 Feb 2025 17:36:58 +0000
Subject: [PATCH 64/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 7861ab719..ce3c0d6e1 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+795",
+  "version": "v1.0.0+797",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/1e9d449f2f0572481b85a62187d94cd2c414720e"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/ea7a7a9420f156fa963e48f2e9b347bbd47c3d2f"
 }

From 7981875ceb12e94129cbc559cdc387d18b50e667 Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Mon, 10 Feb 2025 15:16:35 -0500
Subject: [PATCH 65/98] Added delete permission for program admin

---
 src/config/ability.ts | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/config/ability.ts b/src/config/ability.ts
index f26ee2578..1e08aa268 100644
--- a/src/config/ability.ts
+++ b/src/config/ability.ts
@@ -56,6 +56,7 @@ const rolePermissions: Record<string, DefinePermissions> = {
     can('access', 'Ontology');
     can('access', 'Germplasm');
     can('access', 'SampleManagement');
+    can('delete', 'Submission');
     can('access', 'ProgramAdministration');
     can('access', 'BrAPI');
     can('access', 'JobManagement');

From 457c4f70d905472a8bfcbb98f2e775fb85752c38 Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Tue, 11 Feb 2025 11:45:33 -0500
Subject: [PATCH 66/98] Fixed console errors and display success banner on
 success

---
 src/views/sample-mgmt/SubmissionDetails.vue | 54 +++++++++++++++++----
 1 file changed, 44 insertions(+), 10 deletions(-)

diff --git a/src/views/sample-mgmt/SubmissionDetails.vue b/src/views/sample-mgmt/SubmissionDetails.vue
index 0c993923f..bf4d4271d 100644
--- a/src/views/sample-mgmt/SubmissionDetails.vue
+++ b/src/views/sample-mgmt/SubmissionDetails.vue
@@ -20,14 +20,23 @@
       &lt; Sample Management
     </router-link>
 
-    <SampleSubmissionDeleteModal
-      v-bind:active="deleteModalActive"
-      v-bind:submission-id="submissionId"
-      v-bind:modal-title="`Delete Submission`"
-      v-on:show-error-notification="$emit('show-error-notification', $event)"
-      v-on:deactivate="deleteModalActive = false"
-      v-on:submission-deleted="deleteSuccess"
-    />
+    <template v-if="!submissionDetailsLoading">
+      <ConfirmationModal
+          v-bind:unique-id="submissionId"
+          v-bind:modal-title="`Delete Submission ${submission.name}`"
+          v-bind:confirmedAction="deleteSampleSubmission"
+          v-bind:active="deleteModalActive"
+          modal-class="germplasm-list-deletion-button"
+          v-on:deactivate="deleteModalActive = false"
+          v-on:show-error-notification="$emit('show-error-notification', $event)"
+      >
+        <template #form>
+          <p><strong>{{submission.samples.length}} samples</strong> will be deleted. Are you sure you want to delete the sample submission?</p>
+        </template>
+        <slot />
+      </ConfirmationModal>
+    </template>
+
     <!-- ${submission.name} -->
 
     <div class="mb-4"/>
@@ -370,11 +379,12 @@ import StatusEnum = VendorOrderStatusResponseResult.StatusEnum;
 import {Plate} from "@/breeding-insight/brapi/model/geno/plate";
 import * as XLSX from "xlsx";
 import {WorkBook} from "xlsx";
-import SampleSubmissionDeleteModal from "@/components/modals/SampleSubmissionDeleteModal.vue";
 import GermplasmListDeletionModal from "@/components/germplasm/GermplasmListDeletionlModal.vue";
+import ConfirmationModal from "@/components/modals/ConfirmationModal.vue";
 
 @Component({
   components: {
+    ConfirmationModal,
     GermplasmListDeletionModal,
     GenericModal,
     ExpandableTable,
@@ -382,7 +392,6 @@ import GermplasmListDeletionModal from "@/components/germplasm/GermplasmListDele
     PlusCircleIcon,
     ExperimentObservationsDownloadModal,
     ActionMenu,
-    SampleSubmissionDeleteModal
   },
   computed: {
     ...mapGetters([
@@ -426,6 +435,7 @@ export default class SubmissionDetails extends ProgramsBase {
   private deleteSuccess() {
     // Navigate to the submissions table since this submission no longer exists
     this.$router.push({ name: "sample-management" });
+    this.$emit('show-success-notification', `Successfully deleted sample submission`);
   }
 
   async getSubmission(showLoading: boolean = true) {
@@ -749,5 +759,29 @@ export default class SubmissionDetails extends ProgramsBase {
   deleteSubmission() {
     this.deleteModalActive = true;
   }
+
+  async deleteSampleSubmission(): Promise<void> {
+    if (this.activeProgram) {
+      try {
+        const result: Result<Error, Void> = await SampleSubmissionService.deleteSubmission(this.activeProgram.id, this.submissionId);
+        if (result.isErr()) {
+          const response = result.value.response;
+
+          if (response && response.status === 405) {
+            this.$emit('show-error-notification', `Cannot delete a submission with submitted or completed status`);
+            return;
+          }
+        }
+        this.deleteSuccess();
+
+      } catch (error) {
+        this.$emit('show-error-notification', `Error while trying to delete the sample submission`);
+      }
+    }
+  }
+
+  cancelDelete(){
+    this.$emit('deactivate');
+  }
 }
 </script>
\ No newline at end of file

From b2101cdc9845a0e4dba0fe02e21a66be0896fb53 Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Tue, 11 Feb 2025 14:45:39 -0500
Subject: [PATCH 67/98] Removed unused modal component

---
 .../modals/SampleSubmissionDeleteModal.vue    | 90 -------------------
 1 file changed, 90 deletions(-)
 delete mode 100644 src/components/modals/SampleSubmissionDeleteModal.vue

diff --git a/src/components/modals/SampleSubmissionDeleteModal.vue b/src/components/modals/SampleSubmissionDeleteModal.vue
deleted file mode 100644
index 1200eafea..000000000
--- a/src/components/modals/SampleSubmissionDeleteModal.vue
+++ /dev/null
@@ -1,90 +0,0 @@
-<!--
-- See the NOTICE file distributed with this work for additional information
-- regarding copyright ownership.
--
-- Licensed under the Apache License, Version 2.0 (the "License");
-- you may not use this file except in compliance with the License.
-- You may obtain a copy of the License at
--
--     http://www.apache.org/licenses/LICENSE-2.0
--
-- Unless required by applicable law or agreed to in writing, software
-- distributed under the License is distributed on an "AS IS" BASIS,
-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-- See the License for the specific language governing permissions and
-- limitations under the License.
--->
-
-<template>
-  <ConfirmationModal
-      v-bind:unique-id="submissionId"
-      v-bind:modal-title="modalTitle"
-      v-bind:confirmedAction="deleteSampleSubmission"
-      v-bind:active="active"
-      modal-class="germplasm-list-deletion-button"
-      v-on:deactivate="cancelDelete"
-  >
-    <template #form>
-      <p>Are you sure you want to delete the sample submission?</p>
-    </template>
-    <slot />
-  </ConfirmationModal>
-</template>
-
-<script lang="ts">
-import {Component, Vue, Prop} from "vue-property-decorator";
-import {validationMixin} from "vuelidate";
-import {mapGetters} from "vuex";
-import {Program} from "@/breeding-insight/model/Program";
-import {AlertTriangleIcon} from 'vue-feather-icons';
-import ConfirmationModal from "@/components/modals/ConfirmationModal.vue";
-import {SampleSubmissionService} from "@/breeding-insight/service/SampleSubmissionService";
-import {Result} from "@/breeding-insight/model/Result";
-import {SampleSubmission} from "@/breeding-insight/model/SampleSubmission";
-
-@Component({
-  mixins: [validationMixin],
-  components: {ConfirmationModal, AlertTriangleIcon},
-  computed: {
-    ...mapGetters([
-      'activeProgram'
-    ])
-  }
-})
-export default class SampleSubmissionDeleteModal extends Vue {
-
-  @Prop()
-  active!: boolean;
-  @Prop()
-  submissionId!: string;
-  @Prop()
-  modalTitle?: string;
-
-  private activeProgram?: Program;
-
-  // TODO: move this to parent and get rid of this modal component
-  async deleteSampleSubmission(): Promise<void> {
-    if (this.activeProgram) {
-      try {
-        const result: Result<Error, Void> = await SampleSubmissionService.deleteSubmission(this.activeProgram.id, this.submissionId);
-        if (result.isErr()) {
-          const response = result.value.response;
-
-          if (response && response.status === 405) {
-            this.$emit('show-error-notification', `Cannot delete a submission with submitted or completed status`);
-            return;
-          }
-        }
-        this.$emit('submission-deleted');
-
-      } catch (error) {
-        this.$emit('show-error-notification', `Error while trying to delete the sample submission`);
-      }
-    }
-  }
-
-  cancelDelete(){
-    this.$emit('deactivate');
-  }
-}
-</script>
\ No newline at end of file

