`
// }
};
+
+ this.permissionID = WebUtils.getPermissionID(this.toolbarConfig.resource, "WRITE");
}
- fetchClinicalAnalysis(rows, casesLimit) {
+ fetchClinicalAnalysis(rows, individuals, casesLimit) {
if (rows && rows.length > 0) {
return this.opencgaSession.opencgaClient.clinical()
.search({
- individual: rows.map(sample => sample.individualId).join(","),
+ individual: individuals,
study: this.opencgaSession.study.fqn,
include: "id,proband.id,family.members",
limit: casesLimit * 10,
@@ -229,7 +233,14 @@ export default class SampleGrid extends LitElement {
.then(response => {
sampleResponse = response;
// Fetch clinical analysis to display the Case ID
- return this.fetchClinicalAnalysis(sampleResponse?.responses?.[0]?.results || [], casesLimit);
+ const samples = sampleResponse?.responses?.[0]?.results;
+ const individuals = (samples || [])
+ .map(sample => sample.individualId)
+ .filter(individualId => !!individualId)
+ .join(",");
+ if (individuals) {
+ return this.fetchClinicalAnalysis(samples || [], individuals, casesLimit);
+ }
})
.then(() => {
// Prepare data for columns extensions
@@ -345,7 +356,7 @@ export default class SampleGrid extends LitElement {
case "download-json":
UtilsNew.downloadData([JSON.stringify(row, null, "\t")], row.id + ".json");
break;
- case "qualityControl":
+ case "quality-control":
alert("Not implemented yet");
break;
}
@@ -431,67 +442,78 @@ export default class SampleGrid extends LitElement {
title: "Actions",
field: "actions",
align: "center",
- formatter: (value, row) => `
-
-
-
+
+ `;
+ },
events: {
"click a": this.onActionClick.bind(this)
},
diff --git a/src/webcomponents/sample/sample-update.js b/src/webcomponents/sample/sample-update.js
index 4d0c075ceb..c88d83b800 100644
--- a/src/webcomponents/sample/sample-update.js
+++ b/src/webcomponents/sample/sample-update.js
@@ -206,14 +206,6 @@ export default class SampleUpdate extends LitElement {
placeholder: "Add an ID",
}
},
- {
- title: "Name",
- field: "status.name",
- type: "input-text",
- display: {
- placeholder: "Add source name"
- }
- },
{
title: "Description",
field: "status.description",
diff --git a/src/webcomponents/sample/sample-variant-stats-browser.js b/src/webcomponents/sample/sample-variant-stats-browser.js
index 0542ec3ba7..a763cbb379 100644
--- a/src/webcomponents/sample/sample-variant-stats-browser.js
+++ b/src/webcomponents/sample/sample-variant-stats-browser.js
@@ -407,7 +407,11 @@ export default class SampleVariantStatsBrowser extends LitElement {
modalTitle: "Save Variant Stats",
modalButtonIcon: "fas fa-save",
modalButtonClassName: "btn btn-primary",
- modalDisabled: !OpencgaCatalogUtils.checkPermissions(this.opencgaSession.study, this.opencgaSession.user.id, "WRITE_CLINICAL_ANALYSIS"),
+ modalDisabled: !OpencgaCatalogUtils.getStudyEffectivePermission(
+ this.opencgaSession.study,
+ this.opencgaSession.user.id,
+ "WRITE_CLINICAL_ANALYSIS",
+ this.opencgaSession?.organization?.configuration?.optimizations?.simplifyPermissions),
labelWidth: 3,
labelAlign: "right",
defaultValue: "",
diff --git a/src/webcomponents/sample/sample-variant-stats-view.js b/src/webcomponents/sample/sample-variant-stats-view.js
index b644146dc3..6f20dcf8b9 100644
--- a/src/webcomponents/sample/sample-variant-stats-view.js
+++ b/src/webcomponents/sample/sample-variant-stats-view.js
@@ -194,31 +194,31 @@ class SampleVariantStatsView extends LitElement {
return html`
No Variant Stats found.
-
`;
+
+ `;
}
return html`
- ${this.sample ?
- html`
-
-
-
-
-
-
-
` : nothing
- }
-
+ ${this.sample ? html`
+
+
+
+
+
+
+
+ ` : nothing}
diff --git a/src/webcomponents/sample/sample-view.js b/src/webcomponents/sample/sample-view.js
index f081202e4c..01dfe18c6d 100644
--- a/src/webcomponents/sample/sample-view.js
+++ b/src/webcomponents/sample/sample-view.js
@@ -194,7 +194,10 @@ export default class SampleView extends LitElement {
},
{
title: "Individual ID",
- field: "individualId"
+ field: "individualId",
+ display: {
+ defaultValue: "No individuals or no clinical analyses",
+ }
},
{
title: "Files",
@@ -217,7 +220,7 @@ export default class SampleView extends LitElement {
title: "Status",
type: "complex",
display: {
- template: "${internal.status.name} (${internal.status.date})",
+ template: "${internal.status.id} (${internal.status.date})",
format: {
"internal.status.date": date => UtilsNew.dateFormatter(date),
}
diff --git a/src/webcomponents/study/admin/study-admin-audit.js b/src/webcomponents/study/admin/study-admin-audit.js
index 9fd0a6f1e3..8cacd90148 100644
--- a/src/webcomponents/study/admin/study-admin-audit.js
+++ b/src/webcomponents/study/admin/study-admin-audit.js
@@ -235,7 +235,7 @@ export default class StudyAdminAudit extends LitElement {
},
{
title: "Status",
- field: "status.name",
+ field: "status.id",
},
];
}
diff --git a/src/webcomponents/study/admin/study-admin-iva.js b/src/webcomponents/study/admin/study-admin-iva.js
index cbb7d34eab..a69d3cd295 100644
--- a/src/webcomponents/study/admin/study-admin-iva.js
+++ b/src/webcomponents/study/admin/study-admin-iva.js
@@ -21,6 +21,7 @@ import "../../commons/tool-settings-update.js";
import LitUtils from "../../commons/utils/lit-utils";
import NotificationUtils from "../../commons/utils/notification-utils";
import UtilsNew from "../../../core/utils-new";
+import OpencgaCatalogUtils from "../../../core/clients/opencga/opencga-catalog-utils";
export default class StudyAdminIva extends LitElement {
@@ -36,6 +37,9 @@ export default class StudyAdminIva extends LitElement {
static get properties() {
return {
+ organizationId: {
+ type: String,
+ },
studyId: {
type: String,
},
@@ -61,6 +65,9 @@ export default class StudyAdminIva extends LitElement {
}
update(changedProperties) {
+ if (changedProperties.has("organizationId")) {
+ this.organizationIdObserver();
+ }
if (changedProperties.has("studyId")) {
this.studyIdObserver();
}
@@ -76,9 +83,31 @@ export default class StudyAdminIva extends LitElement {
}
/* -- OBSERVER METHODS -- */
- opencgaSessionObserver() {
- this.study = this.opencgaSession.study;
- this._config = this.getDefaultConfig();
+ organizationIdObserver() {
+ // FIXME Vero: on creating a new group, for instance,
+ // the session is updated but the org id does not change.
