Release/1.1

.env.template

@@ -3,6 +3,8 @@
 USER_ID=<user id of system user>
 GROUP_ID=<group id of system user>
 
+ORCID_SANDBOX_AUTHENTICATION=<true or false; true=>use the Sandbox Orcid, false=>use the Production Orcid.  Defaults to false.>
+
 # Authentication variables
 OAUTH_CLIENT_ID=<oauth app client id>
 OAUTH_CLIENT_SECRET=<ouath_client_secret goes here>
@@ -59,4 +61,12 @@ AWS_GENO_BUCKET=<s3 bucket for genotypic data uploads>
 AWS_S3_ENDPOINT=<s3 endpoint, default https://s3.us-east-1.amazonaws.com>
 
 BRAPI_VENDOR_SUBMISSION_ENABLED=false #can a submission be sent to a vendor via BrAPI
-BRAPI_VENDOR_CHECK_FREQUENCY=1d #how often to check for vendor updates for sample submissions
+BRAPI_VENDOR_CHECK_FREQUENCY=1d #how often to check for vendor updates for sample submissions
+
+#The initial caching of each type of object needs to be staggered by the prescribed number of seconds
+GERMPLASM_START_DELAY=5s
+STUDY_START_DELAY=10s
+TRIAL_START_DELAY=15s
+TRAIT_START_DELAY=20s
+OBSERVATION_START_DELAY=25s
+OBSERVATION_UNIT_START_DELAY=30s

pom.xml

@@ -490,7 +490,7 @@
                             <goal>shade</goal>
                         </goals>
                         <configuration>
-	                    <filters>
+                            <filters>
                                 <filter>
                                     <artifact>*:*</artifact>
                                     <excludes>
@@ -499,9 +499,9 @@
                                         <exclude>META-INF/*.RSA</exclude>
                                     </excludes>
                                 </filter>
-                            </filters>	
-				
-			    <transformers>
+                            </filters>
+
+                            <transformers>
                                 <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                     <mainClass>${exec.mainClass}</mainClass>
                                 </transformer>
@@ -536,98 +536,98 @@
                     <target>${maven.compiler.target}</target>
                 </configuration>
             </plugin>
-        <plugin>
-            <groupId>org.jooq</groupId>
-            <artifactId>jooq-codegen-maven</artifactId>
-            <version>${jooq.version}</version>
-            <executions>
-                <execution>
-                    <goals>
-                        <goal>generate</goal>
-                    </goals>
-                </execution>
-            </executions>
+            <plugin>
+                <groupId>org.jooq</groupId>
+                <artifactId>jooq-codegen-maven</artifactId>
+                <version>${jooq.version}</version>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>generate</goal>
+                        </goals>
+                    </execution>
+                </executions>
+
+                <configuration>
+                    <jdbc>
+                        <driver>org.postgresql.Driver</driver>
+                        <url>jdbc:postgresql://${DB_SERVER}/${DB_NAME}</url>
+                        <user>${DB_USER}</user>
+                        <password>${DB_PASSWORD}</password>
+                    </jdbc>
+                    <generator>
+                        <name>org.breedinginsight.generation.JooqDaoGenerator</name>
+                        <database>
+                            <name>org.jooq.meta.postgres.PostgresDatabase</name>
+                            <includes>.*</includes>
+                            <inputSchema>public</inputSchema>
+                            <includeTables>true</includeTables>
+                            <includeUDTs>true</includeUDTs>
+                            <includeRoutines>false</includeRoutines>
+                            <includePrimaryKeys>true</includePrimaryKeys>
+                            <includeUniqueKeys>true</includeUniqueKeys>
+                            <includeForeignKeys>true</includeForeignKeys>
+                            <includeCheckConstraints>true</includeCheckConstraints>
+                            <includeIndexes>false</includeIndexes>
+                            <excludes>
+                                flyway_schema_history|base_entity|base_track_edit_entity|spatial_ref_sys
+                            </excludes>
+                        </database>
 