From 0f271026760c845334e7bfa3efc6670f50ee7cd9 Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Tue, 11 Feb 2025 14:48:14 -0500
Subject: [PATCH 68/98] Removed unused import

---
 src/breeding-insight/service/SampleSubmissionService.ts | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/breeding-insight/service/SampleSubmissionService.ts b/src/breeding-insight/service/SampleSubmissionService.ts
index 1c9042a3e..f37bb2d59 100644
--- a/src/breeding-insight/service/SampleSubmissionService.ts
+++ b/src/breeding-insight/service/SampleSubmissionService.ts
@@ -20,7 +20,6 @@ import {SampleSubmission} from "@/breeding-insight/model/SampleSubmission";
 import {SampleSubmissionDAO} from "@/breeding-insight/dao/SampleSubmissionDAO";
 import {Result, ResultGenerator} from "@/breeding-insight/model/Result";
 import {VendorOrderSubmission} from "@/breeding-insight/brapi/model/geno/vendorOrderSubmission";
-import {programManagement} from "@/store/program-management";
 
 export class SampleSubmissionService {
   private static getSampleSubmissionUnknown: string = 'An unknown error occurred while retrieving sample submissions';

From 9aafcb11ab2da57774cb992617639ecf05d06c31 Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Tue, 11 Feb 2025 14:51:09 -0500
Subject: [PATCH 69/98] Removed unused import

---
 src/views/sample-mgmt/SubmissionDetails.vue | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/views/sample-mgmt/SubmissionDetails.vue b/src/views/sample-mgmt/SubmissionDetails.vue
index bf4d4271d..2c0372280 100644
--- a/src/views/sample-mgmt/SubmissionDetails.vue
+++ b/src/views/sample-mgmt/SubmissionDetails.vue
@@ -37,8 +37,6 @@
       </ConfirmationModal>
     </template>
 
-    <!-- ${submission.name} -->
-
     <div class="mb-4"/>
     <template v-if="submissionLoading">
       <div class="loading-indicator"></div>
@@ -379,13 +377,11 @@ import StatusEnum = VendorOrderStatusResponseResult.StatusEnum;
 import {Plate} from "@/breeding-insight/brapi/model/geno/plate";
 import * as XLSX from "xlsx";
 import {WorkBook} from "xlsx";
-import GermplasmListDeletionModal from "@/components/germplasm/GermplasmListDeletionlModal.vue";
 import ConfirmationModal from "@/components/modals/ConfirmationModal.vue";
 
 @Component({
   components: {
     ConfirmationModal,
-    GermplasmListDeletionModal,
     GenericModal,
     ExpandableTable,
     GermplasmLink,

From 6b09aa0b9a0bd4e60b167585eee366e4b9b1f0bb Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Wed, 12 Feb 2025 16:59:09 -0500
Subject: [PATCH 70/98] Don't show success notification on 500 error

---
 src/views/sample-mgmt/SubmissionDetails.vue | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/views/sample-mgmt/SubmissionDetails.vue b/src/views/sample-mgmt/SubmissionDetails.vue
index 2c0372280..9202a6789 100644
--- a/src/views/sample-mgmt/SubmissionDetails.vue
+++ b/src/views/sample-mgmt/SubmissionDetails.vue
@@ -767,8 +767,11 @@ export default class SubmissionDetails extends ProgramsBase {
             this.$emit('show-error-notification', `Cannot delete a submission with submitted or completed status`);
             return;
           }
+          this.$emit('show-error-notification', `Unknown error deleting submission`);
+
+        } else {
+          this.deleteSuccess();
         }
-        this.deleteSuccess();
 
       } catch (error) {
         this.$emit('show-error-notification', `Error while trying to delete the sample submission`);

From 60b4b9e335026e4831cfdf77bf6cebb4c39bcfcf Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Thu, 13 Feb 2025 11:15:53 -0500
Subject: [PATCH 71/98] Removed old unused code

---
 src/views/sample-mgmt/SampleManagement.vue | 15 ---------------
 1 file changed, 15 deletions(-)

diff --git a/src/views/sample-mgmt/SampleManagement.vue b/src/views/sample-mgmt/SampleManagement.vue
index c81277e27..fb720caa9 100644
--- a/src/views/sample-mgmt/SampleManagement.vue
+++ b/src/views/sample-mgmt/SampleManagement.vue
@@ -99,21 +99,6 @@
         </ExpandableTable>
       </div>
     </div>
-    <!-- The following seems to be some old dead code so commented out for now, was causing console errors -->
-    <!--
-    <GenericModal
-        v-bind:active.sync="showGenerateFileModal"
-        v-bind:msg-title="'Generate Sample Management File'"
-        v-on:deactivate="closeModal()"
-        v-bind:modalClass="'generate-sample-file'"
-    >
-      <h2>Visible!</h2>
-      <template v-slot:footer>
-        <button class="button is-success" v-on:click="closeModal()">Generate</button>
-        <button class="button" v-on:click="closeModal()">Cancel</button>
-      </template>
-    </GenericModal>
-    -->
   </div>
 </template>
 

From e519001edc3ae47d25abb2ca97b534c47fe03bea Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Thu, 13 Feb 2025 19:42:34 +0000
Subject: [PATCH 72/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index ce3c0d6e1..c798ae9d9 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+797",
+  "version": "v1.0.0+799",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/ea7a7a9420f156fa963e48f2e9b347bbd47c3d2f"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/b083834195205c93ef19a28e29c5be30ccda3a92"
 }

From ae3df3143f64ad9b3c4328887bf3ecd8c040b814 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Tue, 4 Feb 2025 09:30:44 -0500
Subject: [PATCH 73/98] WIP

