4.0.0 (#80)

Fix #48, Fix #35 Fix #29 , * Fix account page Updated the react on the account page to parse the new user object correctly. Changes to be committed: modified: views/account/AccountView/Permissions.js modified: views/account/AccountView/ServerInfo.js * 1st fix for account page Account page will now load. it is still not functional for account details or groups and permissions Changes to be committed: modified: views/account/AccountView/AddServer.js modified: views/account/AccountView/Permissions.js modified: views/account/AccountView/Profile.js modified: views/account/AccountView/ServerInfo.js * Commit before re-factoring the object listing page. * Some more fixes. * update (#46) * Add versioning to bottom bar App.js now has a version object to indicate the version for each of the repositories associated with BCO portal and db Changes to be committed: modified: App.js deleted: layouts/DashboardLayout/index.js deleted: layouts/ObjectViewLayout/BottomBar.js modified: layouts/shared/BottomBar.js modified: routes.js * fix bad url Changes to be committed: modified: layouts/shared/BottomBar.js * Initialize 4.0.0 On branch 4.0.0 Changes to be committed: modified: src/App.js * Prefix int (#57) * bottom bar (#49) * Add versioning to bottom bar App.js now has a version object to indicate the version for each of the repositories associated with BCO portal and db Changes to be committed: modified: App.js deleted: layouts/DashboardLayout/index.js deleted: layouts/ObjectViewLayout/BottomBar.js modified: layouts/shared/BottomBar.js modified: routes.js * fix bad url Changes to be committed: modified: layouts/shared/BottomBar.js * Fix Published object page Changes to be committed: modified: .env.example modified: src/layouts/shared/BottomBar.js modified: src/views/builder/BuilderView/Tools/ServerList.js modified: src/views/builder/BuilderView/index.js modified: src/views/objects/ObjectView/Views.js * Object View page Changes to be committed: modified: src/App.js new file: src/components/API/ModifyDraftObject.js new file: src/components/API/RetrieveDraftObject.js new file: src/components/API/RetrieveDraftObjectPermissions.js new file: src/components/API/RetrieveObjectsFromToken.js new file: src/components/API/untitled.txt renamed: src/views/objects/ObjectsListView/Linker.js -> src/components/Linker.js renamed: src/views/objects/ObjectsListView/Toolbar.js -> src/components/ObjectsListViewToolbar.js new file: src/components/PermissionTools.js modified: src/routes.js new file: src/utils/AddCondition.js new file: src/utils/Groups.js new file: src/utils/LogicField.js new file: src/utils/PublishDialog.js new file: src/utils/RegexBox.js new file: src/utils/SearchField.js new file: src/utils/ServerList.js new file: src/utils/Sharing.js modified: src/views/builder/BuilderView/Tools.js modified: src/views/builder/BuilderView/index.js deleted: src/views/objects/ObjectView/ProductCard.js modified: src/views/objects/ObjectsListView/Results.js modified: src/views/objects/ObjectsListView/index.js new file: src/views/permissions/PermissionView/index.js * Update to API calls for User accounts Separate API components created for new accounts, login, and profile. Changes to be committed: new file: src/components/API/ApiNewAccount.js new file: src/components/API/TokenAuthentication.js new file: src/components/API/UserdbNewAccount.js new file: src/components/API/UserdbTokenAuth.js modified: src/components/PermissionTools.js modified: src/views/account/AccountView/AccountDetails.js modified: src/views/account/AccountView/ProfileDetails.js modified: src/views/account/AccountView/index.js modified: src/views/auth/LoginView.js modified: src/views/auth/RegisterView.js * Account updates Changes to be committed: modified: package.json modified: src/App.js new file: src/components/API/CreateDraftObject.js modified: src/components/API/RetrieveObjectsFromToken.js modified: src/components/API/UserdbNewAccount.js new file: src/components/API/UserdbUpdateAccount.js modified: src/components/Linker.js modified: src/components/PermissionTools.js modified: src/views/account/AccountView/AccountDetails.js modified: src/views/account/AccountView/Profile.js deleted: src/views/account/AccountView/ProfileDetails.js modified: src/views/account/AccountView/index.js modified: src/views/auth/RegisterView.js modified: src/views/builder/BuilderView/ColorCoded/DescriptionDomain.js modified: src/views/builder/BuilderView/ColorCoded/ProvenanceDomain.js new file: src/views/builder/BuilderView/Raw/RawOld/index.js renamed: src/views/builder/BuilderView/Raw/json2.js -> src/views/builder/BuilderView/Raw/RawOld/json2.js renamed: src/views/builder/BuilderView/Raw/jsonlint.js -> src/views/builder/BuilderView/Raw/RawOld/jsonlint.js modified: src/views/builder/BuilderView/Raw/index.js new file: src/views/builder/BuilderView/SaveDraft.js modified: src/views/builder/BuilderView/Tools/Sharing.js modified: src/views/builder/BuilderView/Views.js new file: src/views/builder/BuilderView/index copy.js modified: src/views/builder/BuilderView/index.js modified: src/views/objects/ObjectsListView/index.js * Updates to Provenance Domain Fixed Reviewer fields Added local storage on changes Changes to be committed: modified: package.json modified: src/App.js modified: src/views/builder/BuilderView/ColorCoded/DescriptionDomain.js modified: src/views/builder/BuilderView/ColorCoded/ProvenanceDomain.js modified: src/views/builder/BuilderView/ColorCoded/index.js modified: src/views/builder/BuilderView/index.js modified: src/views/objects/ObjectView/ColorCoded/index.js modified: src/views/objects/ObjectsListView/index.js * Prefix int (#58) * bottom bar (#49) * Add versioning to bottom bar App.js now has a version object to indicate the version for each of the repositories associated with BCO portal and db Changes to be committed: modified: App.js deleted: layouts/DashboardLayout/index.js deleted: layouts/ObjectViewLayout/BottomBar.js modified: layouts/shared/BottomBar.js modified: routes.js * fix bad url Changes to be committed: modified: layouts/shared/BottomBar.js * Fix Published object page Changes to be committed: modified: .env.example modified: src/layouts/shared/BottomBar.js modified: src/views/builder/BuilderView/Tools/ServerList.js modified: src/views/builder/BuilderView/index.js modified: src/views/objects/ObjectView/Views.js * Object View page Changes to be committed: modified: src/App.js new file: src/components/API/ModifyDraftObject.js new file: src/components/API/RetrieveDraftObject.js new file: src/components/API/RetrieveDraftObjectPermissions.js new file: src/components/API/RetrieveObjectsFromToken.js new file: src/components/API/untitled.txt renamed: src/views/objects/ObjectsListView/Linker.js -> src/components/Linker.js renamed: src/views/objects/ObjectsListView/Toolbar.js -> src/components/ObjectsListViewToolbar.js new file: src/components/PermissionTools.js modified: src/routes.js new file: src/utils/AddCondition.js new file: src/utils/Groups.js new file: src/utils/LogicField.js new file: src/utils/PublishDialog.js new file: src/utils/RegexBox.js new file: src/utils/SearchField.js new file: src/utils/ServerList.js new file: src/utils/Sharing.js modified: src/views/builder/BuilderView/Tools.js modified: src/views/builder/BuilderView/index.js deleted: src/views/objects/ObjectView/ProductCard.js modified: src/views/objects/ObjectsListView/Results.js modified: src/views/objects/ObjectsListView/index.js new file: src/views/permissions/PermissionView/index.js * Update to API calls for User accounts