+ // I need to get the organization info again to refresh the grid.
+ // For now, I will query org info only with property opencgaSession change.
+ // TO think about it.
+ // if (this.organizationId && this.opencgaSession) {
+ if (this.organizationId || this.opencgaSession) {
+ let error;
+ this.#setLoading(true);
+ this.opencgaSession.opencgaClient.organization()
+ .info(this.opencgaSession.organization.id)
+ .then(response => {
+ this.organization = UtilsNew.objectClone(response.responses[0].results[0]);
+ })
+ .catch(reason => {
+ // this.organization = {};
+ error = reason;
+ console.error(reason);
+ })
+ .finally(() => {
+ LitUtils.dispatchCustomEvent(this, "organizationInfo", this.organization, {}, error);
+ this.#setLoading(false);
+ });
+ }
}
studyIdObserver() {
@@ -102,9 +131,27 @@ export default class StudyAdminIva extends LitElement {
}
}
+ opencgaSessionObserver() {
+ this.study = this.opencgaSession.study;
+ this._config = this.getDefaultConfig();
+ }
+
// --- RENDER METHOD ---
render() {
- return html`
+ if (this.opencgaSession.study && this.organization) {
+ if (!OpencgaCatalogUtils.isOrganizationAdmin(this.organization, this.opencgaSession.user.id) &&
+ !OpencgaCatalogUtils.isAdmin(this.opencgaSession.study, this.opencgaSession.user.id)) {
+ return html`
+
+
+
Restricted access
+ The page you are trying to access has restricted access.
+ Please refer to your system administrator.
+
+ `;
+ }
+
+ return html`
`;
+ }
}
getDefaultConfig() {
diff --git a/src/webcomponents/study/admin/study-admin-permissions.js b/src/webcomponents/study/admin/study-admin-permissions.js
index 5cd5f4110d..087500d182 100644
--- a/src/webcomponents/study/admin/study-admin-permissions.js
+++ b/src/webcomponents/study/admin/study-admin-permissions.js
@@ -70,11 +70,11 @@ export default class StudyAdminPermissions extends LitElement {
active: true,
render: (study, active, opencgaSession) => {
return html`
-
- `;
+ `;
}
},
{
diff --git a/src/webcomponents/study/admin/study-admin-users.js b/src/webcomponents/study/admin/study-admin-users.js
index b91f7f408e..8ea61f04ea 100644
--- a/src/webcomponents/study/admin/study-admin-users.js
+++ b/src/webcomponents/study/admin/study-admin-users.js
@@ -99,9 +99,11 @@ export default class StudyAdminUsers extends LitElement {
studyObserver() {
if (this.study) {
+ // FIXME!!!!!: admin/owner organization. Ask Pedro again
this.owner = this.study.fqn.split("@")[0];
this.groupsMap = new Map();
- this.opencgaSession.opencgaClient.studies().groups(this.study.fqn)
+ this.opencgaSession.opencgaClient.studies()
+ .groups(this.study.fqn)
.then(response => {
const groups = response.responses[0].results;
// Remove in OpenCGA 2.1
@@ -157,14 +159,36 @@ export default class StudyAdminUsers extends LitElement {
}
groupFormatter(value, row) {
- // const isOwner = this.field.owner === this.field.loggedUser;
- const isOwner = OpencgaCatalogUtils.checkUserAccountView(this.field.owner, this.field.loggedUser);
+ // NOTE:
+ // - Only organization owner/admin can manage study admins
+ // - Study admins can add/remove users to the study and groups (except group admins)
+ // - Regular users (no org owner/admin, no study admin) can not access this site
+ const isOrganizationAdmin = OpencgaCatalogUtils.isOrganizationAdmin(this.field.opencgaSession.organization, row.id);
+ const isLoggedUserOrganizationAdmin = OpencgaCatalogUtils.isOrganizationAdmin(this.field.opencgaSession.organization, this.field.loggedUser);
+ const isStudyAdmin = OpencgaCatalogUtils.isAdmin(this.field.study, row.id);
+ const isLoggedUserStudyAdmin = OpencgaCatalogUtils.isAdmin(this.field.study, this.field.loggedUser);
const checked = this.field.groupsMap?.get(this.field.groupId).findIndex(e => e.id === row.id) !== -1;
if (this.field.groupId === "@admins") {
- return `
`;
+ if (isLoggedUserOrganizationAdmin) {
+ // return `
`;
+ return `
`;
+ } else {
+ return `
`;
+ }
} else {
- return `
`;
+ // return `
`;
+ return `
`;
}
+ // Todo: the checked attribute is not working. Investigate why and fix
+ // return `
+ //
+ //
+ //
+ // `;
}
async onCheck(e, value, row, group, context) {
@@ -189,9 +213,8 @@ export default class StudyAdminUsers extends LitElement {
NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, {
message: messageAlert,
});
- // this.notifyStudyUpdateRequest();
LitUtils.dispatchCustomEvent(this, "studyUpdateRequest", this.study.fqn);
- this.requestUpdate();
+ // this.requestUpdate();
} catch (error) {
// console.error("Message error: ", error);
NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_RESPONSE, error);
@@ -212,7 +235,10 @@ export default class StudyAdminUsers extends LitElement {
groupId: group,
groupsMap: this.groupsMap,
owner: this.owner,
- loggedUser: this.opencgaSession?.user?.id
+ loggedUser: this.opencgaSession?.user?.id,
+ // Terrible two hacks for having access to the organization