---
 src/breeding-insight/dao/ExperimentDAO.ts            | 2 +-
 src/breeding-insight/service/ExperimentService.ts    | 8 +++++++-
 src/components/experiments/ExperimentDeleteModal.vue | 4 +++-
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/breeding-insight/dao/ExperimentDAO.ts b/src/breeding-insight/dao/ExperimentDAO.ts
index 9e1f77c0c..e4aa10f12 100644
--- a/src/breeding-insight/dao/ExperimentDAO.ts
+++ b/src/breeding-insight/dao/ExperimentDAO.ts
@@ -110,6 +110,7 @@ export class ExperimentDAO {
 
 
     static async deleteExperiment(programId: string, experimentId: string, softDelete: boolean): Promise<Result<Error, boolean>> {
+          console.info("....deleteExperiment()....");
         const config: any = {};
         config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}`;
         config.method = 'delete';
@@ -127,7 +128,6 @@ export class ExperimentDAO {
                 throw new Error(`Unexpected status code: ${response.status}`);
             }
         } catch (error) {
-            console.info("F");
             return ResultGenerator.err(error);
         }
     }
diff --git a/src/breeding-insight/service/ExperimentService.ts b/src/breeding-insight/service/ExperimentService.ts
index 3a2c3b84e..20b2cd25d 100644
--- a/src/breeding-insight/service/ExperimentService.ts
+++ b/src/breeding-insight/service/ExperimentService.ts
@@ -23,6 +23,7 @@ import {DatasetMetadata} from "@/breeding-insight/model/DatasetMetadata";
 import {SubEntityDatasetNewRequest} from "@/breeding-insight/model/SubEntityDatasetNewRequest";
 import {BrAPIUtils} from "@/breeding-insight/utils/BrAPIUtils";
 import {Collaborator} from "@/breeding-insight/model/Collaborator";
+import {BiResponse} from "@/breeding-insight/model/BiResponse";
 
 export class ExperimentService {
 
@@ -105,6 +106,11 @@ export class ExperimentService {
         if (!programId) {
             return ResultGenerator.err(new Error('Missing or invalid program id'));
         }
-        return await ExperimentDAO.deleteExperiment(programId, experimentId, hasObsUnits);
+        let response: Result<Error, boolean>;
+        response = await ExperimentDAO.deleteExperiment(programId, experimentId, hasObsUnits);
+        if(response.isErr()) { console.info('ERRRRROR');}
+        else (console.info('Noooo Errrror'));
+        if(response.isErr()) throw response.value;
+        return response;
     }
 }
diff --git a/src/components/experiments/ExperimentDeleteModal.vue b/src/components/experiments/ExperimentDeleteModal.vue
index ff782035f..2a4bf6029 100644
--- a/src/components/experiments/ExperimentDeleteModal.vue
+++ b/src/components/experiments/ExperimentDeleteModal.vue
@@ -41,6 +41,7 @@ import {AlertTriangleIcon} from 'vue-feather-icons';
 import {Trial} from "@/breeding-insight/model/Trial";
 import ConfirmationModal from "@/components/modals/ConfirmationModal.vue";
 import {ExperimentService} from "@/breeding-insight/service/ExperimentService";
+import {ResultGenerator} from "@/breeding-insight/model/Result";
 
 @Component({
   mixins: [validationMixin],
@@ -78,6 +79,7 @@ export default class ExperimentDeleteModal extends Vue {
             this.trialId,
             hasObsUnits,
         );
+
         // now switch screen to the list of remaining experiments
         this.$router.push({
           name: 'experiments-observations',
@@ -85,7 +87,7 @@ export default class ExperimentDeleteModal extends Vue {
             programId: this.activeProgram!.id!
           },
         });
-        this.$emit('show-success-notification', `Success! The experiment has been deleted.`);
+        this.$emit('show-success-notification', `Success!! The experiment has been deleted.`);
 
       } catch (error) {
         // Handle any errors that might occur during the async operation

From bfa17005c5dbeda184acff4b0e700790f6e665ff Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Thu, 6 Feb 2025 11:23:03 -0500
Subject: [PATCH 74/98] [BI-2496] resond to HTTP-Status code

---
 src/breeding-insight/dao/ExperimentDAO.ts            | 1 -
 src/breeding-insight/service/ExperimentService.ts    | 3 ---
 src/components/experiments/ExperimentDeleteModal.vue | 4 +---
 3 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/src/breeding-insight/dao/ExperimentDAO.ts b/src/breeding-insight/dao/ExperimentDAO.ts
index e4aa10f12..3141133f5 100644
--- a/src/breeding-insight/dao/ExperimentDAO.ts
+++ b/src/breeding-insight/dao/ExperimentDAO.ts
@@ -110,7 +110,6 @@ export class ExperimentDAO {
 
 
     static async deleteExperiment(programId: string, experimentId: string, softDelete: boolean): Promise<Result<Error, boolean>> {
-          console.info("....deleteExperiment()....");
         const config: any = {};
         config.url = `${process.env.VUE_APP_BI_API_V1_PATH}/programs/${programId}/experiments/${experimentId}`;
         config.method = 'delete';
diff --git a/src/breeding-insight/service/ExperimentService.ts b/src/breeding-insight/service/ExperimentService.ts
index 20b2cd25d..ad27a535a 100644
--- a/src/breeding-insight/service/ExperimentService.ts
+++ b/src/breeding-insight/service/ExperimentService.ts
@@ -23,7 +23,6 @@ import {DatasetMetadata} from "@/breeding-insight/model/DatasetMetadata";
 import {SubEntityDatasetNewRequest} from "@/breeding-insight/model/SubEntityDatasetNewRequest";
 import {BrAPIUtils} from "@/breeding-insight/utils/BrAPIUtils";
 import {Collaborator} from "@/breeding-insight/model/Collaborator";
-import {BiResponse} from "@/breeding-insight/model/BiResponse";
 
 export class ExperimentService {
 
@@ -108,8 +107,6 @@ export class ExperimentService {
         }
         let response: Result<Error, boolean>;
         response = await ExperimentDAO.deleteExperiment(programId, experimentId, hasObsUnits);
-        if(response.isErr()) { console.info('ERRRRROR');}
-        else (console.info('Noooo Errrror'));
         if(response.isErr()) throw response.value;
         return response;
     }
diff --git a/src/components/experiments/ExperimentDeleteModal.vue b/src/components/experiments/ExperimentDeleteModal.vue
index 2a4bf6029..ff782035f 100644
--- a/src/components/experiments/ExperimentDeleteModal.vue
+++ b/src/components/experiments/ExperimentDeleteModal.vue
@@ -41,7 +41,6 @@ import {AlertTriangleIcon} from 'vue-feather-icons';
 import {Trial} from "@/breeding-insight/model/Trial";
 import ConfirmationModal from "@/components/modals/ConfirmationModal.vue";
 import {ExperimentService} from "@/breeding-insight/service/ExperimentService";
-import {ResultGenerator} from "@/breeding-insight/model/Result";
 
 @Component({
   mixins: [validationMixin],
@@ -79,7 +78,6 @@ export default class ExperimentDeleteModal extends Vue {
             this.trialId,
             hasObsUnits,
         );
-
         // now switch screen to the list of remaining experiments
         this.$router.push({
           name: 'experiments-observations',
@@ -87,7 +85,7 @@ export default class ExperimentDeleteModal extends Vue {
             programId: this.activeProgram!.id!
           },
         });
-        this.$emit('show-success-notification', `Success!! The experiment has been deleted.`);
+        this.$emit('show-success-notification', `Success! The experiment has been deleted.`);
 
       } catch (error) {
         // Handle any errors that might occur during the async operation

From 6c03d4e39e3dbae842919a510a4cf6a64785cb8e Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 17 Feb 2025 19:46:44 +0000
Subject: [PATCH 75/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index c798ae9d9..42b2ee81d 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+799",
+  "version": "v1.0.0+801",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/b083834195205c93ef19a28e29c5be30ccda3a92"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/8bbddf34e0499229f65400adc0c19749d151d07d"
 }

From b95285cc5345cb1479847b41d63914e207ef4aad Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Mon, 17 Feb 2025 16:26:14 -0500
Subject: [PATCH 76/98] [BI-2449-fix] - Correct Exp Preview Summary Stats, QA
 fix

