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TASK-6272: IVA Catalog browser have "Edit" greyed-out in the Actions drop-down for non-admin #935

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merged 6 commits into from
Jun 27, 2024
Merged

TASK-6272: IVA Catalog browser have "Edit" greyed-out in the Actions drop-down for non-admin #935

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a4aa9f2
wc - Fix permissions rights, #TASK-6272
gpveronica Jun 20, 2024
8e3338a
Merge branch 'release-2.12.x' into TASK-6272
gpveronica Jun 20, 2024
ae4a93e
Merge branch 'release-2.12.x' into TASK-6272
gpveronica Jun 21, 2024
4e603d6
wc - Fix permissions method, #TASK-5866, #TASK-5809
gpveronica Jun 21, 2024
e641df2
wc - Fix issues found in the PR, #TASK-6272
gpveronica Jun 21, 2024
1f1fa6f
Merge branch 'release-2.12.x' into TASK-6272
jmjuanes Jun 27, 2024
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4 changes: 2 additions & 2 deletions src/webcomponents/clinical/clinical-analysis-grid.js
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Expand Up @@ -22,7 +22,7 @@ import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
import "../commons/opencb-grid-toolbar.js";
import LitUtils from "../commons/utils/lit-utils.js";
import NotificationUtils from "../commons/utils/notification-utils.js";
import ModalUtils from "../commons/modal/modal-utils";
import ModalUtils from "../commons/modal/modal-utils.js";

export default class ClinicalAnalysisGrid extends LitElement {

Expand Down Expand Up @@ -641,7 +641,7 @@ export default class ClinicalAnalysisGrid extends LitElement {
const session = this.opencgaSession;
const url = `#interpreter/${session.project.id}/${session.study.id}/${row.id}`;
const hasWriteAccess = OpencgaCatalogUtils.checkPermissions(session.study, session.user.id, "WRITE_CLINICAL_ANALYSIS");
const hasAdminAccess = OpencgaCatalogUtils.isAdmin(this.opencgaSession.study, this.opencgaSession.user.id) || "disabled";
const hasAdminAccess = hasWriteAccess || "disabled";
const lockActionIcon = row.locked ? "fa-unlock" : "fa-lock";
const lockActionText = row.locked ? "Unlock" : "Lock";
const isOwnOrIsLocked = row.locked || !row.analysts?.some(analyst => analyst.id === this.opencgaSession?.user?.id) ? "disabled" : "";
Expand Down
9 changes: 6 additions & 3 deletions src/webcomponents/cohort/cohort-grid.js
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Expand Up @@ -21,8 +21,9 @@ import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
import PolymerUtils from "../PolymerUtils.js";
import "../commons/opencb-grid-toolbar.js";
import NotificationUtils from "../commons/utils/notification-utils.js";
import ModalUtils from "../commons/modal/modal-utils";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils";
import ModalUtils from "../commons/modal/modal-utils.js";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils.js";
import WebUtils from "../commons/utils/web-utils.js";


export default class CohortGrid extends LitElement {
Expand Down Expand Up @@ -144,6 +145,8 @@ export default class CohortGrid extends LitElement {
// </catalog-browser-grid-config>`
// }
};

this.permissionID = WebUtils.getPermissionID(this.toolbarConfig.resource, "WRITE");
}

renderTable() {
Expand Down Expand Up @@ -320,7 +323,7 @@ export default class CohortGrid extends LitElement {
</button>
<ul class="dropdown-menu dropdown-menu-right">
<li>
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.isAdmin(this.opencgaSession.study, this.opencgaSession.user.id) || "disabled" }">
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.checkPermissions(this.opencgaSession.study, this.opencgaSession.user.id, this.permissionID) || "disabled" }">
<i class="fas fa-edit icon-padding" aria-hidden="true"></i> Edit ...
</a>
</li>
Expand Down
7 changes: 5 additions & 2 deletions src/webcomponents/commons/opencb-grid-toolbar.js
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Expand Up @@ -21,6 +21,7 @@ import LitUtils from "./utils/lit-utils";
import ModalUtils from "./modal/modal-utils.js";
import "./opencga-export.js";
import "../variant/interpretation/variant-interpreter-grid-config.js";
import WebUtils from "./utils/web-utils.js";