+ opencgaSession: this.opencgaSession,
+ study: this.study,
},
rowspan: 1,
colspan: 1,
@@ -231,9 +257,6 @@ export default class StudyAdminUsers extends LitElement {
{
title: "User Name",
field: "name",
- formatter: (value, row) => {
- return value === this.owner ? `
${value} (owner)` : value;
- },
rowspan: 2,
colspan: 1,
sortable: true
@@ -252,8 +275,8 @@ export default class StudyAdminUsers extends LitElement {
},
{
title: "Created on",
- field: "account.creationDate",
- formatter: (value, row) => {
+ field: "creationDate",
+ formatter: value => {
return value ? UtilsNew.dateFormatter(value) : "NA";
},
rowspan: 2,
@@ -334,20 +357,18 @@ export default class StudyAdminUsers extends LitElement {
console.log("User already exists in the study");
return;
}
+ const params = {
+ study: this.study.fqn,
+ template: "",
+ permissions: "",
+ };
- this.opencgaSession.opencgaClient.studies().updateUsers(this.study.fqn, "@members", {users: [this.addUserId]}, {action: "ADD"})
- .then(res => {
+ this.opencgaSession.opencgaClient.studies()
+ // .updateUsers(this.study.fqn, "@members", {users: [this.addUserId]}, {action: "ADD"})
+ .updateAcl(this.addUserId, {action: "ADD"}, params)
+ .then(() => {
this.addUserId = "";
- this.requestUpdate();
-
- this.dispatchEvent(new CustomEvent("studyUpdateRequest", {
- detail: {
- value: this.study.fqn
- },
- bubbles: true,
- composed: true
- }));
-
+ LitUtils.dispatchCustomEvent(this, "studyUpdateRequest", this.study.fqn);
NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, {
message: "User added.",
});
@@ -373,20 +394,31 @@ export default class StudyAdminUsers extends LitElement {
onRemoveUserTest(e, row) {
NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_CONFIRMATION, {
title: `Remove user '${row.id}'`,
- message: `Are you sure you want to remove user
'${row.id}'?`,
+ message: `Are you sure you want to remove user
'${row.id}' from the study ${this.study.fqn}?`,
display: {
okButtonText: "Yes, remove user",
},
ok: () => {
- this.opencgaSession.opencgaClient.studies().updateUsers(this.study.fqn, "@members", {users: [row.id]}, {action: "REMOVE"})
+ // this.opencgaSession.opencgaClient.studies()
+ // .updateUsers(this.study.fqn, "@members", {users: [row.id]}, {action: "REMOVE"})
+ const params= {
+ includeResult: true,
+ action: "REMOVE",
+ };
+ const data = {
+ users: [row.id],
+ };
+ this.opencgaSession.opencgaClient.studies()
+ .updateGroupsUsers(this.study.fqn, "@members", data, params)
.then(() => {
- this.requestUpdate();
LitUtils.dispatchCustomEvent(this, "studyUpdateRequest", this.study.fqn);
- this.requestUpdate();
-
NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, {
message: "User removed",
});
+ NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, {
+ title: `User in Group Update`,
+ message: `User ${row.id} REMOVED from @members in study ${this.study.id} correctly`,
+ });
}).catch(err => {
console.error(err);
});
@@ -403,16 +435,8 @@ export default class StudyAdminUsers extends LitElement {
this.opencgaSession.opencgaClient.studies().updateUsers(this.study.fqn, "@members", {users: userIds}, {action: "REMOVE"})
.then(res => {
this.removeUserSet = new Set();
- this.requestUpdate();
-
- this.dispatchEvent(new CustomEvent("studyUpdateRequest", {
- detail: {
- value: this.study.fqn
- },
- bubbles: true,
- composed: true
- }));
-
+ // this.requestUpdate();
+ LitUtils.dispatchCustomEvent(this, "studyUpdateRequest", this.study.fqn);
NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, {
message: "User removed",
});
@@ -436,8 +460,7 @@ export default class StudyAdminUsers extends LitElement {
this.opencgaSession.opencgaClient.studies().updateGroups(this.study.fqn, {id: this.addGroupId}, {action: "ADD"})
.then(res => {
this.addGroupId = "";
- this.requestUpdate();
- // this.notifyStudyUpdateRequest();
+ // this.requestUpdate();
LitUtils.dispatchCustomEvent(this, "studyUpdateRequest", this.study.fqn);
NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, {
@@ -492,20 +515,8 @@ export default class StudyAdminUsers extends LitElement {
NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_INFO, {
message: messageAlert,
});
-
- // this.notifyStudyUpdateRequest();
LitUtils.dispatchCustomEvent(this, "studyUpdateRequest", this.study.fqn);
- this.requestUpdate();
- }
-
- notifyStudyUpdateRequest() {
- this.dispatchEvent(new CustomEvent("studyUpdateRequest", {
- detail: {
- value: this.study.fqn
- },
- bubbles: true,
- composed: true
- }));
+ // this.requestUpdate();
}
render() {
@@ -543,9 +554,16 @@ export default class StudyAdminUsers extends LitElement {
-
`;
}
diff --git a/src/webcomponents/user/user-password-change.js b/src/webcomponents/user/user-password-change.js
index 70a514cc8b..af0140f566 100644
--- a/src/webcomponents/user/user-password-change.js
+++ b/src/webcomponents/user/user-password-change.js
@@ -1,7 +1,8 @@