---
 src/views/import/Dataset.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/views/import/Dataset.vue b/src/views/import/Dataset.vue
index 626392b8c..6ef10f365 100644
--- a/src/views/import/Dataset.vue
+++ b/src/views/import/Dataset.vue
@@ -42,7 +42,7 @@
                   <b>Total observations:</b>
                 </div>
                 <div class="column pl-1 is-three-quarters pb-0">
-                  {{ totalObservationsCount }}
+                  {{ observationsWithData }}
                 </div>
               </div>
             </div>

From 47cf72646c06460968863114f2769819c2416eb2 Mon Sep 17 00:00:00 2001
From: HMS17 <hms243@cornell.edu>
Date: Wed, 19 Feb 2025 11:24:53 -0500
Subject: [PATCH 77/98] [BI-2449-fix] - Correct Exp Preview Summary Stats,
 preview stat mod

---
 src/views/import/ImportExperiment.vue | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/views/import/ImportExperiment.vue b/src/views/import/ImportExperiment.vue
index 425752fb1..add420509 100644
--- a/src/views/import/ImportExperiment.vue
+++ b/src/views/import/ImportExperiment.vue
@@ -68,9 +68,6 @@
           </div>
           <div id="experiment-summary" class ="right-confirm-column">
             <p class="is-size-5 mb-2"><strong>Import Summary</strong></p>
-            Dataset: {{ rows[0].observationUnit.brAPIObject.additionalInfo.observationLevel }}
-            <br>Germplasm: {{ statistics.GIDs.newObjectCount }}
-            <br>Environment(s): {{ statistics.Environments.newObjectCount }}
             <br>Observation Variables: {{ dynamicColumns.length }}
 
             <span v-if="isExisting(rows)" >

From 51879f1f23cccbe1955c6c1448b346bd927cd8ba Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Wed, 19 Feb 2025 19:05:22 +0000
Subject: [PATCH 78/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 42b2ee81d..a11c9a851 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+801",
+  "version": "v1.0.0+803",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/8bbddf34e0499229f65400adc0c19749d151d07d"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/b12591f646517d3b518c9f68d559848426c32fd0"
 }

From 2eceff92a9f47374ecb7a2f4aa7487379ed62ffc Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Wed, 26 Feb 2025 21:59:11 +0000
Subject: [PATCH 79/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index a11c9a851..b48b01abe 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+803",
+  "version": "v1.0.0+805",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/b12591f646517d3b518c9f68d559848426c32fd0"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/67f92175b92345ef70818753cd0c2c0453841304"
 }

From 796538de7937667b035a406869d69a795027097d Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Tue, 25 Feb 2025 13:53:01 -0500
Subject: [PATCH 80/98] [BI-2140] Accessibility: Home Page

---
 src/components/layouts/NoSideBarLayout.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/layouts/NoSideBarLayout.vue b/src/components/layouts/NoSideBarLayout.vue
index 9efa42628..4b6147e2e 100644
--- a/src/components/layouts/NoSideBarLayout.vue
+++ b/src/components/layouts/NoSideBarLayout.vue
@@ -32,7 +32,7 @@
         </div>
         <div class="level-right">
           <div class="level-item">
-            <h1 class="title has-text-primary level-item">{{title}}</h1>
+            <h1 v-if="title" class="title has-text-primary level-item">{{title}}</h1>
           </div>
           <div class="level-item">
             <UserStatusMenu v-bind:username="username" v-on:logout="$emit('logout')"/>

From 5fb835fdfde0804194c0b307feb59ea68c94f642 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 3 Mar 2025 18:57:41 +0000
Subject: [PATCH 81/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index b48b01abe..e42c945df 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+805",
+  "version": "v1.0.0+807",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/67f92175b92345ef70818753cd0c2c0453841304"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/1f11389b2e6b40b2911f119a6d44a867939dd1ca"
 }

From 8c3100762a44fdc6c6f95bd3e5add52ba3c957a6 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Fri, 14 Mar 2025 16:52:34 -0400
Subject: [PATCH 82/98] [BI-2555] - fixed unexpected default sort

---
 src/components/germplasm/GermplasmTable.vue | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/components/germplasm/GermplasmTable.vue b/src/components/germplasm/GermplasmTable.vue
index 2691c40ba..e1722fdf8 100644
--- a/src/components/germplasm/GermplasmTable.vue
+++ b/src/components/germplasm/GermplasmTable.vue
@@ -149,6 +149,16 @@ export default class GermplasmTable extends Vue {
       .reduce((obj, key) => Object.assign({}, obj, { [this.fieldMap[key]]: key }), {});
 
   mounted() {
+    // The initial request was using the default value of the mapped getter, germplasmSort.
+    // This component is used for both AllGermplasm.vue and GermplasmByList.vue with different default sorts
+    // and the built-in buefy properties (default-sort) doesn't seem to do what we want with backend sorting.
+    // Because germplasmSort is persistent client-side state, it needs to be set properly for the initial
+    // request in for both cases.
+    if (this.entryNumberVisible) {
+      this.updateSort(new GermplasmSort("importEntryNumber", "ASC"));
+    } else {
+      this.updateSort(new GermplasmSort("accessionNumber", "DESC"));
+    }
     this.paginationController.pageSize = 200
     this.germplasmCallStack = new CallStack(this.germplasmFetch(
         this.activeProgram!.id!,

From 6a816e6375db4c9ddb6b3812f4fc05d0c2dfdcc9 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Tue, 18 Mar 2025 17:13:59 -0400
Subject: [PATCH 83/98] [BI-2555] - implemented an alternative approach

---
 src/components/germplasm/GermplasmTable.vue | 36 +++++++++++----------
 src/store/sorting/getters.ts                | 16 ++++++---
 src/store/sorting/index.ts                  |  3 ++
 src/store/sorting/mutation-types.ts         |  3 ++
 src/store/sorting/mutations.ts              |  7 ++++
 src/store/sorting/types.ts                  |  7 ++--
 6 files changed, 48 insertions(+), 24 deletions(-)

diff --git a/src/components/germplasm/GermplasmTable.vue b/src/components/germplasm/GermplasmTable.vue
index e1722fdf8..85b12e254 100644
--- a/src/components/germplasm/GermplasmTable.vue
+++ b/src/components/germplasm/GermplasmTable.vue
@@ -92,7 +92,7 @@ import {
   GermplasmSortField,
   Sort
 } from "@/breeding-insight/model/Sort";
-import {UPDATE_GERMPLASM_SORT} from "@/store/sorting/mutation-types";
+import {UPDATE_GERMPLASM_SORT, UPDATE_GERMPLASM_BY_LIST_SORT} from "@/store/sorting/mutation-types";
 import { PaginationQuery } from '@/breeding-insight/model/PaginationQuery';
 import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
 