export default class OpencbGridToolbar extends LitElement {

Expand Down Expand Up @@ -74,6 +75,8 @@ export default class OpencbGridToolbar extends LitElement {
...this.getDefaultConfig(),
...this.config,
};

this.permissionID = WebUtils.getPermissionID(this._config.resource, "WRITE");
}

super.update(changedProperties);
Expand Down Expand Up @@ -120,7 +123,7 @@ export default class OpencbGridToolbar extends LitElement {
isCreateDisabledTooltip = this._config?.create?.display?.disabledTooltip;
} else {
const hasPermissions = OpencgaCatalogUtils
.checkPermissions(this.opencgaSession?.study, this.opencgaSession?.user?.id, `WRITE_${this._config.resource}`);
.checkPermissions(this.opencgaSession?.study, this.opencgaSession?.user?.id, this.permissionID);
if (!hasPermissions) {
isCreateDisabled = true;
isCreateDisabledTooltip = "Creating a new instance requires write permissions on the study. Please, contact your administrator if you need different access rights.";
Expand Down Expand Up @@ -194,7 +197,7 @@ export default class OpencbGridToolbar extends LitElement {
<!-- Add modals-->
${(this._config?.create &&
(this._settings.showCreate || this._settings.showNew) &&
OpencgaCatalogUtils.checkPermissions(this.opencgaSession?.study, this.opencgaSession?.user?.id, `WRITE_${this._config.resource}`)) ?
OpencgaCatalogUtils.checkPermissions(this.opencgaSession?.study, this.opencgaSession?.user?.id, this.permissionID)) ?
ModalUtils.create(this, `${this._prefix}CreateModal`, this._config.create) :
nothing}

Expand Down
16 changes: 16 additions & 0 deletions src/webcomponents/commons/utils/web-utils.js
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Expand Up @@ -32,6 +32,22 @@ export default class WebUtils {
}
}

static getPermissionID(resource, mode) {
// Note 20240620 Vero: The permissions IDs have been retrieved from the following document:
// https://github.com/opencb/opencga/blob/develop/docs/manual/data-management/sharing-and-permissions/permissions.md
const mapResourcePermissionId = {
"INDIVIDUAL": "INDIVIDUALS",
"SAMPLE": "SAMPLES",
"COHORT": "COHORTS",
"FAMILY": "FAMILIES",
"DISEASE_PANEL": "PANELS",
"JOB": "JOBS",
"FILE": "FILES",
"CLINICAL_ANALYSIS": "CLINICAL_ANALYSIS",
};
return (resource && mapResourcePermissionId[resource] && mode) ? `${mode.toUpperCase()}_${mapResourcePermissionId[resource]}` : "";
}

static getIVALink(opencgaSession, tool, query = {}) {
const baseUrl = (new URL(window.location.pathname, window.location.origin));
let queryStr = "";
Expand Down
10 changes: 8 additions & 2 deletions src/webcomponents/disease-panel/disease-panel-grid.js
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Expand Up @@ -23,8 +23,9 @@ import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-util
import LitUtils from "../commons/utils/lit-utils.js";
import "../commons/catalog-browser-grid-config.js";
import "../commons/opencb-grid-toolbar.js";
import ModalUtils from "../commons/modal/modal-utils";
import CatalogGridFormatter from "../commons/catalog-grid-formatter";
import ModalUtils from "../commons/modal/modal-utils.js";
import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
import WebUtils from "../commons/utils/web-utils.js";

export default class DiseasePanelGrid extends LitElement {

Expand Down Expand Up @@ -142,6 +143,8 @@ export default class DiseasePanelGrid extends LitElement {
// </catalog-browser-grid-config>`
// }
};

this.permissionID = WebUtils.getPermissionID(this.toolbarConfig.resource, "WRITE");
}

