Merge branch 'master' into dependabot/npm_and_yarn/moment-2.29.4

CIMAC-CIDC · Oct 27, 2022 · 200e0b9 · 200e0b9
2 parents 0cdfcc6 + b3f4370
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,24 @@ This Changelog tracks changes to this project. The notes below include a summary
 - `fixed` for any bug fixes.
 - `security` in case of vulnerabilities.
 
+## 27 Oct 2022
+
+- `removed` analysis for ctdna
+
+## 25 Oct 2022
+
+- `added` N/A organization for users
+
+## 17 Oct 2022
+
+- `changed` Data Exploration > Code-based View, update for new templates and permissions scheme
+- `fixed` bug in pipelines docs pointing to chips instead of atacseq
+- `changed` Data Exploration links to open in new tab
+
+## 14 Sep 2022
+
+- `changed` template download button to point to /templates/assays not /templates/metadata
+
 ## 11 Aug 2022
 
 - `changed` clinical data NOT included in cross-assay permissions

diff --git a/src/components/data-exploration/code-based/CodeBasedExploration.tsx b/src/components/data-exploration/code-based/CodeBasedExploration.tsx
@@ -9,6 +9,7 @@ import {
 } from "@material-ui/core";
 import { useRootStyles } from "../../../rootStyles";
 import exampleScreenShot from "../../../img/example-colab-screenshot.png";
+import exampleUpsetPlot from "../../../img/example-colab-screenshot.upset.png";
 
 const CodeBasedExplorationPage: React.FC<{
     history: any;
@@ -55,65 +56,98 @@ const CodeBasedExplorationPage: React.FC<{
                             Some data from CIDC is available for direct querying
                             and exploration via Google's BigQuery database
                             system. We provide tables of participant- and
-                            sample-level metadata, including some clinical data.
-                            Additionally, we are working with researchers and
-                            statisticians to support some widely-used and
-                            high-impact assay data tables for direct analysis
-                            with minimal setup.
+                            sample-level metadata. Additionally, we are working
+                            with researchers and statisticians to figure out
+                            some widely-used and high-impact assay data tables
+                            for direct analysis with minimal setup.
                         </Typography>
                         <Typography>
                             These datasets are most easily accessed via python
                             notebooks hosted on Google's Colaboratory, for which
-                            we have several examples listed below. CIDC will
-                            allow data access for all approved users. Please
-                            contact CIDC at{" "}
+                            we have a few templates and examples listed below.
+                            CIDC enables data access for all approved users.
+                            Please contact CIDC at&nbsp;
                             <a href="mailto:[email protected]">
                                 [email protected]
-                            </a>{" "}
-                            for access to the data tables. The same data
-                            restrictions and security apply to all data accessed
-                            via this mechanism as via the portal.
+                            </a>
+                            &nbsp; if you have any issues accessing the data
+                            tables. The same data restrictions and security
+                            apply to all data accessed via this mechanism as via
+                            the portal.
                         </Typography>
                     </CardContent>
                 </Card>
             </Grid>
             <Grid item>
                 <Card style={{ maxWidth: 1100, width: 1100 }}>
-                    <CardHeader title="Examples" />
+                    <CardHeader title="Templates and Examples" />
                     <CardContent className="markdown-body">
                         <ul>
                             {[
                                 {
-                                    name: "Introductory Tutorial",
-                                    destination: null
-                                },
-                                {
-                                    name: "Participant and sample exploration",
+                                    name:
+                                        "Template: Upset Plot by Trial and/or Assay",
                                     destination:
-                                        "https://colab.research.google.com/drive/1VXVLpLE9_D7fW5cZP4j2jyTOA4q42sJk#scrollTo=R_PNmBI99t4G"
+                                        "https://colab.research.google.com/drive/14xys5GrZ7OzCC5eUYMrexM9Imq4szw7o",
+                                    description:
+                                        "a template meant for copying and modification by the user to generate their own upset plots " +
+                                        "showing the number of participants with a given subset of assays across a given subset of trials"
                                 },
                                 {
                                     name:
-                                        "Analysis of WES variants for 10021 from filtered .maf files",
+                                        "Template: Upset Plot for Collection Events on a Single Trial",
                                     destination:
-                                        "https://colab.research.google.com/drive/11BfQsD5QgShJCGWjpnhhq6OPtUVwiPgN"
+                                        "https://colab.research.google.com/drive/1kheXUtozN6dcxdrf_U_WtnXUiDBhEMt2",
+                                    description:
+                                        "a template meant for copying and modification by the user to generate their own upset plots " +
+                                        "showing the number of participants with a given subset of collection events across a single trial"
                                 },
                                 {
                                     name:
-                                        "Analysis of RNAseq with sample metadata for 10021 from quant.sf",
+                                        "Example: Participant and Sample Exploration",
                                     destination:
-                                        "https://colab.research.google.com/drive/1mdm4ONM0BwoBCbyGk0N2DVFEDN8Ob9Iw"
+                                        "https://colab.research.google.com/drive/1VXVLpLE9_D7fW5cZP4j2jyTOA4q42sJk",
+                                    description:
+                                        "a demonstration of more complex code-based filtering and exploration of samples and participants"
                                 }
                             ].map(item =>
                                 item.destination == null ? (
+                                    item.description == null ? (
+                                        <li key={item.name}>
+                                            <b>
+                                                {item.name} (under construction)
+                                            </b>
+                                        </li>
+                                    ) : (
+                                        <li key={item.name}>
+                                            <b>
+                                                {item.name} (under construction)
+                                            </b>{" "}
+                                            - {item.description}
+                                        </li>
+                                    )
+                                ) : item.description == null ? (
                                     <li key={item.name}>
-                                        {item.name} (under construction)
+                                        <a
+                                            href={item.destination}
+                                            target="_blank"
+                                            rel="noopener noreferrer"
+                                        >
+                                            {item.name}
+                                        </a>
                                     </li>
                                 ) : (
                                     <li key={item.name}>
-                                        <a href={item.destination}>
-                                            {item.name}
-                                        </a>
+                                        <b>
+                                            <a
+                                                href={item.destination}
+                                                target="_blank"
+                                                rel="noopener noreferrer"
+                                            >
+                                                {item.name}
+                                            </a>
+                                        </b>{" "}
+                                        - {item.description}
                                     </li>
                                 )
                             )}
@@ -128,7 +162,13 @@ const CodeBasedExplorationPage: React.FC<{
                         <img
                             src={exampleScreenShot}
                             alt={
-                                "Screenshot of a Kaplan-Meier curve for trial 10021. One subplot per cohort, one line per trial arm."
+                                "Screenshot of Google Colaboratory interface for Upset Plot Template, showing the top of Section 3. Parameters where you can choose trials to include in the plot."
+                            }
+                        ></img>
+                        <img
+                            src={exampleUpsetPlot}
+                            alt={
+                                "Upset plot as generated in Google Colaboratory using the Upset Plot Template."
                             }
                         ></img>
                     </CardContent>