import {LitElement, html} from "lit";
-import UtilsNew from "../../core/utils-new.js";
import NotificationUtils from "../commons/utils/notification-utils.js";
import "../commons/forms/data-form.js";
+import LitUtils from "../commons/utils/lit-utils";
+import UtilsNew from "../../core/utils-new";
export default class UserPasswordChange extends LitElement {
@@ -16,55 +17,101 @@ export default class UserPasswordChange extends LitElement {
static get properties() {
return {
+ userId: {
+ type: String,
+ },
opencgaSession: {
type: Object
},
+ organizationId: {
+ type: String,
+ },
+ displayConfig: {
+ type: Object
+ },
};
}
#init() {
- this.updateParams = {};
- this.config = this.getDefaultConfig();
+ this._password = {};
+ this.displayConfigDefault = {
+ style: "margin: 10px",
+ titleWidth: 3,
+ titleStyle: "color: var(--main-bg-color);margin-bottom:16px;font-weight:bold;",
+ defaultLayout: "horizontal",
+ buttonOkText: "Change password",
+ };
+ this._config = this.getDefaultConfig();
+ }
+
+ #setLoading(value) {
+ this.isLoading = value;
+ this.requestUpdate();
+ }
+
+ #initOriginalObjects() {
+ this._password = {};
+ this._config = this.getDefaultConfig();
+ this.requestUpdate();
+ }
+
+ update(changedProperties) {
+ if (changedProperties.has("displayConfig")) {
+ this.displayConfig = {
+ ...this.displayConfigDefault,
+ ...this.displayConfig
+ };
+ this._config = this.getDefaultConfig();
+ }
+ super.update(changedProperties);
}
onFieldChange(e) {
- this.updateParams[e.detail.param] = e.detail.value;
- this.updateParams = {...this.updateParams};
+ this._password = {...e.detail.data}; // force to refresh the object-list
this.requestUpdate();
}
onSubmit() {
- this.opencgaSession.opencgaClient.getClient("user").password({
- user: this.opencgaSession.user.id,
- password: this.updateParams.oldPassword,
- newPassword: this.updateParams.newPassword,
- })
+ const params = {
+ user: this.userId,
+ password: this._password.oldPassword,
+ newPassword: this._password.newPassword,
+ organizationId: this.organizationId,
+ };
+ let error;
+ this.#setLoading(true);
+ this.opencgaSession.opencgaClient.users()
+ .password(params)
.then(() => {
NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, {
message: "Your password has been changed",
});
- this.onClear();
+ LitUtils.dispatchCustomEvent(this, "userUpdate");
+ this.#initOriginalObjects();
+ })
+ .catch(reason => {
+ error = reason;
+ NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_RESPONSE, error);
})
- .catch(response => {
- // console.error(response);
- NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_RESPONSE, response);
+ .finally(() => {
+ this.#setLoading(false);
});
}
onClear() {
- this.updateParams = {};
- // Terrible hack to reset the values in the input elements
- // eslint-disable-next-line no-param-reassign
- Array.from(this.querySelectorAll("input")).forEach(el => el.value = "");
- this.requestUpdate();
+ NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_CONFIRMATION, {
+ title: "Clear password",
+ message: "Are you sure to clear?",
+ ok: () => this.#initOriginalObjects(),
+ });
}
render() {
// TODO: check if opencgaSession has been provided
return html`
@@ -74,45 +121,47 @@ export default class UserPasswordChange extends LitElement {
getDefaultConfig() {
return {
- icon: "",
- display: {
- buttonOkText: "Change password",
- },
- // validation: {
- // validate: () => this.updateParams.newPassword === this.updateParams.confirmNewPassword,
- // message: "New passwords do not match",
+ // icon: "",
+ // display: {
+ // buttonOkText: "Change password",
// },
+ // // validation: {
+ // // validate: () => this.updateParams.newPassword === this.updateParams.confirmNewPassword,
+ // // message: "New passwords do not match",
+ // // },
+ title: "Change Password",
+ display: this.displayConfig || this.displayConfigDefault,
sections: [
{
// title: "Change password",
// description: "Here you can change your password. Make sure it has at least 8 characters.",
elements: [
- {
- type: "text",
- text: "Change password",
- display: {
- icon: "user-shield",
- textClassName: "h2",
- textStyle: "color: var(--main-bg-color);margin-bottom:16px;font-weight:bold;",
- },
- },
- {
- type: "text",
- text: `
- Here you can change your password. We recommend that your new password has at least
- 8 characters long and uses uppercase and lowercase letters and numbers.
- `,
- display: {
- textStyle: "margin-bottom:16px;",
- },
- },
+ // {
+ // type: "text",
+ // text: "Change password",
+ // display: {
+ // icon: "user-shield",
+ // textClassName: "h2",
+ // textStyle: "color: var(--main-bg-color);margin-bottom:16px;font-weight:bold;",
+ // },
+ // },
+ // {
+ // type: "text",
+ // text: `
+ // Here you can change your password. We recommend that your new password has at least
+ // 8 characters long and uses uppercase and lowercase letters and numbers.