renderTable() {
Expand Down Expand Up @@ -460,6 +463,9 @@ export default class DiseasePanelGrid extends LitElement {
<a data-action="edit" class="btn force-text-left ${isAdmin ? "" : "disabled"}">
<i class="fas fa-edit icon-padding" aria-hidden="true"></i> Edit ...
</a>
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.checkPermissions(this.opencgaSession.study, this.opencgaSession.user.id, this.permissionID) || "disabled" }">
<i class="fas fa-edit icon-padding" aria-hidden="true"></i> Edit ...
</a>
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</li>
<li>
<a data-action="delete" href="javascript: void 0" class="btn force-text-left ${isAdmin ? "" : "disabled"}">
Expand Down
9 changes: 6 additions & 3 deletions src/webcomponents/family/family-grid.js
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Expand Up @@ -19,9 +19,10 @@ import UtilsNew from "../../core/utils-new.js";
import GridCommons from "../commons/grid-commons.js";
import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
import NotificationUtils from "../commons/utils/notification-utils.js";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils";
import ModalUtils from "../commons/modal/modal-utils";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils.js";
import ModalUtils from "../commons/modal/modal-utils.js";
import "../commons/opencb-grid-toolbar.js";
import WebUtils from "../commons/utils/web-utils.js";

export default class FamilyGrid extends LitElement {

Expand Down Expand Up @@ -138,6 +139,8 @@ export default class FamilyGrid extends LitElement {
// </catalog-browser-grid-config>`
// }
};

this.permissionID = WebUtils.getPermissionID(this.toolbarConfig.resource, "WRITE");
}

renderTable() {
Expand Down Expand Up @@ -534,7 +537,7 @@ export default class FamilyGrid extends LitElement {
</li>
<li role="separator" class="divider"></li>
<li>
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.isAdmin(this.opencgaSession.study, this.opencgaSession.user.id) || "disabled" }">
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.checkPermissions(this.opencgaSession.study, this.opencgaSession.user.id, this.permissionID) || "disabled" }">
<i class="fas fa-edit icon-padding" aria-hidden="true"></i> Edit ...
</a>
</li>
Expand Down
7 changes: 5 additions & 2 deletions src/webcomponents/file/file-grid.js
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Expand Up @@ -21,7 +21,8 @@ import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
import "../commons/opencb-grid-toolbar.js";
import "../loading-spinner.js";
import NotificationUtils from "../commons/utils/notification-utils.js";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils.js";
import WebUtils from "../commons/utils/web-utils.js";


export default class OpencgaFileGrid extends LitElement {
Expand Down Expand Up @@ -117,6 +118,8 @@ export default class OpencgaFileGrid extends LitElement {
`,
},
};

this.permissionID = WebUtils.getPermissionID(this.toolbarConfig.resource, "WRITE");
}

renderTable() {
Expand Down Expand Up @@ -415,7 +418,7 @@ export default class OpencgaFileGrid extends LitElement {
</li>
<li role="separator" class="divider"></li>
<li>
<a data-action="edit" class="btn force-text-left disabled ${OpencgaCatalogUtils.isAdmin(this.opencgaSession.study, this.opencgaSession.user.id) || "disabled" }">
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.checkPermissions(this.opencgaSession.study, this.opencgaSession.user.id, this.permissionID) || "disabled" }">
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<i class="fas fa-edit icon-padding" aria-hidden="true"></i> Edit ...
</a>
</li>
Expand Down
9 changes: 6 additions & 3 deletions src/webcomponents/individual/individual-grid.js
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Expand Up @@ -19,9 +19,10 @@ import UtilsNew from "../../core/utils-new.js";
import GridCommons from "../commons/grid-commons.js";
import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
import NotificationUtils from "../commons/utils/notification-utils.js";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils";
import ModalUtils from "../commons/modal/modal-utils";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils.js";
import ModalUtils from "../commons/modal/modal-utils.js";
import "../commons/opencb-grid-toolbar.js";
import WebUtils from "../commons/utils/web-utils.js";

export default class IndividualGrid extends LitElement {

Expand Down Expand Up @@ -142,6 +143,8 @@ export default class IndividualGrid extends LitElement {
// </catalog-browser-grid-config>`
// }
};