@@ -105,12 +105,14 @@ import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
     ]),
     ...mapGetters('sorting',
         [
-          'germplasmSort'
+          'germplasmSort',
+          'germplasmByListSort',
       ])
   },
   methods: {
     ...mapMutations('sorting', {
-      updateSort: UPDATE_GERMPLASM_SORT
+      updateGermplasmSort: UPDATE_GERMPLASM_SORT,
+      updateGermplasmByListSort: UPDATE_GERMPLASM_BY_LIST_SORT,
     })
   },
   data: () => ({Trait, StringFormatters, TraitStringFormatters, Pedigree, GermplasmUtils, BrAPIUtils, Sort})
@@ -133,7 +135,9 @@ export default class GermplasmTable extends Vue {
   private germplasmCallStack?: CallStack;
 
   private germplasmSort!: GermplasmSort;
-  private updateSort!: (sort: GermplasmSort) => void;
+  private germplasmByListSort!: GermplasmSort;
+  private updateGermplasmSort!: (sort: GermplasmSort) => void;
+  private updateGermplasmByListSort!: (sort: GermplasmSort) => void;
   private fieldMap: any = {
     'importEntryNumber': GermplasmSortField.ImportEntryNumber,
     'accessionNumber': GermplasmSortField.AccessionNumber,
@@ -149,20 +153,13 @@ export default class GermplasmTable extends Vue {
       .reduce((obj, key) => Object.assign({}, obj, { [this.fieldMap[key]]: key }), {});
 
   mounted() {
-    // The initial request was using the default value of the mapped getter, germplasmSort.
-    // This component is used for both AllGermplasm.vue and GermplasmByList.vue with different default sorts
-    // and the built-in buefy properties (default-sort) doesn't seem to do what we want with backend sorting.
-    // Because germplasmSort is persistent client-side state, it needs to be set properly for the initial
-    // request in for both cases.
-    if (this.entryNumberVisible) {
-      this.updateSort(new GermplasmSort("importEntryNumber", "ASC"));
-    } else {
-      this.updateSort(new GermplasmSort("accessionNumber", "DESC"));
-    }
-    this.paginationController.pageSize = 200
+    // Set default page size to 200.
+    this.paginationController.pageSize = 200;
+    // Germplasm and Germplasm by List use different sorts.
+    let sort: GermplasmSort = this.entryNumberVisible ? this.germplasmByListSort : this.germplasmSort;
     this.germplasmCallStack = new CallStack(this.germplasmFetch(
         this.activeProgram!.id!,
-        this.germplasmSort,
+        sort,
         this.paginationController
     ));
 
@@ -211,7 +208,12 @@ export default class GermplasmTable extends Vue {
 
   setSort(field: string, order: string) {
     if (field in this.fieldMap) {
-      this.updateSort(new GermplasmSort(this.fieldMap[field], Sort.orderAsBI(order)));
+      // Update the appropriate sort.
+      if (this.entryNumberVisible) {
+        this.updateGermplasmByListSort(new GermplasmSort(this.fieldMap[field], Sort.orderAsBI(order)));
+      } else {
+        this.updateGermplasmSort(new GermplasmSort(this.fieldMap[field], Sort.orderAsBI(order)));
+      }
       this.getGermplasm();
     }
   }
diff --git a/src/store/sorting/getters.ts b/src/store/sorting/getters.ts
index 012c2383a..5f7dd847e 100644
--- a/src/store/sorting/getters.ts
+++ b/src/store/sorting/getters.ts
@@ -15,9 +15,9 @@
  * limitations under the License.
  */
 
-import {GetterTree} from 'vuex';
-import {RootState} from "@/store/types";
-import {SortState} from "@/store/sorting/types";
+import { GetterTree } from 'vuex';
+import { RootState } from "@/store/types";
+import { SortState } from "@/store/sorting/types";
 import {
     ExperimentSort,
     GermplasmSort,
@@ -31,7 +31,7 @@ import {
     UserSortField
 } from "@/breeding-insight/model/Sort";
 
-const orderMap: any = {[SortOrder.Ascending]: 'asc', [SortOrder.Descending]: 'desc'};
+const orderMap: any = { [SortOrder.Ascending]: 'asc', [SortOrder.Descending]: 'desc' };
 
 export const getters: GetterTree<SortState, RootState> = {
 
@@ -40,7 +40,7 @@ export const getters: GetterTree<SortState, RootState> = {
         return state.activeOntologySort;
     },
     activeOntologySortOrder(state: SortState): SortOrder {
-      return state.activeOntologySort.order;
+        return state.activeOntologySort.order;
     },
 
     // archived ontology table
@@ -123,6 +123,12 @@ export const getters: GetterTree<SortState, RootState> = {
         return state.germplasmSort;
     },
 
+    // germplasm (by list)
+    germplasmByListSort(state: SortState): GermplasmSort {
+        return state.germplasmByListSort;
+    },
+
+    // germplmas list
     germplasmListSort(state: SortState): GermplasmListSort {
         return state.germplasmListSort;
     },
diff --git a/src/store/sorting/index.ts b/src/store/sorting/index.ts
index 80a4debc6..78a607345 100644
--- a/src/store/sorting/index.ts
+++ b/src/store/sorting/index.ts
@@ -66,6 +66,9 @@ state = {
     // germplasm table
     germplasmSort: new GermplasmSort(GermplasmSortField.AccessionNumber, SortOrder.Descending),
 
+    // germplasm (by list) table
+    germplasmByListSort: new GermplasmSort(GermplasmSortField.ImportEntryNumber, SortOrder.Ascending),
+
     // germplasm list table
     germplasmListSort: new GermplasmListSort(GermplasmListSortField.Name, SortOrder.Ascending),
 
diff --git a/src/store/sorting/mutation-types.ts b/src/store/sorting/mutation-types.ts
index 5d9f69d68..02b3af43f 100644
--- a/src/store/sorting/mutation-types.ts
+++ b/src/store/sorting/mutation-types.ts
@@ -40,6 +40,9 @@ export const UPDATE_PROGRAM_SORT = 'updateProgramSort';
 // germplasm table
 export const UPDATE_GERMPLASM_SORT = 'updateGermplasmSort';
 
+// germplasm (by list) table
+export const UPDATE_GERMPLASM_BY_LIST_SORT = 'updateGermplasmByListSort';
+
 // germplasm list table
 export const UPDATE_GERMPLASM_LIST_SORT = 'updateGermplasmListSort';
 
diff --git a/src/store/sorting/mutations.ts b/src/store/sorting/mutations.ts
index 50850c547..e6b743ef2 100644
--- a/src/store/sorting/mutations.ts
+++ b/src/store/sorting/mutations.ts
@@ -24,6 +24,7 @@ import {
     IMPORT_PREVIEW_ONT_TOGGLE_SORT_ORDER,
     IMPORT_PREVIEW_ONT_NEW_SORT_COLUMN,
     UPDATE_GERMPLASM_SORT,
+    UPDATE_GERMPLASM_BY_LIST_SORT,
     UPDATE_GERMPLASM_LIST_SORT,
     UPDATE_EXPERIMENT_SORT, UPDATE_ACTIVE_ONT_SORT, UPDATE_ARCHIVED_ONT_SORT
 } from "@/store/sorting/mutation-types";
@@ -89,6 +90,12 @@ export const mutations: MutationTree<SortState> = {
         state.germplasmSort.order = sort.order;
     },
 
+    //germplasm (by list) table
+    [UPDATE_GERMPLASM_BY_LIST_SORT](state: SortState, sort: GermplasmSort) {
+        state.germplasmByListSort.field = sort.field;
+        state.germplasmByListSort.order = sort.order;
+    },
+
     //germplasm list table
     [UPDATE_GERMPLASM_LIST_SORT](state: SortState, sort: GermplasmListSort) {
         state.germplasmListSort.field = sort.field;
diff --git a/src/store/sorting/types.ts b/src/store/sorting/types.ts
index ebedb8923..ecf5ad1b2 100644
--- a/src/store/sorting/types.ts
+++ b/src/store/sorting/types.ts
@@ -32,10 +32,13 @@ export interface SortState {
     programSort: ProgramSort,
 
     // germplasm table
-    germplasmSort: GermplasmSort
+    germplasmSort: GermplasmSort,
+
+    // germplasm (by list) table
+    germplasmByListSort: GermplasmSort,
 
     // germplasm list table
-    germplasmListSort: GermplasmListSort
+    germplasmListSort: GermplasmListSort,
 
     // experiment and observation table
     experimentSort: ExperimentSort

From 9d0818ab6ad3f6ce74f3b77d00ddadf35368262a Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Wed, 19 Mar 2025 17:40:51 -0400
Subject: [PATCH 84/98] [BI-2555] - refactored