+ // `,
+ // display: {
+ // textStyle: "margin-bottom:16px;",
+ // },
+ // },
{
title: "Current password",
type: "input-password",
field: "oldPassword",
defaultValue: "",
validation: {
- validate: () => !!this.updateParams.oldPassword,
+ validate: () => !!this._password.oldPassword,
message: "Please enter your existing password.",
},
},
@@ -122,7 +171,7 @@ export default class UserPasswordChange extends LitElement {
field: "newPassword",
defaultValue: "",
validation: {
- validate: () => !!this.updateParams.newPassword,
+ validate: () => !!this._password.newPassword,
message: "Your new password can not be empty.",
},
},
@@ -133,7 +182,7 @@ export default class UserPasswordChange extends LitElement {
defaultValue: "",
validation: {
validate: () => {
- return !!this.updateParams.confirmNewPassword && this.updateParams.confirmNewPassword === this.updateParams.newPassword;
+ return !!this._password.confirmNewPassword && this._password.confirmNewPassword === this._password.newPassword;
},
message: "New passwords do not match.",
},
diff --git a/src/webcomponents/user/user-password-reset.js b/src/webcomponents/user/user-password-reset.js
index 3773f0c89f..790740ad58 100644
--- a/src/webcomponents/user/user-password-reset.js
+++ b/src/webcomponents/user/user-password-reset.js
@@ -1,12 +1,28 @@
+/**
+ * Copyright 2015-2024 OpenCB
+ *
+ * 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 {LitElement, html} from "lit";
import LitUtils from "../commons/utils/lit-utils.js";
import NotificationUtils from "../commons/utils/notification-utils.js";
-
export default class UserPasswordReset extends LitElement {
constructor() {
super();
+
this.#init();
}
@@ -16,83 +32,129 @@ export default class UserPasswordReset extends LitElement {
static get properties() {
return {
+ user: {
+ type: Object,
+ },
opencgaSession: {
type: Object
},
+ displayConfig: {
+ type: Object
+ },
};
}
#init() {
- this.hasEmptyUser = false;
+ this._user = {};
+ this.displayConfigDefault = {
+ style: "margin: 10px",
+ titleWidth: 3,
+ titleStyle: "color: var(--main-bg-color);margin-bottom:16px;font-weight:bold;",
+ defaultLayout: "horizontal",
+ buttonOkText: "Reset password",
+ };
+ this._config = this.getDefaultConfig();
}
- redirect(to) {
- LitUtils.dispatchCustomEvent(this, "redirect", null, {hash: to});
+ #setLoading(value) {
+ this.isLoading = value;
+ this.requestUpdate();
}
- onSubmit(e) {
- e.preventDefault();
- const user = (this.querySelector("#user").value || "").trim();
+ #initOriginalObjects() {
+ this._config = this.getDefaultConfig();
+ this.requestUpdate();
+ }
- // Check for empty user ID
- this.hasEmptyUser = user.length === 0;
- if (this.hasEmptyUser) {
- return this.requestUpdate();
+ update(changedProperties) {
+ if (changedProperties.has("displayConfig") || changedProperties.has("user")) {
+ this.displayConfig = {
+ ...this.displayConfigDefault,
+ ...this.displayConfig
+ };
+ this._config = this.getDefaultConfig();
}
+ super.update(changedProperties);
+ }
- // Reset password mockup
- // TODO: call openCGA to the correct endpoint
- Promise.resolve().then(() => {
- NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, {
- "message": "We have just send you an email with the new password.",
+ onSubmit() {
+ // QUESTION:
+ // - TASK-1667, includeResult
+ // - JS client do not have argument for params, only user
+ let error;
+ this.#setLoading(true);
+ // Reset password
+ this.opencgaSession.opencgaClient.users()
+ .resetPassword(this.user.id)
+ .then(() => {
+ this.#initOriginalObjects();
+ NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, {
+ title: `User Reset Password`,
+ message: `User ${this.user.id} password reset correctly`,
+ });
+ })
+ .catch(reason => {
+ error = reason;
+ NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_RESPONSE, reason);
+ })
+ .finally(() => {
+ LitUtils.dispatchCustomEvent(this, "userUpdate", this.user.id, {}, error);
+ this.#setLoading(false);
});
- this.querySelector("#user").value = "";
- this.hasEmptyUser = false;
- this.requestUpdate();
- });
- }
-
- // Handle keyup event --> check for enter key to submit the form
- onKeyUp(e) {
- if (e.key === "Enter") {
- return this.onSubmit(e);
- }
}
render() {
+ // TODO: check if opencgaSession has been provided
return html`
-
-
-
-
-
- Reset your password
-
-
-
- Please enter your user ID and we will send you an email with your password reset link.
