update all links that refer to the repo itself

breadbox/README.md

@@ -1,6 +1,6 @@
 # Breadbox
 
-Breadbox is a persistent service for storing and retrieving data for the [DepMap portal](https://github.com/broadinstitute/depmap). It aims to simplify and consolidate formats across datasets that are uploaded by CDS during portal database re-builds, by users transiently, and by users for private groups. It consists of a persistent database to store the datasets and an API for uploading and fetching from the dataset.
+Breadbox is a persistent service for storing and retrieving data for the [DepMap portal](https://github.com/broadinstitute/depmap-portal). It aims to simplify and consolidate formats across datasets that are uploaded by CDS during portal database re-builds, by users transiently, and by users for private groups. It consists of a persistent database to store the datasets and an API for uploading and fetching from the dataset.
 
 ## Setup
 
@@ -54,7 +54,7 @@ To run tests, run
 
 ### Running Elara
 
-Elara is the UI containing tools that use and interface with the Breadbox service. To run the elara app, see instructions for setup at https://github.com/broadinstitute/depmap/tree/master/frontend/packages/elara-frontend.
+Elara is the UI containing tools that use and interface with the Breadbox service. To run the elara app, see instructions for setup at https://github.com/broadinstitute/depmap-portal/tree/master/frontend/packages/elara-frontend/README.md
 
 If trying to access Elara from the Depmap app (behind the `/breadbox` url prefix) locally, the Elara static files must exist at `depmap/breadbox/app/static/elara/` which are produced by running `yarn build` from the `elara/` directory. Additionally, the environment variable `HOST_SCHEME_OVERRIDE=http:127.0.0.1:5000` should be added to the `depmap/breadbox/.env` file. The Breadbox app must also be running first with the flag option `--use_proxy`. See instructions below for running Breadbox behind a proxy.
 

frontend/README.md

@@ -13,15 +13,15 @@ directory. If two different packages share the same dependency, only one copy
 is installed in frontend/node_modules.
 
 But you won't often need to do this because it's run for you as part of the
-[portal-backend/install_prereqs.sh](https://github.com/broadinstitute/depmap/blob/master/portal-backend/install_prereqs.sh#L16)
+[portal-backend/install_prereqs.sh](https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/portal-backend/install_prereqs.sh#L39)
 script.
 
 ## Main packages
 
 In the ./packages directory you'll find two main projects:
 
-- [elara-frontend](https://github.com/broadinstitute/depmap/tree/master/frontend/packages/elara-frontend#readme)
-- [portal-frontend](https://github.com/broadinstitute/depmap/tree/master/frontend/packages/portal-frontend#readme)
+- [elara-frontend](https://github.com/broadinstitute/depmap-portal/tree/master/frontend/packages/elara-frontend#readme)
+- [portal-frontend](https://github.com/broadinstitute/depmap-portal/tree/master/frontend/packages/portal-frontend#readme)
 
 Each of these represents a different set of UI features. The Elara frontend is
 limited to Data Explorer (the original version, also known as the "interactive
@@ -50,7 +50,7 @@ that's what you're used to. All it does is call `yarn dev:portal` for you).
 
 The two main frontends described above share a fair amount of code. The shared
 code is distributed across several libraries, scoped under the
-[@depmap](https://github.com/broadinstitute/depmap/tree/master/frontend/packages/%40depmap)
+[@depmap](https://github.com/broadinstitute/depmap-portal/tree/master/frontend/packages/%40depmap)
 directory. This is a naming convention to make them easily distinguishable from
 3rd party libraries.
 

frontend/packages/@depmap/data-explorer-2/README.md

@@ -5,7 +5,7 @@ Data Explorer 2.0 is the replacement for the original Data Explorer (a.k.a.
 original.
 
 Note that most of of the DE2 UI code is located in the
-[../../portal-frontend/src/data-explorer-2/](https://github.com/broadinstitute/depmap/tree/0fa2d2e/frontend/packages/portal-frontend/src/data-explorer-2)
+[../../portal-frontend/src/data-explorer-2/](https://github.com/broadinstitute/depmap-portal/tree/master/frontend/packages/portal-frontend/src/data-explorer-2)
 directory. That code will be migrated here over time. For now, only the
 ContextSelector is exported from this package.
 

frontend/packages/@depmap/data-explorer-2/src/utils/misc.ts

@@ -93,7 +93,7 @@ export const isPartialSliceId = (value: string | null) => {
 };
 