diff --git a/src/components/data-exploration/interactive/InteractiveExploration.tsx b/src/components/data-exploration/interactive/InteractiveExploration.tsx
@@ -132,7 +132,11 @@ const InteractiveExplorationPage: React.FC<{
                                     }
                                 ].map(item => (
                                     <li>
-                                        <a href={item.destination}>
+                                        <a
+                                            href={item.destination}
+                                            target="_blank"
+                                            rel="noopener noreferrer"
+                                        >
                                             {item.name}
                                         </a>
                                     </li>

diff --git a/src/components/data-overview/DataOverviewPage.tsx b/src/components/data-overview/DataOverviewPage.tsx
@@ -38,7 +38,6 @@ const NONASSAY_FIELDS = [
 
 const ASSAYS_WITH_ANALYSIS = [
     "atacseq",
-    "ctdna",
     "cytof",
     "rna",
     "tcr",

diff --git a/src/components/generic/TemplateDownloadButton.tsx b/src/components/generic/TemplateDownloadButton.tsx
@@ -9,9 +9,7 @@ export function nameToURL(
     name: string
 ) {
     const fmtedName = name.toLowerCase().replace(" ", "_");
-    // Assay templates have type "metadata" on the server
-    const fixedType = type === "assays" ? "metadata" : type;
-    return `${process.env.REACT_APP_API_URL}/info/templates/${fixedType}/${fmtedName}`;
+    return `${process.env.REACT_APP_API_URL}/info/templates/${type}/${fmtedName}`;
 }
 
 export interface ITemplateDownloadButtonProps extends ButtonProps {

diff --git a/src/components/identity/Register.tsx b/src/components/identity/Register.tsx
@@ -178,6 +178,9 @@ const Register: React.FC<RouteComponentProps> = ({ history }) => {
                                     <MenuItem value="ANDERSON">
                                         {ORGANIZATION_NAME_MAP.ANDERSON}
                                     </MenuItem>
+                                    <MenuItem value="N/A">
+                                        {ORGANIZATION_NAME_MAP["N/A"]}
+                                    </MenuItem>
                                 </Select>
                             </FormControl>
                         </Grid>