-            <configuration>
-                <jdbc>
-                    <driver>org.postgresql.Driver</driver>
+                        <strategy>
+                            <matchers>
+                                <tables>
+                                    <table>
+                                        <pojoClass>
+                                            <transform>PASCAL</transform>
+                                            <expression>$0_ENTITY</expression>
+                                        </pojoClass>
+                                        <tableClass>
+                                            <transform>PASCAL</transform>
+                                            <expression>$0_TABLE</expression>
+                                        </tableClass>
+                                    </table>
+                                </tables>
+                            </matchers>
+                        </strategy>
+
+                        <target>
+                            <packageName>org.breedinginsight.dao.db</packageName>
+                            <directory>target/generated-sources/jooq</directory>
+                        </target>
+                        <generate>
+                            <pojos>true</pojos>
+                            <daos>true</daos>
+                            <fluentSetters>false</fluentSetters>
+                            <javaTimeTypes>true</javaTimeTypes>
+                        </generate>
+                    </generator>
+                </configuration>
+                <dependencies>
+                    <dependency>
+                        <groupId>org.breedinginsight</groupId>
+                        <artifactId>bi-jooq-codegen</artifactId>
+                        <version>${jooq.version}</version>
+                    </dependency>
+                </dependencies>
+            </plugin>
+            <plugin>
+                <groupId>org.flywaydb</groupId>
+                <artifactId>flyway-maven-plugin</artifactId>
+                <version>${flyway.version}</version>
+                <configuration>
                     <url>jdbc:postgresql://${DB_SERVER}/${DB_NAME}</url>
                     <user>${DB_USER}</user>
                     <password>${DB_PASSWORD}</password>
-                </jdbc>
-                <generator>
-                    <name>org.breedinginsight.generation.JooqDaoGenerator</name>
-                    <database>
-                        <name>org.jooq.meta.postgres.PostgresDatabase</name>
-                        <includes>.*</includes>
-                        <inputSchema>public</inputSchema>
-                        <includeTables>true</includeTables>
-                        <includeUDTs>true</includeUDTs>
-                        <includeRoutines>false</includeRoutines>
-                        <includePrimaryKeys>true</includePrimaryKeys>
-                        <includeUniqueKeys>true</includeUniqueKeys>
-                        <includeForeignKeys>true</includeForeignKeys>
-                        <includeCheckConstraints>true</includeCheckConstraints>
-                        <includeIndexes>false</includeIndexes>
-                        <excludes>
-                            flyway_schema_history|base_entity|base_track_edit_entity|spatial_ref_sys
-                        </excludes>
-                    </database>
-
-                    <strategy>
-                        <matchers>
-                            <tables>
-                                <table>
-                                    <pojoClass>
-                                        <transform>PASCAL</transform>
-                                        <expression>$0_ENTITY</expression>
-                                    </pojoClass>
-                                    <tableClass>
-                                        <transform>PASCAL</transform>
-                                        <expression>$0_TABLE</expression>
-                                    </tableClass>
-                                </table>
-                            </tables>
-                        </matchers>
-                    </strategy>
-
-                    <target>
-                        <packageName>org.breedinginsight.dao.db</packageName>
-                        <directory>target/generated-sources/jooq</directory>
-                    </target>
-                    <generate>
-                        <pojos>true</pojos>
-                        <daos>true</daos>
-                        <fluentSetters>false</fluentSetters>
-                        <javaTimeTypes>true</javaTimeTypes>
-                    </generate>
-                </generator>
-            </configuration>
-            <dependencies>
-                <dependency>
-                    <groupId>org.breedinginsight</groupId>
-                    <artifactId>bi-jooq-codegen</artifactId>
-                    <version>${jooq.version}</version>
-                </dependency>
-            </dependencies>
-        </plugin>
-        <plugin>
-            <groupId>org.flywaydb</groupId>
-            <artifactId>flyway-maven-plugin</artifactId>
-            <version>${flyway.version}</version>
-            <configuration>
-                <url>jdbc:postgresql://${DB_SERVER}/${DB_NAME}</url>
-                <user>${DB_USER}</user>
-                <password>${DB_PASSWORD}</password>
-            </configuration>
-            <dependencies>
-                <dependency>
-                    <groupId>org.postgresql</groupId>
-                    <artifactId>postgresql</artifactId>
-                    <version>${postgres.version}</version>
-                </dependency>
-            </dependencies>
-        </plugin>
+                </configuration>
+                <dependencies>
+                    <dependency>
+                        <groupId>org.postgresql</groupId>
+                        <artifactId>postgresql</artifactId>
+                        <version>${postgres.version}</version>
+                    </dependency>
+                </dependencies>
+            </plugin>
         </plugins>
         <pluginManagement>
             <plugins>