-
-
-
-
-
-
-
diff --git a/src/webcomponents/variant/annotation/variant-annotation-clinical-view.js b/src/webcomponents/variant/annotation/variant-annotation-clinical-view.js
index 4da83bc067..91d4af34fe 100644
--- a/src/webcomponents/variant/annotation/variant-annotation-clinical-view.js
+++ b/src/webcomponents/variant/annotation/variant-annotation-clinical-view.js
@@ -22,7 +22,6 @@ export default class VariantAnnotationClinicalView extends LitElement {
constructor() {
super();
-
this.#init();
}
@@ -44,6 +43,10 @@ export default class VariantAnnotationClinicalView extends LitElement {
assembly: {
type: String
},
+ groupedBySource: {
+ type: Object,
+ state: true
+ },
opencgaSession: {
type: Object
},
@@ -52,16 +55,21 @@ export default class VariantAnnotationClinicalView extends LitElement {
#init() {
this._prefix = UtilsNew.randomString(8);
+ this.traitAssociation = [];
+ this.groupedBySource = {};
}
- firstUpdated() {
- this.renderVariantTraitTable();
- }
-
- updated(changedProperties) {
+ update(changedProperties) {
if (changedProperties.has("variantId")) {
this.variantIdObserver();
}
+ if (changedProperties.has("traitAssociation")) {
+ this.traitAssociationObserver();
+ }
+ super.update(changedProperties);
+ }
+
+ updated(changedProperties) {
if (changedProperties.has("traitAssociation")) {
this.renderVariantTraitTable();
}
@@ -80,6 +88,13 @@ export default class VariantAnnotationClinicalView extends LitElement {
}
}
+ traitAssociationObserver() {
+ this.groupedBySource = {};
+ if (this.traitAssociation?.length > 0) {
+ this.groupedBySource = UtilsNew.groupBy(this.traitAssociation, "source.name");
+ }
+ }
+
idFormatter(value, row) {
let html = "-";
if (row) {
@@ -94,6 +109,9 @@ export default class VariantAnnotationClinicalView extends LitElement {
case "cosmic":
html = `${row.id}`;
break;
+ case "hgmd":
+ html = `${row.id}`;
+ break;
}
}
return html;
@@ -101,11 +119,13 @@ export default class VariantAnnotationClinicalView extends LitElement {
sourceFormatter(value) {
if (value) {
- switch (value.name) {
+ switch (value.name?.toLowerCase()) {
case "clinvar":
- return "ClinVar";
+ return `ClinVar (${value.version})`;
case "cosmic":
- return "COSMIC";
+ return `COSMIC (${value.version})`;
+ case "hgmd":
+ return `HGMD (${value.version})`;
default:
console.error("Source not valid: " + value.name);
return "-";
@@ -162,14 +182,6 @@ export default class VariantAnnotationClinicalView extends LitElement {
let result, data;
const name = row?.source?.name;
switch (name.toLowerCase()) {
- case "cosmic":
- data = row?.additionalProperties?.filter(item => item.id === "FATHMM_PREDICTION");
- result = `
-
- ${Number.parseFloat(data?.[0]?.value) || "NA"}
-
- `;
- break;
case "clinvar":
data = row?.additionalProperties?.filter(item => item.name === "ClinicalSignificance_in_source_file");
// Prepare star rating HTML
@@ -191,6 +203,14 @@ export default class VariantAnnotationClinicalView extends LitElement {
`;
break;
+ case "cosmic":
+ data = row?.additionalProperties?.filter(item => item.id === "FATHMM_PREDICTION");
+ result = `
+
+ ${Number.parseFloat(data?.[0]?.value) || "NA"}
+
+ `;
+ break;
default:
result = "-";
break;
@@ -236,15 +256,76 @@ export default class VariantAnnotationClinicalView extends LitElement {
}
renderVariantTraitTable() {
- if (!this.traitAssociation) {
- this.traitAssociation = [];
- }
+ $("#" + this._prefix + "ClinvarTraitAssociation").bootstrapTable("destroy");
+ $("#" + this._prefix + "ClinvarTraitAssociation").bootstrapTable({
+ data: this.groupedBySource.clinvar,
+ theadClasses: "table-light",
+ buttonsClass: "light",
+ pagination: false,
+ columns: [
+ {
+ title: "ID",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.idFormatter,
+ halign: "center"
+ },
+ {
+ title: "Source",
+ field: "source",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.sourceFormatter,
+ halign: "center"
+ },
+ {
+ title: "Gene",
+ field: "genomicFeatures",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.geneFormatter,
+ halign: "center"
+ },
+ {
+ title: "Heritable Traits",
+ field: "heritableTraits",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.heritableTraitsFormatter,
+ halign: "center"
+ },
+ {
+ title: "Mode of Inheritance",
+ field: "heritableTraits",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.inheritanceModeFormatter,
+ halign: "center"
+ },
+ {
+ title: "Clinical Significance",
+ field: "variantClassification",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.clinicalSignificanceFormatter,
+ halign: "center"
+ },
+ {
+ title: "Origin Type",
+ field: "alleleOrigin",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.alleleOriginFormatter,
+ halign: "center"
+ },
+ ]
+ });
- $("#" + this._prefix + "VariantTraitAssociation").bootstrapTable("destroy");
- $("#" + this._prefix + "VariantTraitAssociation").bootstrapTable({
+ $("#" + this._prefix + "CosmicTraitAssociation").bootstrapTable("destroy");
+ $("#" + this._prefix + "CosmicTraitAssociation").bootstrapTable({
+ data: this.groupedBySource.cosmic,
theadClasses: "table-light",
buttonsClass: "light",
- data: this.traitAssociation,
pagination: false,
columns: [
[
@@ -271,22 +352,6 @@ export default class VariantAnnotationClinicalView extends LitElement {