---
 src/components/germplasm/GermplasmTable.vue | 32 ++++++---------------
 src/views/germplasm/AllGermplasm.vue        | 16 ++++++++++-
 src/views/germplasm/GermplasmByList.vue     | 19 ++++++++++--
 3 files changed, 40 insertions(+), 27 deletions(-)

diff --git a/src/components/germplasm/GermplasmTable.vue b/src/components/germplasm/GermplasmTable.vue
index 85b12e254..5c89c20c5 100644
--- a/src/components/germplasm/GermplasmTable.vue
+++ b/src/components/germplasm/GermplasmTable.vue
@@ -103,17 +103,6 @@ import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
     ...mapGetters([
       'activeProgram'
     ]),
-    ...mapGetters('sorting',
-        [
-          'germplasmSort',
-          'germplasmByListSort',
-      ])
-  },
-  methods: {
-    ...mapMutations('sorting', {
-      updateGermplasmSort: UPDATE_GERMPLASM_SORT,
-      updateGermplasmByListSort: UPDATE_GERMPLASM_BY_LIST_SORT,
-    })
   },
   data: () => ({Trait, StringFormatters, TraitStringFormatters, Pedigree, GermplasmUtils, BrAPIUtils, Sort})
 })
@@ -125,6 +114,10 @@ export default class GermplasmTable extends Vue {
   entryNumberVisible?: Boolean;
   @Prop()
   referenceId?: string;
+  @Prop()
+  germplasmSort!: GermplasmSort;
+  @Prop()
+  updateGermplasmSort!: (sort: GermplasmSort) => void;
 
   private activeProgram?: Program;
   private paginationController: PaginationController = new PaginationController();
@@ -134,10 +127,7 @@ export default class GermplasmTable extends Vue {
 
   private germplasmCallStack?: CallStack;
 
-  private germplasmSort!: GermplasmSort;
-  private germplasmByListSort!: GermplasmSort;
-  private updateGermplasmSort!: (sort: GermplasmSort) => void;
-  private updateGermplasmByListSort!: (sort: GermplasmSort) => void;
+
   private fieldMap: any = {
     'importEntryNumber': GermplasmSortField.ImportEntryNumber,
     'accessionNumber': GermplasmSortField.AccessionNumber,
@@ -155,11 +145,9 @@ export default class GermplasmTable extends Vue {
   mounted() {
     // Set default page size to 200.
     this.paginationController.pageSize = 200;
-    // Germplasm and Germplasm by List use different sorts.
-    let sort: GermplasmSort = this.entryNumberVisible ? this.germplasmByListSort : this.germplasmSort;
     this.germplasmCallStack = new CallStack(this.germplasmFetch(
         this.activeProgram!.id!,
-        sort,
+        this.germplasmSort,
         this.paginationController
     ));
 
@@ -208,12 +196,8 @@ export default class GermplasmTable extends Vue {
 
   setSort(field: string, order: string) {
     if (field in this.fieldMap) {
-      // Update the appropriate sort.
-      if (this.entryNumberVisible) {
-        this.updateGermplasmByListSort(new GermplasmSort(this.fieldMap[field], Sort.orderAsBI(order)));
-      } else {
-        this.updateGermplasmSort(new GermplasmSort(this.fieldMap[field], Sort.orderAsBI(order)));
-      }
+      // Update the sort.
+      this.updateGermplasmSort(new GermplasmSort(this.fieldMap[field], Sort.orderAsBI(order)));
       this.getGermplasm();
     }
   }
diff --git a/src/views/germplasm/AllGermplasm.vue b/src/views/germplasm/AllGermplasm.vue
index 9f75aa960..c272ae017 100644
--- a/src/views/germplasm/AllGermplasm.vue
+++ b/src/views/germplasm/AllGermplasm.vue
@@ -2,6 +2,8 @@
   <section id="germplasmTable">
     <GermplasmTable
       v-bind:germplasmFetch="germplasmFetch"
+      v-bind:germplasm-sort="germplasmSort"
+      v-bind:update-germplasm-sort="updateGermplasmSort"
       >
     </GermplasmTable>
   </section>
@@ -10,7 +12,7 @@
 <script lang="ts">
 import {Component, Vue} from "vue-property-decorator";
 import {validationMixin} from "vuelidate";
-import {mapGetters} from "vuex";
+import {mapGetters, mapMutations} from "vuex";
 import {Trait} from "@/breeding-insight/model/Trait";
 import {StringFormatters} from "@/breeding-insight/utils/StringFormatters";
 import {TraitStringFormatters} from "@/breeding-insight/utils/TraitStringFormatters";
@@ -29,6 +31,7 @@ import {
 } from "@/breeding-insight/model/Sort";
 import GermplasmTable from "@/components/germplasm/GermplasmTable.vue";
 import {PaginationController} from "@/breeding-insight/model/view_models/PaginationController";
+import {UPDATE_GERMPLASM_SORT} from "@/store/sorting/mutation-types";
 
 @Component({
   mixins: [validationMixin],
@@ -37,12 +40,23 @@ import {PaginationController} from "@/breeding-insight/model/view_models/Paginat
     ...mapGetters([
       'activeProgram'
     ]),
+    ...mapGetters('sorting',
+        [
+          'germplasmSort',
+        ])
+  },
+  methods: {
+    ...mapMutations('sorting', {
+      updateGermplasmSort: UPDATE_GERMPLASM_SORT,
+    })
   },
   data: () => ({Trait, StringFormatters, TraitStringFormatters, Pedigree, GermplasmUtils, Sort})
 })
 export default class AllGermplasm extends Vue {
 
   private activeProgram?: Program;
+  private germplasmSort!: GermplasmSort;
+  private updateGermplasmSort!: (sort: GermplasmSort) => void;
 
   // Set the method used to populate the germplasm table
   private germplasmFetch: (programId: string, sort: GermplasmSort, paginationController: PaginationController) => ((filters: any) => Promise<BiResponse>) =
diff --git a/src/views/germplasm/GermplasmByList.vue b/src/views/germplasm/GermplasmByList.vue
index 8db93ead0..bf47103ce 100644
--- a/src/views/germplasm/GermplasmByList.vue
+++ b/src/views/germplasm/GermplasmByList.vue
@@ -116,6 +116,8 @@
         v-bind:germplasmFetch="germplasmFetch"
         entryNumberVisible="true"
         v-bind:reference-id="referenceId"
+        v-bind:germplasm-sort="germplasmByListSort"
+        v-bind:update-germplasm-sort="updateGermplasmByListSort"
     >
     </GermplasmTable>
   </div>
@@ -128,7 +130,7 @@ import GermplasmTable from '@/components/germplasm/GermplasmTable.vue';
 import {GermplasmListSortField, GermplasmSort, SortOrder, GermplasmSortField} from '@/breeding-insight/model/Sort';
 import {BiResponse} from '@/breeding-insight/model/BiResponse';
 import {PaginationQuery} from '@/breeding-insight/model/PaginationQuery';
-import {mapGetters} from 'vuex';
+import {mapGetters, mapMutations} from 'vuex';
 import {Program} from '@/breeding-insight/model/Program';
 import {StringFormatters} from "@/breeding-insight/utils/StringFormatters";
 import GermplasmDownloadButton from '@/components/germplasm/GermplasmDownloadButton.vue';
@@ -142,13 +144,23 @@ import {ListService} from '@/breeding-insight/service/ListService';
 import {ListType} from "@/util/ListType";
 import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
 import {GermplasmService} from "@/breeding-insight/service/GermplasmService";
+import {UPDATE_GERMPLASM_BY_LIST_SORT} from "@/store/sorting/mutation-types";
 