Separate API components created for new accounts, login, and profile. Changes to be committed: new file: src/components/API/ApiNewAccount.js new file: src/components/API/TokenAuthentication.js new file: src/components/API/UserdbNewAccount.js new file: src/components/API/UserdbTokenAuth.js modified: src/components/PermissionTools.js modified: src/views/account/AccountView/AccountDetails.js modified: src/views/account/AccountView/ProfileDetails.js modified: src/views/account/AccountView/index.js modified: src/views/auth/LoginView.js modified: src/views/auth/RegisterView.js * Account updates Changes to be committed: modified: package.json modified: src/App.js new file: src/components/API/CreateDraftObject.js modified: src/components/API/RetrieveObjectsFromToken.js modified: src/components/API/UserdbNewAccount.js new file: src/components/API/UserdbUpdateAccount.js modified: src/components/Linker.js modified: src/components/PermissionTools.js modified: src/views/account/AccountView/AccountDetails.js modified: src/views/account/AccountView/Profile.js deleted: src/views/account/AccountView/ProfileDetails.js modified: src/views/account/AccountView/index.js modified: src/views/auth/RegisterView.js modified: src/views/builder/BuilderView/ColorCoded/DescriptionDomain.js modified: src/views/builder/BuilderView/ColorCoded/ProvenanceDomain.js new file: src/views/builder/BuilderView/Raw/RawOld/index.js renamed: src/views/builder/BuilderView/Raw/json2.js -> src/views/builder/BuilderView/Raw/RawOld/json2.js renamed: src/views/builder/BuilderView/Raw/jsonlint.js -> src/views/builder/BuilderView/Raw/RawOld/jsonlint.js modified: src/views/builder/BuilderView/Raw/index.js new file: src/views/builder/BuilderView/SaveDraft.js modified: src/views/builder/BuilderView/Tools/Sharing.js modified: src/views/builder/BuilderView/Views.js new file: src/views/builder/BuilderView/index copy.js modified: src/views/builder/BuilderView/index.js modified: src/views/objects/ObjectsListView/index.js * Updates to Provenance Domain Fixed Reviewer fields Added local storage on changes Changes to be committed: modified: package.json modified: src/App.js modified: src/views/builder/BuilderView/ColorCoded/DescriptionDomain.js modified: src/views/builder/BuilderView/ColorCoded/ProvenanceDomain.js modified: src/views/builder/BuilderView/ColorCoded/index.js modified: src/views/builder/BuilderView/index.js modified: src/views/objects/ObjectView/ColorCoded/index.js modified: src/views/objects/ObjectsListView/index.js * Docs Changes to be committed: new file: docs/App.js.html new file: docs/FetchContext.html new file: docs/fonts/OpenSans-Bold-webfont.eot new file: docs/fonts/OpenSans-Bold-webfont.svg new file: docs/fonts/OpenSans-Bold-webfont.woff new file: docs/fonts/OpenSans-BoldItalic-webfont.eot new file: docs/fonts/OpenSans-BoldItalic-webfont.svg new file: docs/fonts/OpenSans-BoldItalic-webfont.woff new file: docs/fonts/OpenSans-Italic-webfont.eot new file: docs/fonts/OpenSans-Italic-webfont.svg new file: docs/fonts/OpenSans-Italic-webfont.woff new file: docs/fonts/OpenSans-Light-webfont.eot new file: docs/fonts/OpenSans-Light-webfont.svg new file: docs/fonts/OpenSans-Light-webfont.woff new file: docs/fonts/OpenSans-LightItalic-webfont.eot new file: docs/fonts/OpenSans-LightItalic-webfont.svg new file: docs/fonts/OpenSans-LightItalic-webfont.woff new file: docs/fonts/OpenSans-Regular-webfont.eot new file: docs/fonts/OpenSans-Regular-webfont.svg new file: docs/fonts/OpenSans-Regular-webfont.woff new file: docs/global.html new file: docs/index.html new file: docs/scripts/linenumber.js new file: docs/scripts/prettify/Apache-License-2.0.txt new file: docs/scripts/prettify/lang-css.js new file: docs/scripts/prettify/prettify.js new file: docs/styles/jsdoc-default.css