diff --git a/src/components/identity/UserProvider.test.tsx b/src/components/identity/UserProvider.test.tsx
@@ -112,7 +112,7 @@ describe("download access", () => {
 
             expect(
                 await findByText(
-                    role === "network-viewer"
+                    ["network-viewer", "pact-user"].includes(role)
                         ? /cannot download/i
                         : /can download/i
                 )
@@ -140,6 +140,7 @@ describe("role-based tab display", () => {
 
     const expectedTabs = [
         { role: "cimac-user", tabs: [] },
+        { role: "pact-user", tabs: [] },
         { role: "network-viewer", tabs: [] },
         { role: "cimac-biofx-user", tabs: ["transfer data"] },
         { role: "cidc-biofx-user", tabs: ["transfer data", "analyses"] },

diff --git a/src/components/identity/UserProvider.tsx b/src/components/identity/UserProvider.tsx
@@ -82,7 +82,8 @@ const UserProvider: React.FunctionComponent<RouteComponentProps> = props => {
         user?.role && ["nci-biobank-user", "cidc-admin"].includes(user.role);
     const showAnalyses =
         user?.role && ["cidc-biofx-user", "cidc-admin"].includes(user.role);
-    const canDownload = user?.role !== "network-viewer";
+    const canDownload =
+        user?.role && !["network-viewer", "pact-user"].includes(user.role);
 
     const value =
         authData.state === "logged-in" && user && permissions

diff --git a/src/components/pipelines/PipelinesPage.tsx b/src/components/pipelines/PipelinesPage.tsx
@@ -38,10 +38,10 @@ const pipelineMarkdowns = {
             />
         </div>
     ),
-    chips: (
-        <div role="document" id="chips-docs">
+    atacseq: (
+        <div role="document" id="atacseq-docs">
             <CIDCGithubMarkdown
-                path={`cidc-ngs-pipeline-api/master/cidc_ngs_pipeline_api/chips/chips.md`}
+                path={`cidc-ngs-pipeline-api/master/cidc_ngs_pipeline_api/atacseq/atacseq.md`}
             />
         </div>
     )
@@ -75,18 +75,18 @@ const PipelinesPage: React.FC<RouteComponentProps> = props => {
                                 path={`/pipelines/rna`}
                             />
                             <DocsListItem
-                                label={"WES (Whole Exome Sequencing"}
+                                label={"WES (Whole Exome Sequencing) Analysis"}
                                 path={`/pipelines/wes`}
                             />
                             <DocsListItem
                                 label={
-                                    "TCR (T-cell Receptor Repertoire Analysis)"
+                                    "TCR (T-cell Receptor) Repertoire Analysis"
                                 }
                                 path={`/pipelines/tcr`}
                             />
                             <DocsListItem
-                                label={"CHIPS ATAC-seq Analysis"}
-                                path={`/pipelines/chips`}
+                                label={"ATAC-seq Analysis"}
+                                path={`/pipelines/atacseq`}
                             />
                         </List>
                     </Grid>

diff --git a/src/img/example-colab-screenshot.png b/src/img/example-colab-screenshot.png
diff --git a/src/img/example-colab-screenshot.upset.png b/src/img/example-colab-screenshot.upset.png
diff --git a/src/model/account.ts b/src/model/account.ts
@@ -8,7 +8,8 @@ type Role =
     | "devops"
     | "nci-biobank-user"
     | "system"
-    | "network-viewer";
+    | "network-viewer"
+    | "pact-user";
 
 type Organization = "CIDC" | "DFCI" | "ICAHN" | "STANFORD" | "ANDERSON";
 

diff --git a/src/util/constants.ts b/src/util/constants.ts
@@ -3,7 +3,8 @@ export const ORGANIZATION_NAME_MAP = {
     CIDC: "Dana-Farber Cancer Institute (CIDC)",
     ICAHN: "Icahn School of Medicine at Mount Sinai (CIMAC)",
     STANFORD: "Stanford Cancer Institute (CIMAC)",
-    ANDERSON: "MD Anderson Cancer Center (CIMAC)"
+    ANDERSON: "MD Anderson Cancer Center (CIMAC)",
+    "N/A": "Not Applicable"
 };
 
 export const ROLES = [
@@ -14,7 +15,8 @@ export const ROLES = [
     "developer",
     "devops",
     "nci-biobank-user",
-    "network-viewer"
+    "network-viewer",
+    "pact-user"
 ];
 
 export const DATE_OPTIONS = {