 // A more aggressive version of encodeURIComponent() to match this:
-// https://github.com/broadinstitute/depmap/blob/af83d4d/portal-backend/depmap/vector_catalog/models.py#L358
+// https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/portal-backend/depmap/vector_catalog/models.py#L358
 export const urlLibEncode = (s: string) => {
   return encodeURIComponent(s).replace(
     /[()*!']/g,

frontend/packages/@depmap/globals/src/globals.ts

@@ -20,35 +20,35 @@ function makeMockEnabledFeatures() {
 }
 
 // In the Portal, this is defined here:
-// https://github.com/broadinstitute/depmap/blob/c1ecacb/portal-backend/depmap/templates/nav_footer/layout.html#L88
+// https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/portal-backend/depmap/templates/nav_footer/layout.html#L88
 // In Elara, it's defined here:
-// https://github.com/broadinstitute/depmap/blob/c1ecacb/frontend/packages/elara-frontend/webpack.common.js#L34-L36
+// https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/frontend/packages/elara-frontend/webpack.common.js#L34-L36
 export const depmapContactUrl: string = (window as any).depmapContactUrl;
 
 // This is injected into the HTML by the Portal backend:
-// https://github.com/broadinstitute/depmap/blob/c1ecacb/portal-backend/depmap/templates/nav_footer/layout.html#L87
+// https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/portal-backend/depmap/templates/nav_footer/layout.html#L88
 // In Elara, it's instead "baked in" as a hardcoded feature list at build time:
-// https://github.com/broadinstitute/depmap/blob/c1ecacb/frontend/packages/elara-frontend/webpack.common.js#L29-L33
+// https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/frontend/packages/elara-frontend/webpack.common.js#L29-L33
 // If it doesn't exist on `window` then we assume we're running in a test
 // environment (like Jest or Storybook) and return a mock.
 export const enabledFeatures: Record<string, boolean> =
   (window as any).enabledFeatures || makeMockEnabledFeatures();
 
 // Currently, the `errorHandler` doesn't really do anything special outside of
 // logging to the console. In the Portal, it's defined here:
-// https://github.com/broadinstitute/depmap/blob/c1ecacb/portal-backend/depmap/templates/nav_footer/layout.html#L102
+// https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/portal-backend/depmap/templates/nav_footer/layout.html#L103
 // In Elara, it's defined here:
-// https://github.com/broadinstitute/depmap/blob/c1ecacb/frontend/packages/elara-frontend/webpack.common.js#L37
+// https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/frontend/packages/elara-frontend/webpack.common.js#L37
 export const errorHandler: {
   report: (message: string) => void;
 } = (window as any).errorHandler;
 
 // The DepMap global is created by the portal-frontend's Webpack config.
 // There is no equivalent in elara-frontend and should be avoided there.
 // This is "set" by Webpack as part of its module loader.
-// https://github.com/broadinstitute/depmap/blob/70396b2/frontend/packages/portal-frontend/webpack.common.js#L7-L13
-// All exported functions in file become its properties:
-// https://github.com/broadinstitute/depmap/blob/70396b2/frontend/packages/portal-frontend/src/index.tsx
+// https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/frontend/packages/portal-frontend/webpack.common.js#L7-L13
+// All exported functions in this file become its properties:
+// https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/frontend/packages/portal-frontend/src/index.tsx
 // eslint-disable-next-line @typescript-eslint/ban-types
 export const DepMap: Record<string, Function> =
   "Proxy" in window

portal-backend/README.md

@@ -622,9 +622,9 @@ def view_MY_APP():
 ```
 
 👉 Make sure to
-[import it here](https://github.com/broadinstitute/depmap/blob/54005fb/portal-backend/depmap/app.py#L37)
+[import it here](https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/portal-backend/depmap/app.py#L36)
 and
-[register it here](https://github.com/broadinstitute/depmap/blob/54005fb/portal-backend/depmap/app.py#L383).
+[register it here](https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/portal-backend/depmap/app.py#L382).
 
 #### Step #3: Create a new React app
 
@@ -665,7 +665,7 @@ ReactDOM.render(<App />, container);
 #### Step #4: Configure Webpack
 
 Now Webpack needs to know that your app should be considered its own bundle. To the
-[webpack config](https://github.com/broadinstitute/depmap/blob/54005fb/frontend/packages/portal-frontend/webpack.common.js#L31),
+[webpack config](https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/frontend/packages/portal-frontend/webpack.common.js#L31),
 add this line:
 
 ```js

portal-backend/depmap/data_explorer_2/views.py

@@ -422,7 +422,7 @@ def unique_values_or_range():
     # HACK: Infer if the values are lists by looking at the first member of the
     # series. If so, we assume it's a list of strings. When we rework this to
     # use BreadBox, we can take advantage of its "list_strings" AnnotationType.
-    # https://github.com/broadinstitute/depmap/blob/6f2b043/breadbox/app/models/dataset.py#L66
+    # https://github.com/broadinstitute/depmap-portal/blob/a2e2cc9/breadbox-client/breadbox_client/models/annotation_type.py#L8
     if isinstance(series[0], list):
         all_values = series.explode()
         if dataset_id == "mutation_protein_change_by_gene":

portal-backend/depmap/package.json

@@ -6,7 +6,7 @@
   "scripts": {
     "test": "jest"
   },
-  "repository": "https://github.com/broadinstitute/depmap",
+  "repository": "https://github.com/broadinstitute/depmap-portal",
   "author": "CDS Team <[email protected]>",
   "license": "MIT",
   "dependencies": {