new file: docs/styles/prettify-jsdoc.css new file: docs/styles/prettify-tomorrow.css new file: jsdoc.conf.json modified: src/App.js modified: src/views/builder/BuilderView/ColorCoded/index.js * Fix issue with public state (#72) * fix issue with public state * Return proper message when retrieving token and failed. * Cleanup * Make biocompute ojbect servers update on close of window to add server. * Clean the hostname, email, server info, token on closing of the add server popover. Write out failed message to log; update timeout to be a little quicker. * Set success or error handle properly. * Cleanup of result parsing, update state variable properly for changing information. Add new API Account call for requesting a Token. * Support for deleting API servers. * Remove erroneous todo Co-authored-by: John Torcivia <[email protected]> Co-authored-by: John Torcivia <[email protected]> Co-authored-by: John Torcivia <[email protected]> * Added UI fixes from 3.96.3 to 4.0.0 Changes to be committed: modified: src/views/account/AccountView/ServerInfo.js modified: src/views/builder/BuilderView/ColorCoded/DescriptionDomain.js modified: src/views/builder/BuilderView/ColorCoded/ProvenanceDomain.js modified: src/views/builder/BuilderView/ColorCoded/index.js modified: src/views/builder/BuilderView/index.js renamed: src/views/builder/BuilderView/index copy.js -> src/views/builder/BuilderView/index_bk.js modified: src/views/objects/ObjectView/ColorCoded/DescriptionDomain.js modified: src/views/objects/ObjectView/ColorCoded/ProvenanceDomain.js modified: src/views/objects/ObjectsListView/index.js * added dockerfile to cover build of web server in a container * readme with some basic build instructions for docker * Small tweaks to dockerfile * support multiple different servers to return biocompute objects from * Fix Add server button Changes to be committed: modified: src/views/account/AccountView/AddServer.js Co-authored-by: Chris Armstrong <[email protected]> Co-authored-by: John Torcivia <[email protected]> Co-authored-by: John Torcivia <[email protected]>
biocompute-objects · Nov 11, 2021 · 28bd043 · 28bd043
1 parent 73bd869
commit 28bd043
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diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,20 @@
+FROM ubuntu:21.04
+LABEL org.opencontainers.image.source https://github.com/biocompute-objects/portal
+ENV DEBIAN_FRONTEND=noninteractive
+
+EXPOSE 3000
+
+RUN apt-get update && apt-get install -y nodejs npm vim
+
+WORKDIR /portal
+
+COPY src ./src
+COPY package.json .
+COPY jsconfig.json .
+COPY public public
+COPY docs docs
+
+RUN npm install --quiet --legacy-peer-deps
+#RUN npm audit fix --legacy-peer-deps
+
+CMD ["npm", "run", "start"]
diff --git a/README.md b/README.md
@@ -27,3 +27,20 @@ The git folder (application) that contains all of the user information for the p
 
 1. python3 manage.py runserver 8000
 
+## Containerization
+
+The web portal can be containerized for easier development and deployment.
+
+### Building in a container with docker
+
+You can build the container by running the build command:
+
+`docker build -t bco_portal .`
+
+### Running the container with docker
+
+You can run the container via docker through the following command:
+
+`docker run --network host --rm -t bco_portal`
+
+This will set the portal to be available at `localhost:3000` on the host machine.
diff --git a/src/views/account/AccountView/ServerInfo.js b/src/views/account/AccountView/ServerInfo.js
@@ -212,7 +212,7 @@ const EnhancedTableToolbar = (props) => {
           // This will allow the background to update with
           // the updated server list.
           setServerAdded(true);
-
+          // setSelected(false);
         } else {
           // Display whatever the server said.