src/main/java/org/breedinginsight/api/v1/controller/ExperimentController.java

@@ -298,4 +298,43 @@ public HttpResponse deleteExperimentalCollaborator(
         }
 
     }
+
+    /**
+     * Deletes an experiment.
+     * @param programId The UUID of the program
+     * @param experimentId The UUID of the experiment
+     * @param hard Specifies hard or soft delete
+     * @return A Http Response
+     */
+    @Delete("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}{?hard}")
+    @ProgramSecured(roles = {ProgramSecuredRole.PROGRAM_ADMIN, ProgramSecuredRole.SYSTEM_ADMIN})
+    @Produces(MediaType.APPLICATION_JSON)
+    public HttpResponse deleteExperiment(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("experimentId") UUID experimentId,
+            @QueryValue(defaultValue = "false") Boolean hard
+    ) throws ApiException {
+        try {
+            Optional<Program> program = programService.getById(programId);
+            if(program.isEmpty()) {
+                return HttpResponse.notFound();
+            }
+            int observationCount = experimentService.deleteExperiment(program.get(), experimentId, hard);
+            if (observationCount > 0 && hard) {
+                // 409 Conflict. https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/409
+                return HttpResponse.status(HttpStatus.CONFLICT);
+            }
+            // 204 No Content indicates successful delete. https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/204
+            return HttpResponse.noContent();
+        } catch (ApiException e) {
+            log.error("Error deleting experiment.\n\tprogramId: " + programId +  "\n\texperimentId: " + experimentId + "\n\thard: " + hard);
+            if (e.getCode() == 404) {
+                return HttpResponse.notFound();
+            } else {
+                return HttpResponse.serverError();
+            }
+        }
+    }
+
+
 }

src/main/java/org/breedinginsight/api/v1/controller/geno/SampleSubmissionController.java

@@ -281,4 +281,42 @@ public HttpResponse<Response<SampleSubmission>> checkVendorStatus(@PathVariable
             return HttpResponse.serverError();
         }
     }
+
+    /**
+     * Delete sample submission.
+     * Deletes the bidb submission record and BrAPI samples & plates
+     * @param programId bi-api id of program
+     * @param submissionId bi-api id of submission
+     * @return HttpResponse
+     * @throws ApiException
+     */
+    @Delete("programs/{programId}/submissions/{submissionId}")
+    @Produces(MediaType.APPLICATION_JSON)
+    // sys admin and program admin roles to match file import permissions
+    @ProgramSecured(roles = {ProgramSecuredRole.SYSTEM_ADMIN, ProgramSecuredRole.PROGRAM_ADMIN})
+    public HttpResponse deleteSubmissionById(@PathVariable UUID programId, @PathVariable UUID submissionId) throws ApiException {
+
+        // program validation
+        Optional<Program> program = programService.getById(programId);
+        if(program.isEmpty()) {
+            log.info(String.format("programId not found: %s", programId.toString()));
+            return HttpResponse.notFound();
+        }
+
+        // sample status validation
+        Optional<SampleSubmission> submissionOpt = sampleSubmissionService.getSampleSubmission(program.get(), submissionId, false);
+
+        if(submissionOpt.isEmpty()) {
+            return HttpResponse.notFound();
+        }
+        SampleSubmission submission = submissionOpt.get();
+        if (!submission.isDeletable()) {
+            return HttpResponse.notAllowed();
+        }
+
+        sampleSubmissionService.deleteSampleSubmission(program.get(), submissionId);
+
+        return HttpResponse.ok();
+    }
+
 }