 @Component({
   components: { FormModal, GermplasmTable, GermplasmDownloadButton, GermplasmListDeletionModal, ActionMenu },
   computed: {
     ...mapGetters([
       'activeProgram'
-    ])
+    ]),
+    ...mapGetters('sorting',
+        [
+          'germplasmByListSort',
+        ])
+  },
+  methods: {
+    ...mapMutations('sorting', {
+      updateGermplasmByListSort: UPDATE_GERMPLASM_BY_LIST_SORT,
+    })
   }
 })
 export default class GermplasmByList extends GermplasmBase {
@@ -165,6 +177,9 @@ export default class GermplasmByList extends GermplasmBase {
     new ActionMenuItem('germplasm-list-download-file', 'download-file', 'Download',  true)
   ];
 
+  private germplasmByListSort: GermplasmSort;
+  private updateGermplasmByListSort: (sort: GermplasmSort) => void;
+
   // Formatting filters
   private toYMD(date: string | null | undefined): string {
     if (!date) return ''; // Return an empty string if date is null, undefined, or empty

From b90bfe89484070d44adb7c1959019da5281088e1 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Fri, 21 Mar 2025 10:37:13 -0400
Subject: [PATCH 85/98] [BI-2555] - removed unused import

---
 src/components/germplasm/GermplasmTable.vue | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/components/germplasm/GermplasmTable.vue b/src/components/germplasm/GermplasmTable.vue
index 5c89c20c5..b47df5684 100644
--- a/src/components/germplasm/GermplasmTable.vue
+++ b/src/components/germplasm/GermplasmTable.vue
@@ -92,7 +92,6 @@ import {
   GermplasmSortField,
   Sort
 } from "@/breeding-insight/model/Sort";
-import {UPDATE_GERMPLASM_SORT, UPDATE_GERMPLASM_BY_LIST_SORT} from "@/store/sorting/mutation-types";
 import { PaginationQuery } from '@/breeding-insight/model/PaginationQuery';
 import {GermplasmFilter} from "@/breeding-insight/model/ListFilter";
 
@@ -127,7 +126,6 @@ export default class GermplasmTable extends Vue {
 
   private germplasmCallStack?: CallStack;
 
-
   private fieldMap: any = {
     'importEntryNumber': GermplasmSortField.ImportEntryNumber,
     'accessionNumber': GermplasmSortField.AccessionNumber,

From 557d6191bf0e0242fec011c0528a1798b8c19ac5 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Mon, 24 Mar 2025 16:56:00 -0400
Subject: [PATCH 86/98] [BI-2574] - updated import template links

---
 src/components/trait/TraitImportTemplateMessageBox.vue | 2 +-
 src/views/import/ImportExperiment.vue                  | 2 +-
 src/views/import/ImportGermplasm.vue                   | 2 +-
 src/views/import/ImportSample.vue                      | 2 +-
 src/views/trait/TraitsImport.vue                       | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/components/trait/TraitImportTemplateMessageBox.vue b/src/components/trait/TraitImportTemplateMessageBox.vue
index 57b6c4771..40536a6a6 100644
--- a/src/components/trait/TraitImportTemplateMessageBox.vue
+++ b/src/components/trait/TraitImportTemplateMessageBox.vue
@@ -32,7 +32,7 @@
             <div class="level-item">
               <div class="has-text-dark has-text-centered is-size-7">
                 <!-- temporary link until the backend card is done -->
-                <a href="https://cornell.box.com/shared/static/8sp0qvccpjotosiv8576tczeg09nnvao.xls"
+                <a href="https://cornell.box.com/shared/static/pgi6ncysrdnxkb3sbk2bijmemcqqrygd.xls"
                   class="button is-outlined is-primary" :id="downloadTraitTemplateId">Download the Trait Import Template</a>
                 <br/>Template version placeholder
               </div>
diff --git a/src/views/import/ImportExperiment.vue b/src/views/import/ImportExperiment.vue
index add420509..86066a410 100644
--- a/src/views/import/ImportExperiment.vue
+++ b/src/views/import/ImportExperiment.vue
@@ -33,7 +33,7 @@
 
       <template v-slot:importInfoTemplateMessageBox>
         <ImportInfoTemplateMessageBox v-bind:import-type-name="'Experiments & Observations'"
-                                      v-bind:template-url="'https://cornell.box.com/shared/static/7ziyhhnia5i7bdvekawhb2ldyobrecmw.xls'"
+                                      v-bind:template-url="'https://cornell.box.com/shared/static/x53n1x8fhccgij8hroel0zuz3y4l31iu.xls'"
                                       class="mb-5">
           <strong>Before You Import...</strong>
           <br/>
diff --git a/src/views/import/ImportGermplasm.vue b/src/views/import/ImportGermplasm.vue
index f0dd23532..32fa30cf2 100644
--- a/src/views/import/ImportGermplasm.vue
+++ b/src/views/import/ImportGermplasm.vue
@@ -31,7 +31,7 @@
 
       <template v-slot:importInfoTemplateMessageBox>
         <ImportInfoTemplateMessageBox v-bind:import-type-name="'Germplasm'"
-                                      v-bind:template-url="'https://cornell.box.com/shared/static/nx22mqw2y2q7uod0xt388zq5t04ejai3.xls'"
+                                      v-bind:template-url="'https://cornell.box.com/shared/static/qr9raqf70xcotoa7747dybxgjdunt7o0.xls'"
                                       class="mb-5">
           <strong>Before You Import...</strong>
           <br/>
diff --git a/src/views/import/ImportSample.vue b/src/views/import/ImportSample.vue
index 11b445dcc..4f78a2a02 100644
--- a/src/views/import/ImportSample.vue
+++ b/src/views/import/ImportSample.vue
@@ -30,7 +30,7 @@
     >
       <template v-slot:importInfoTemplateMessageBox>
         <ImportInfoTemplateMessageBox v-bind:import-type-name="'Sample Submission'"
-                                      v-bind:template-url="'https://cornell.box.com/shared/static/trakiri85mhazfd0gfika6ubpnt7gum5.xlsx'"
+                                      v-bind:template-url="'https://cornell.box.com/shared/static/yketd2s1353g62p0psem64w0awob5toz.xls'"
                                       class="mb-5">
           <strong>Before You Import...</strong>
           <br/>
diff --git a/src/views/trait/TraitsImport.vue b/src/views/trait/TraitsImport.vue
index d4189f6b5..add461d46 100644
--- a/src/views/trait/TraitsImport.vue
+++ b/src/views/trait/TraitsImport.vue
@@ -178,7 +178,7 @@ export default class TraitsImport extends ProgramsBase {
   private showAbortModal = false;
 
   private yesAbortId: string = "traitsimport-yes-abort";
-  private templateUrl: string = "https://cornell.box.com/shared/static/rxmj35d0wracg15ubemrshizdytmn731.xls";
+  private templateUrl: string = "https://cornell.box.com/shared/static/pgi6ncysrdnxkb3sbk2bijmemcqqrygd.xls";
 
   private confirmImportState: DataFormEventBusHandler = new DataFormEventBusHandler();
 

From 8ffdd881a184f4dc0f4d3f17ac6a6ae9e86db766 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Wed, 26 Mar 2025 13:55:15 +0000
Subject: [PATCH 87/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index e42c945df..226f653d4 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+807",
+  "version": "v1.0.0+809",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/1f11389b2e6b40b2911f119a6d44a867939dd1ca"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/58ea2ca23cff74eed5685a8724b2621fb4c59395"
 }

From e472b4b1ebb9b0117e3ab08675fff73bd90c64a5 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 31 Mar 2025 15:13:34 +0000
Subject: [PATCH 88/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 226f653d4..5d657b1d8 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+809",
+  "version": "v1.0.0+811",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/58ea2ca23cff74eed5685a8724b2621fb4c59395"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/a4a854e14dbe092efdd7fe13015f8b7e5e46d0ae"
 }