           console.log('Failed to remove the API server because: ', result.data.detail);

diff --git a/src/views/objects/ObjectsListView/Results.js b/src/views/objects/ObjectsListView/Results.js
@@ -370,5 +370,5 @@ export default function Results({ rowInfo }) {
 }
 
 Results.propTypes = {
-  rowInfo: PropTypes.object.isRequired,
+  rowInfo: PropTypes.array.isRequired,
 };
diff --git a/src/views/objects/ObjectsListView/index.js b/src/views/objects/ObjectsListView/index.js
@@ -57,10 +57,24 @@ const ObjectsListView = () => {
   // Row data
   const rowData = [];
 
+  const getObjs = function getObjects(item) {
+    return fetch(`${item.public_hostname}/api/objects/token/`, {
+      method: 'POST',
+      body: JSON.stringify({
+        POST_api_objects_token: {}
+      }),
+      headers: {
+        Authorization: `Token ${item.token}`,
+        'Content-type': 'application/json; charset=UTF-8'
+      }
+    }).then((response) => {
+      return [item.public_hostname, response.json()];
+    });
+  };
+
   const getObjectsListing = () => {
     // First get the API info.
     let ApiInfo = JSON.parse(localStorage.getItem('user'));
-
     // If there is no user info stored, assume we're the anonymous user.
     if (ApiInfo === null) {
       // Use the anon token, which is publicly available.
@@ -69,51 +83,47 @@ const ObjectsListView = () => {
       // There was a user.
       ApiInfo = ApiInfo.apiinfo;
     }
-
-    console.log('ApiInfo', ApiInfo);
-
+    // console.log(ApiInfo);
     // Get the info for each API.
-    ApiInfo.forEach((item) => {
-      // Call the API using the server information
-      // associated with the user.
-      fetch(`${item.public_hostname}/api/objects/token/`, {
-        method: 'POST',
-        body: JSON.stringify({
-          POST_api_objects_token: {}
-        }),
-        headers: {
-          Authorization: `Token ${item.token}`,
-          'Content-type': 'application/json; charset=UTF-8'
+    const results = Promise.all(ApiInfo.map(getObjs));
+    results.then((data) => {
+      console.log('Output ', data);
+      // data.forEach((d) => {
+      const promises = data.map((apiAndPromise) => {
+        // The provenance domain name may not be defined.
+        if (apiAndPromise.length !== 2) {
+          console.log("ERROR: This shouldn't ever be hit.");
         }
-      }).then((response) => response.json()).then((data) => {
-        console.log('data: ',item.public_hostname,  data);
-
-        data.map((d_item) => {
-          // The provenance domain name may not be defined.
-          try {
-            d_item.name = d_item.contents.provenance_domain.name;
-          } catch (TypeError) {
-            d_item.name = 'N/A';
-          }
-
-          rowData.push(
-            createData(
-              d_item.name,
-              item.public_hostname,
-              d_item.contents,
-              d_item.last_update,
-              d_item.object_class,
-              d_item.object_id,
-              d_item.owner_group,
-              d_item.owner_user,
-              d_item.prefix,
-              d_item.schema,
-              d_item.state,
-            )
-          );
+        const apiServer = apiAndPromise[0];
+        return apiAndPromise[1].then((dItems) => {
+          dItems.forEach((dItem) => {
+            try {
+              dItem.name = dItem.contents.provenance_domain.name;
+            } catch (TypeError) {
+              dItem.name = 'N/A';
+            }
+
+            rowData.push(
+              createData(
+                dItem.name,
+                apiServer,
+                dItem.contents,
+                dItem.last_update,
+                dItem.object_class,
+                dItem.object_id,
+                dItem.owner_group,
+                dItem.owner_user,
+                dItem.prefix,
+                dItem.schema,
+                dItem.state,
+              )
+            );
+          });
         });
-
-        // We're no longer loading.
+      });
+      // We should have all of the promises for the various servers now
+      // wait for them all to finish and then populate the table.
+      Promise.all(promises).then((r) => {
         setRows(rowData);
         setLoading(false);
       });