@datagrok/helm 1.0.6 → 1.0.9

package/dockerfiles/Dockerfile

@@ -0,0 +1,13 @@
+FROM tomcat:8.0.48-jre8
+
+RUN sed -i 's/port="8080"/port="8081"/' $CATALINA_HOME/conf/server.xml
+
+WORKDIR $CATALINA_HOME/tmp
+
+ENV HELM2_WEBSERVICE_VERSION=2.2.0
+
+RUN curl -o $CATALINA_HOME/webapps/WebService.war "https://oss.sonatype.org/service/local/repositories/releases/content/org/pistoiaalliance/helm/helm2-webservice/${HELM2_WEBSERVICE_VERSION}/helm2-webservice-${HELM2_WEBSERVICE_VERSION}.war"
+
+RUN cp -r $CATALINA_HOME/tmp $CATALINA_HOME/webapps
+
+CMD ["catalina.sh", "run"]

package/package.json

@@ -2,13 +2,13 @@
   "name": "@datagrok/helm",
   "beta": false,
   "friendlyName": "Helm",
-  "version": "1.0.6",
+  "version": "1.0.9",
   "description": "",
   "dependencies": {
     "datagrok-api": "^1.4.12",
     "cash-dom": "latest",
     "dayjs": "latest",
-    "@datagrok-libraries/utils": "latest",
+    "@datagrok-libraries/utils": "^1.4.0",
     "@datagrok-libraries/bio": "^2.8.4",
     "ts-loader": "^9.2.5",
     "typescript": "^4.4.2"

package/src/package.ts

@@ -26,6 +26,11 @@ export async function initHelm(): Promise<void> {
   grid.invalidate();
 }
 
+//name: getLru
+export async function getLru() {
+  return await grok.functions.call('Bio:Lru');
+}
+
 //tags: cellEditor
 //description: Macromolecule
 //input: grid_cell cell
@@ -43,8 +48,8 @@ export function editMoleculeCell(cell: DG.GridCell): void {
     mexfilter: true
   });
   var sizes = app.calculateSizes();
-  app.canvas.resize(sizes.rightwidth, sizes.topheight - 210);
-  var s = {width: sizes.rightwidth + 'px', height: sizes.bottomheight + 'px'};
+  app.canvas.resize(sizes.rightwidth - 100, sizes.topheight - 210);
+  var s = {width: sizes.rightwidth - 100 + 'px', height: sizes.bottomheight + 'px'};
   //@ts-ignore
   scil.apply(app.sequence.style, s);
   //@ts-ignore
@@ -84,8 +89,8 @@ export function editMoleculeCell(cell: DG.GridCell): void {
 //tags: panel, widgets
 //input: string helmString {semType: Macromolecule}
 //output: widget result
-export function detailsPanel(helmString: string) {
-  //return new DG.Widget(ui.divText(lru.get(helmString)));
+export async function detailsPanel(helmString: string) {
+  const lru = await getLru();
   const result = lru.get(helmString).split(',');
   return new DG.Widget(
     ui.tableFromMap({
@@ -103,11 +108,7 @@ export function detailsPanel(helmString: string) {
 
 
 async function loadDialog() {
-  //@ts-ignore
-  let res = await grok.dapi.files.list('System:AppData/Helm/libraries', false, '');
-  //@ts-ignore
-  res = res.map((e) => e.path);
-  //@ts-ignore
+  let res = (await _package.files.list(`${LIB_PATH}`, false, '')).map(it => it.fileName);
   let FilesList = await ui.choiceInput('Monomer Libraries', ' ', res);
   let grid = grok.shell.tv.grid;
   ui.dialog('Load library from file')
@@ -128,7 +129,7 @@ export async function libraryPanel(helmColumn: DG.Column) {
   //@ts-ignore
   let loadButton = ui.button('Load Library');
   loadButton.addEventListener('click', loadDialog);
-  let list = (await grok.dapi.files.list('System:AppData/Helm/libraries', false, '')).toString().split(',');
+  let list = (await _package.files.list(`${LIB_PATH}`, false, '')).map(it => it.fileName);
   let usedLibraries = [];
   for (let j = 0; j <= i; j++) {
     usedLibraries.push(await grok.dapi.userDataStorage.getValue(STORAGE_NAME, j.toString(), true));
@@ -216,14 +217,12 @@ function getRS(smiles: string) {
 
 async function monomerManager(value: string) {
   let df: any[];
-  const libName = value.substring(value.lastIndexOf('/') + 1);
   if (value.endsWith('.sdf')) {
-    const file = await _package.files.readAsBytes(`${LIB_PATH}${libName}`);
+    const file = await _package.files.readAsBytes(`${LIB_PATH}${value}`);
     const dfSdf = await grok.functions.call('Chem:importSdf', {bytes: file});
     df = createJsonMonomerLibFromSdf(dfSdf[0]);
-
   } else {
-    const file = await _package.files.readAsText(`${LIB_PATH}${libName}`);
+    const file = await _package.files.readAsText(`${LIB_PATH}${value}`);
     df = JSON.parse(file);
   }
 

package/npmignore

@@ -1,26 +0,0 @@
-# Developer keys
-upload.keys.json
-
-# Dependency directories
-node_modules/
-
-# IDEs
-# VS Code (https://github.com/github/gitignore/blob/master/Global/VisualStudioCode.gitignore)
-.vscode/*
-!.vscode/settings.json
-!.vscode/tasks.json
-!.vscode/launch.json
-!.vscode/extensions.json
-*.code-workspace
-.history/
-
-# Intellij IDEA/WebStorm (https://github.com/github/gitignore/blob/master/Global/JetBrains.gitignore)
-.idea/inspectionProfiles/
-.idea/**/compiler.xml
-.idea/**/encodings.xml
-.idea/**/workspace.xml
-.idea/**/tasks.xml
-.idea/**/usage.statistics.xml
-.idea/**/dictionaries
-.idea/**/shelf
-.idea/codeStyles/

package/test-Helm-34f75e5127b8-7d82c3f3.html

@@ -1,251 +0,0 @@
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-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Helm Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 7d82c3f3.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-15 17:15:38</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts</div><div class="suite-time warn">14.146s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">1.721s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Helm.Helm.detectMacromolecule : Error: Expected "Macromolecule", got "null"
-Test result : Helm.Helm.detectHelm : Error: Expected "HELM", got "null"
-
-    at /home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:67:20
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:31:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Helm/src/__jest__/test-node.ts:61:11)
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/test-node.ts:28:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:40:11
-    at Generator.next (&lt;anonymous&gt;)
-    at /home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:34:71
-    at new Promise (&lt;anonymous&gt;)
-    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:30:12)
-    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:38:23)
-    at Promise.then.completed (/home/runner/work/public/public/packages/Helm/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Helm package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:65:11
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:31:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message"/></div></div></div></div></body></html>