From 6e1fe04c3239098cddd37a0d8cd81591573f84e0 Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Thu, 3 Apr 2025 15:41:41 -0400
Subject: [PATCH 89/98] [BI-2589] fixed bug:  pageSize, and currentPage were
 not being correctly read from the PaginationController

---
 src/views/germplasm/GermplasmByList.vue | 4 ++--
 src/views/germplasm/GermplasmLists.vue  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/views/germplasm/GermplasmByList.vue b/src/views/germplasm/GermplasmByList.vue
index bf47103ce..66d876dac 100644
--- a/src/views/germplasm/GermplasmByList.vue
+++ b/src/views/germplasm/GermplasmByList.vue
@@ -203,12 +203,12 @@ export default class GermplasmByList extends GermplasmBase {
   private germplasmFetch = (
       programId: string,
       sort: GermplasmSort,
-      { pageSize, currentPage }: PaginationController
+      paginationController: PaginationController
   ) => (filters: any): Promise<BiResponse> =>
       GermplasmService.getAllInList<GermplasmSortField>(
           programId,
           sort,
-          { pageSize, page: currentPage - 1 },
+          { pageSize: paginationController.pageSize, page: paginationController.currentPage - 1 },
           { listDbId: this.$route.params.listId, ...filters }
       );
 
diff --git a/src/views/germplasm/GermplasmLists.vue b/src/views/germplasm/GermplasmLists.vue
index 61dd713c4..9ad9d925b 100644
--- a/src/views/germplasm/GermplasmLists.vue
+++ b/src/views/germplasm/GermplasmLists.vue
@@ -45,13 +45,13 @@ export default class GermplasmLists extends ProgramsBase {
   private germplasmListFetch = (
       programId: string,
       sort: GermplasmListSort,
-      { pageSize, currentPage }: PaginationController
+      paginationController: PaginationController
   ) => (filters: any): Promise<BiResponse> =>
       ListService.getLists<GermplasmListSortField>(
           ListType.GERMPLASM,
           programId,
           sort,
-          { pageSize, page: currentPage - 1 },
+          { pageSize: paginationController.pageSize, page: paginationController.currentPage - 1 },
           filters
       );
 }

From 87ec975f1bba827c05aeb42276c4dbbe0a8b5e57 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Fri, 4 Apr 2025 15:50:05 +0000
Subject: [PATCH 90/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 5d657b1d8..d82122bad 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+811",
+  "version": "v1.0.0+813",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/a4a854e14dbe092efdd7fe13015f8b7e5e46d0ae"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/4a0d66371eaa79c2190b1537f60c53689a82671b"
 }

From 8bdcfb394e7d644de9c3be9a6f78a8f008996d75 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 7 Apr 2025 15:25:43 +0000
Subject: [PATCH 91/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index d82122bad..9be53d36e 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+813",
+  "version": "v1.0.0+815",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/4a0d66371eaa79c2190b1537f60c53689a82671b"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/87ec975f1bba827c05aeb42276c4dbbe0a8b5e57"
 }

From fbdae42a0c4f85b4d9e5c155ba2ce387651f0fa1 Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Tue, 8 Apr 2025 15:11:02 -0400
Subject: [PATCH 92/98] Update version

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index d82122bad..4d2826877 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.0.0+813",
+  "version": "v1.1.0+813",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",

From 03e4b8993ff7ffceec950cc917045670f2126bf8 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Tue, 8 Apr 2025 19:13:13 +0000
Subject: [PATCH 93/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index ce80639a1..bff051d28 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.1.0+815",
+  "version": "v1.1.0+817",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/87ec975f1bba827c05aeb42276c4dbbe0a8b5e57"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/040472f2d12f194b21bf66c3da8f698e2d622ed8"
 }

From 2e2af51cc45942882c9584abaf1d1db5c0c87eaa Mon Sep 17 00:00:00 2001
From: David Randolph Phillips <drp227@cornell.edu>
Date: Mon, 14 Apr 2025 10:41:24 -0400
Subject: [PATCH 94/98] [BI-2124] Set init sort order

---
 src/store/sorting/index.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/store/sorting/index.ts b/src/store/sorting/index.ts
index 78a607345..bc07d7f46 100644
--- a/src/store/sorting/index.ts
+++ b/src/store/sorting/index.ts
@@ -70,7 +70,7 @@ state = {
     germplasmByListSort: new GermplasmSort(GermplasmSortField.ImportEntryNumber, SortOrder.Ascending),
 
     // germplasm list table
-    germplasmListSort: new GermplasmListSort(GermplasmListSortField.Name, SortOrder.Ascending),
+    germplasmListSort: new GermplasmListSort(GermplasmListSortField.CreatedDate, SortOrder.Descending),
 
     //experiment and observation table
     experimentSort: new ExperimentSort(ExperimentSortField.CreatedDate, SortOrder.Descending)

From 459a75ba8c91e89cc6a3461a0bcbc4d2b682b995 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Mon, 21 Apr 2025 13:05:36 +0000
Subject: [PATCH 95/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index bff051d28..5e36e8a65 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.1.0+817",
+  "version": "v1.1.0+821",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/040472f2d12f194b21bf66c3da8f698e2d622ed8"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/12be2273d0d2dabda88d2768ef612214a38d6ec5"
 }

From 63123ad0b4279f95adb2caca582c42a7180d0cb2 Mon Sep 17 00:00:00 2001
From: mlm483 <128052931+mlm483@users.noreply.github.com>
Date: Wed, 30 Apr 2025 10:51:00 -0400
Subject: [PATCH 96/98] [BI-2618] - pin sort-package-json to 3.0.0

---
 task/serve.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/task/serve.js b/task/serve.js
index 08f071e5d..1579e94d4 100755
--- a/task/serve.js
+++ b/task/serve.js
@@ -26,7 +26,7 @@ const port = process.env.PORT || JSON.parse(fs.readFileSync('package.json', 'utf
   let spinner = ora({prefixText: ' ', color: 'yellow'});
   try {
     spinner = spinner.start('sort package.json');
-    await execa('npx', ['sort-package-json'], {preferLocal: true});
+    await execa('npx', ['sort-package-json@3.0.0'], {preferLocal: true});
     spinner = spinner.clear()
                      .succeed('package.json sorted');
 

From 90685f98f16dca0efaeebd4b3da38c2006d39184 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Wed, 30 Apr 2025 15:25:05 +0000
Subject: [PATCH 97/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 5e36e8a65..0af84c4b5 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.1.0+821",
+  "version": "v1.1.0+827",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/12be2273d0d2dabda88d2768ef612214a38d6ec5"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/81d94e74d0512fecda81bae5eb89da4079bcd3b3"
 }

From b8dd020843961493d0d7d5b6b69570a41fd29073 Mon Sep 17 00:00:00 2001
From: rob-ouser-bi <bidevteam@cornell.edu>
Date: Wed, 30 Apr 2025 16:02:07 +0000
Subject: [PATCH 98/98] [autocommit] bumping build number

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 6558b6881..a0076865b 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "bi-web",
-  "version": "v1.1.0+827",
+  "version": "v1.1.0+832",
   "private": true,
   "scripts": {
     "build": "node $npm_package_config_task_path/build.js --dev-audit-level=critical --prod-audit-level=none",
@@ -96,5 +96,5 @@
     "vue-cli-plugin-axios": "0.0.4",
     "vue-template-compiler": "^2.7.14"
   },
-  "versionInfo": "https://github.com/Breeding-Insight/bi-web/releases/tag/v1.1.0"
+  "versionInfo": "https://github.com/Breeding-Insight/bi-web/commit/939aade34a7566e58dfaeb3896904c6e897c764c"
 }