formatter: this.geneFormatter,
halign: "center"
},
- {
- title: "Heritable Traits",
- field: "heritableTraits",
- rowspan: 2,
- colspan: 1,
- formatter: this.heritableTraitsFormatter,
- halign: "center"
- },
- {
- title: "Mode of Inheritance",
- field: "heritableTraits",
- rowspan: 2,
- colspan: 1,
- formatter: this.inheritanceModeFormatter,
- halign: "center"
- },
{
title: "Clinical Significance",
field: "variantClassification",
@@ -296,19 +361,25 @@ export default class VariantAnnotationClinicalView extends LitElement {
halign: "center"
},
{
- title: "Origin Type",
- field: "alleleOrigin",
- rowspan: 2,
- colspan: 1,
- formatter: this.alleleOriginFormatter,
+ title: "Somatic Information",
+ rowspan: 1,
+ colspan: 4,
halign: "center"
},
{
- title: "Cancer",
- rowspan: 1,
- colspan: 3,
+ title: "Bibliography",
+ field: "bibliography",
+ rowspan: 2,
+ colspan: 1,
+ formatter: value => {
+ if (value?.length > 0) {
+ return value
+ .map(v => `
${v}`)
+ .join("
");
+ }
+ },
halign: "center"
- }
+ },
], [
{
title: "Tumour Site",
@@ -332,17 +403,116 @@ export default class VariantAnnotationClinicalView extends LitElement {
rowspan: 1,
colspan: 1,
halign: "center"
- }
+ },
+ {
+ title: "Mutation Zygosity",
+ field: "additionalProperties",
+ rowspan: 1,
+ colspan: 1,
+ formatter: value => {
+ const data = value?.find(item => item.name === "MUTATION_ZYGOSITY");
+ return data?.value || "-";
+ },
+ halign: "center"
+ },
]
]
});
+
+ $("#" + this._prefix + "HgmdTraitAssociation").bootstrapTable("destroy");
+ $("#" + this._prefix + "HgmdTraitAssociation").bootstrapTable({
+ data: this.groupedBySource.hgmd,
+ theadClasses: "table-light",
+ buttonsClass: "light",
+ pagination: false,
+ columns: [
+ {
+ title: "ID",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.idFormatter,
+ halign: "center"
+ },
+ {
+ title: "Source",
+ field: "source",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.sourceFormatter,
+ halign: "center"
+ },
+ {
+ title: "Gene",
+ field: "genomicFeatures",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.geneFormatter,
+ halign: "center"
+ },
+ {
+ title: "Heritable Traits",
+ field: "heritableTraits",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.heritableTraitsFormatter,
+ halign: "center"
+ },
+ {
+ title: "Mode of Inheritance",
+ field: "heritableTraits",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.inheritanceModeFormatter,
+ halign: "center"
+ },
+ {
+ title: "Clinical Significance",
+ field: "variantClassification",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.clinicalSignificanceFormatter,
+ halign: "center"
+ },
+ {
+ title: "Origin Type",
+ field: "alleleOrigin",
+ rowspan: 1,
+ colspan: 1,
+ formatter: this.alleleOriginFormatter,
+ halign: "center"
+ },
+ ]
+ });
}
render() {
return html`
Variant Trait Association
-
+
ClinVar
+
+ ${this.groupedBySource?.clinvar?.length > 0 ? html`
+
+ ` : html`
+
No data available
+ `}
+
+
Cosmic
+
+ ${this.groupedBySource?.cosmic?.length > 0 ? html`
+
+ ` : html`
+
No data available
+ `}
+
+
HGMD
+
+ ${this.groupedBySource?.hgmd?.length > 0 ? html`
+
+ ` : html`
+
No data available
+ `}
+
`;
}
diff --git a/src/webcomponents/variant/annotation/variant-annotation-pharmacogenomics-view.js b/src/webcomponents/variant/annotation/variant-annotation-pharmacogenomics-view.js
new file mode 100644
index 0000000000..9ebbfe29d8
--- /dev/null
+++ b/src/webcomponents/variant/annotation/variant-annotation-pharmacogenomics-view.js
@@ -0,0 +1,234 @@
+/*
+ * Copyright 2015-2016 OpenCB
+ *
+ * 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 {html, LitElement} from "lit";
+import UtilsNew from "../../../core/utils-new.js";
+import BioinfoUtils from "../../../core/bioinfo/bioinfo-utils.js";
+
+export default class VariantAnnotationPharmacogenomicsView extends LitElement {
+
+ constructor() {
+ super();
+
+ this.#init();
+ }
+
+ createRenderRoot() {
+ return this;
+ }
+
+ static get properties() {
+ return {
+ variantId: {
+ type: String
+ },
+ pharmacogenomics: {
+ type: Array
+ },
+ cellbaseClient: {
+ type: Object
+ },
+ assembly: {
+ type: String
+ },
+ opencgaSession: {
+ type: Object
+ },
+ };
+ }
+
+ #init() {
+ this._prefix = UtilsNew.randomString(8);
+
+ this.pharmacogenomics = [];
+ }
+
+ firstUpdated() {
+ this.renderVariantTraitTable();
+ }
+
+ updated(changedProperties) {
+ if (changedProperties.has("variantId")) {
+ this.variantIdObserver();
+ }
+ if (changedProperties.has("pharmacogenomics")) {
+ this.renderVariantTraitTable();
+ }
+ }
+
+ variantIdObserver() {
+ if (this.cellbaseClient) {
+ if (this.variantId) {
+ this.cellbaseClient
+ .get("genomic", "variant", this.variantId, "annotation", {assembly: this.assembly || this.opencgaSession.project.organism.assembly}, {})
+ .then(restResponse => {
+ this.variantAnnotation = restResponse.getResult(0);
+ this.pharmacogenomics = this.variantAnnotation.pharmacogenomics || [];
+ });
+ }
+ }
+ }
+
+ geneFormatter(value) {
+ if (value) {
+ const genes = value
+ .filter(v => v.featureType === "gene")
+ .map(v => v.xrefs.symbol);
+ return genes?.length > 0 ? genes.join(", ") : "-";
+ }
+ return "-";
+ }
+
+ renderVariantTraitTable() {