this.permissionID = WebUtils.getPermissionID(this.toolbarConfig.resource, "WRITE");
}

renderTable() {
Expand Down Expand Up @@ -572,7 +575,7 @@ export default class IndividualGrid extends LitElement {
</li>
<li role="separator" class="divider"></li>
<li>
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.isAdmin(this.opencgaSession.study, this.opencgaSession.user.id) || "disabled" }">
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.checkPermissions(this.opencgaSession.study, this.opencgaSession.user.id, this.permissionID) || "disabled" }">
<i class="fas fa-edit icon-padding" aria-hidden="true"></i> Edit ...
</a>
</li>
Expand Down
9 changes: 6 additions & 3 deletions src/webcomponents/job/job-grid.js
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Expand Up @@ -21,8 +21,9 @@ import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
import "../commons/opencb-grid-toolbar.js";
import "../loading-spinner.js";
import NotificationUtils from "../commons/utils/notification-utils.js";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils";
import ModalUtils from "../commons/modal/modal-utils";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils.js";
import ModalUtils from "../commons/modal/modal-utils.js";
import WebUtils from "../commons/utils/web-utils.js";

export default class JobGrid extends LitElement {

Expand Down Expand Up @@ -148,6 +149,8 @@ export default class JobGrid extends LitElement {
// </catalog-browser-grid-config>`
// }
};

this.permissionID = WebUtils.getPermissionID(this.toolbarConfig.resource, "WRITE");
}

renderTable() {
Expand Down Expand Up @@ -573,7 +576,7 @@ export default class JobGrid extends LitElement {
</li>
<li role="separator" class="divider"></li>
<li>
<a data-action="edit" class="btn force-text-left disabled ${OpencgaCatalogUtils.isAdmin(this.opencgaSession.study, this.opencgaSession.user.id) || "disabled" }">
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.checkPermissions(this.opencgaSession.study, this.opencgaSession.user.id, this.permissionID) || "disabled" }">
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<i class="fas fa-edit icon-padding" aria-hidden="true"></i> Edit ...
</a>
</li>
Expand Down
10 changes: 8 additions & 2 deletions src/webcomponents/sample/sample-grid.js
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Expand Up @@ -22,7 +22,8 @@ import "../commons/opencb-grid-toolbar.js";
import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils.js";
import NotificationUtils from "../commons/utils/notification-utils.js";
import "./sample-update.js";
import ModalUtils from "../commons/modal/modal-utils";
import ModalUtils from "../commons/modal/modal-utils.js";
import WebUtils from "../commons/utils/web-utils.js";


export default class SampleGrid extends LitElement {
Expand Down Expand Up @@ -90,6 +91,8 @@ export default class SampleGrid extends LitElement {
...this.getDefaultConfig(),
...this.config,
};


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this.gridCommons = new GridCommons(this.gridId, this, this._config);

// Config for the grid toolbar
Expand All @@ -116,6 +119,7 @@ export default class SampleGrid extends LitElement {
</sample-create>
`,
},

// Uncomment in case we need to change defaults
// export: {
// display: {
Expand Down Expand Up @@ -143,6 +147,8 @@ export default class SampleGrid extends LitElement {
// </catalog-browser-grid-config>`
// }
};

this.permissionID = WebUtils.getPermissionID(this.toolbarConfig.resource, "WRITE");
}

renderTable() {
Expand Down Expand Up @@ -455,7 +461,7 @@ export default class SampleGrid extends LitElement {
</li>
<li role="separator" class="divider"></li>
<li>
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.isAdmin(this.opencgaSession.study, this.opencgaSession.user.id) || "disabled" }">
<a data-action="edit" class="btn force-text-left ${OpencgaCatalogUtils.checkPermissions(this.opencgaSession.study, this.opencgaSession.user.id, this.permissionID) || "disabled" }">
<i class="fas fa-edit icon-padding" aria-hidden="true"></i> Edit ...
</a>
</li>
Expand Down
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