+ if (!this.pharmacogenomics) {
+ this.pharmacogenomics = [];
+ }
+
+ $("#" + this._prefix + "Pharmacogenomics").bootstrapTable("destroy");
+ $("#" + this._prefix + "Pharmacogenomics").bootstrapTable({
+ data: this.pharmacogenomics,
+ theadClasses: "table-light",
+ buttonsClass: "light",
+ pagination: false,
+ columns: [
+ [
+ {
+ title: "ID",
+ field: "id",
+ rowspan: 2,
+ colspan: 1,
+ formatter: value => `
${value}`,
+ halign: "center"
+ },
+ {
+ title: "Name",
+ field: "name",
+ rowspan: 2,
+ colspan: 1,
+ halign: "center"
+ },
+ {
+ title: "Type",
+ field: "types",
+ rowspan: 2,
+ colspan: 1,
+ formatter: value => value.join(", "),
+ halign: "center"
+ },
+ // {
+ // title: "Source",
+ // field: "source",
+ // rowspan: 2,
+ // colspan: 1,
+ // halign: "center"
+ // },
+ {
+ title: "Annotation",
+ // field: "source",
+ rowspan: 1,
+ colspan: 8,
+ halign: "center"
+ },
+ ],
+ [
+ {
+ title: "Variant ID",
+ field: "annotations",
+ rowspan: 1,
+ colspan: 1,
+ formatter: value => value.map(v => v.variantId).join("
"),
+ halign: "center"
+ },
+ {
+ title: "PharmGKB Annotation",
+ field: "annotations",
+ rowspan: 1,
+ colspan: 1,
+ formatter: value => value.map(v => `
View`).join("
"),
+ halign: "center"
+ },
+ {
+ title: "Gene",
+ field: "annotations",
+ rowspan: 1,
+ colspan: 1,
+ formatter: value => value.map(v => v.geneNames?.join(";")).join("
"),
+ halign: "center"
+ },
+ {
+ title: "Phenotypes",
+ field: "annotations",
+ rowspan: 1,
+ colspan: 1,
+ formatter: value => value.map(v => v.phenotypes?.join(";
")).join("
"),
+ halign: "center"
+ },
+ {
+ title: "Score",
+ field: "annotations",
+ rowspan: 1,
+ colspan: 1,
+ formatter: value => value.map(v => v.score).join("
"),
+ halign: "center"
+ },
+ {
+ title: "Confidence",
+ field: "annotations",
+ rowspan: 1,
+ colspan: 1,
+ formatter: value => value.map(v => v.confidence).join("
"),
+ halign: "center"
+ },
+ {
+ title: "PubMed",
+ field: "annotations",
+ rowspan: 1,
+ colspan: 1,
+ formatter: value => value
+ .map(v => v.pubmed?.map(p => `
${p}`).join("
"))
+ .join("
"),
+ halign: "center"
+ },
+ {
+ title: "Summary",
+ field: "annotations",
+ rowspan: 1,
+ colspan: 1,
+ formatter: value => value.map(v => v.summary).join("
"),
+ halign: "center"
+ },
+ ]
+ ]
+ });
+ }
+
+ render() {
+ return html`
+
Pharmacogenomics
+
+
PharmaGKB
+
+ ${this.pharmacogenomics?.length > 0 ? html`
+
+ ` : html`
No data available
`}
+
+
+ `;
+ }
+
+}
+
+customElements.define("variant-annotation-pharmacogenomics-view", VariantAnnotationPharmacogenomicsView);
diff --git a/src/webcomponents/variant/custom/steiner-report.js b/src/webcomponents/variant/custom/steiner-report.js
index 080ec79b5a..b341941eaa 100644
--- a/src/webcomponents/variant/custom/steiner-report.js
+++ b/src/webcomponents/variant/custom/steiner-report.js
@@ -58,9 +58,9 @@ class SteinerReport extends LitElement {
#init() {
this.gridTypes = {
- snv: "variantInterpreterCancerSNV",
- cnv: "variantInterpreterCancerCNV",
- rearrangements: "variantInterpreterRearrangement",
+ snv: "variant-interpreter-cancer-snv",
+ cnv: "variant-interpreter-cancer-cnv",
+ rearrangements: "variant-interpreter-rearrangement",
};
this.callersInfo = {
@@ -99,7 +99,7 @@ class SteinerReport extends LitElement {
this.clinicalAnalysisObserver();
}
- if (changedProperties.has("config")) {
+ if (changedProperties.has("opencgaSession") || changedProperties.has("config")) {
this._config = {
...this.getDefaultConfig(),
...this.config,
@@ -299,6 +299,19 @@ class SteinerReport extends LitElement {
}
}
+ getGroupedClinicalAnalsysisStatus() {
+ const statusList = this.opencgaSession?.study?.internal?.configuration?.clinical?.interpretation?.status || [];
+ const groupedStatus = UtilsNew.groupBy(statusList, "type");
+ return Object.keys(groupedStatus)
+ .filter(type => ["ACTIVE", "DONE", "CLOSED"].includes(type))
+ .map(type => {
+ return {
+ id: type,
+ fields: groupedStatus[type],
+ };
+ });
+ }
+
onSignatureChange(event, type) {
this.selectedSignatures[type] = event.detail.value;
this._config = {
@@ -1251,7 +1264,7 @@ class SteinerReport extends LitElement {
title: "Case Status",
field: "status",
type: "select",
- allowedValues: ["CLOSED", "REJECTED"],
+ allowedValues: this.getGroupedClinicalAnalsysisStatus(),
required: true,
},
{
diff --git a/src/webcomponents/variant/family-genotype-filter.js b/src/webcomponents/variant/family-genotype-filter.js
index 6ed53e703d..408dc7908d 100644
--- a/src/webcomponents/variant/family-genotype-filter.js
+++ b/src/webcomponents/variant/family-genotype-filter.js
@@ -297,7 +297,7 @@ export default class FamilyGenotypeFilter extends LitElement {
// Return the default genotype values according the role
defaultGenotype(sample) {
- return sample.id === this.clinicalAnalysis.proband.samples[0].id ? ["0/1", "1/1", "1/2"] : [...this._config.defaultGenotypes];
+ return sample.id === this.clinicalAnalysis.proband.samples[0].id ? ["0/1", "1/1", "1", "1/2"] : [...this._config.defaultGenotypes];
}
render() {
@@ -340,12 +340,13 @@ export default class FamilyGenotypeFilter extends LitElement {
${BioinfoUtils.getIdName(this.clinicalAnalysis.disorder.id, this.clinicalAnalysis.disorder.name)}
-
Genotypes |
+
Genotypes |