From 4114c692dbb5163885eb0d3c6d48ca3c3eeb14e7 Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Thu, 21 Sep 2017 12:04:16 +0000
Subject: [PATCH] SSDM-4223 : Jupyter integration - reopening past notebooks +
updating correct parents to children datasets
SVN: 38743
---
.../eln-lims/html/js/config/Profile.js | 6 +-
.../eln-lims/html/js/util/JupyterUtil.js | 87 ++++++++++++++++---
.../widgets/JupyterCopyNotebookController.js | 4 +-
.../widgets/JupyterCopyNotebookView.js | 2 +-
4 files changed, 81 insertions(+), 18 deletions(-)
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
index d2a6a4ad378..60cc1dac5d7 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
@@ -124,9 +124,9 @@ $.extend(DefaultProfile.prototype, {
// jupyterhub -f jupyterhub_config.py --no-ssl
// Jupyter integration config
-// this.jupyterOpenbisEndpoint = "http://10.0.2.2:8888"; //Should not end with slash
-// this.jupyterIntegrationServerEndpoint = "https://127.0.0.1:8123";
-// this.jupyterEndpoint = "http://127.0.0.1:8000/";
+ this.jupyterOpenbisEndpoint = "http://10.0.2.2:8888"; //Should not end with slash
+ this.jupyterIntegrationServerEndpoint = "https://127.0.0.1:8123";
+ this.jupyterEndpoint = "http://127.0.0.1:8000/";
this.forcedDisableRTF = ["FREEFORM_TABLE_STATE","NAME", "SEQUENCE"];
this.forceMonospaceFont = ["SEQUENCE"];
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/JupyterUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/JupyterUtil.js
index 9734331cfc9..6b3235ec958 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/JupyterUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/JupyterUtil.js
@@ -21,19 +21,49 @@ var JupyterUtil = new function() {
jupyterNotebook.init();
}
- this.openJupyterNotebookFromTemplate = function(folder, fileName, template) {
+ this.openJupyterNotebookFromTemplate = function(folder, fileName, template, dataSetId) {
fileName = fileName + ".ipynb";
var jupyterURL = profile.jupyterIntegrationServerEndpoint + "?token=" + mainController.serverFacade.openbisServer.getSession() + "&folder=" + folder + "&filename=" + fileName;
var jupyterNotebookURL = profile.jupyterEndpoint + "user/" + mainController.serverFacade.getUserId() + "/notebooks/" + folder + "/";
$.ajax({
- url : jupyterURL,
+ url : jupyterURL + "&test=True",
type : 'POST',
crossDomain: true,
- data : template,
+ data : "TEST",
success : function(result) {
- var win = window.open(jupyterNotebookURL + result.fileName, '_blank');
- win.focus();
+ fileName = result.fileName;
+ var jupyterNotebookJson = JSON.parse(template);
+
+ var autogeneratedWithOpenBIS = false;
+ for(var cIdx = 0; cIdx < jupyterNotebookJson.cells.length; cIdx++) {
+ //If was autogenerated with openBIS
+ if(jupyterNotebookJson.cells[cIdx].source[0] === "# Mark : Autogenerated with openBIS-ELN/LIMS (System Cell, Don't delete!)") {
+ autogeneratedWithOpenBIS = true;
+ }
+ //Fix Name
+ if(autogeneratedWithOpenBIS && jupyterNotebookJson.cells[cIdx].source[0] === "# Variable - File Name (System Cell, Don't delete!)\n") {
+ jupyterNotebookJson.cells[cIdx].source[1] = "fileName='" + fileName + "'";
+ }
+ //Fix Parents
+ if(autogeneratedWithOpenBIS && jupyterNotebookJson.cells[cIdx].source[0] === "# Variable : Parents used by the automaticaly generated result dataset (System Cell, Don't delete!)\n") {
+ jupyterNotebookJson.cells[cIdx].source[1] = "resultDatasetParents=" + JSON.stringify([dataSetId]);
+ }
+ }
+
+ $.ajax({
+ url : jupyterURL + "&test=False",
+ type : 'POST',
+ crossDomain: true,
+ data : JSON.stringify(jupyterNotebookJson),
+ success : function(result) {
+ var win = window.open(jupyterNotebookURL + result.fileName, '_blank');
+ win.focus();
+ },
+ error : function(result) {
+ alert("error: " + JSON.stringify(result));
+ }
+ });
},
error : function(result) {
alert("error: " + JSON.stringify(result));
@@ -82,10 +112,43 @@ var JupyterUtil = new function() {
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Jupyter notebook autogenerated from openBIS-ELN"
+ "# Jupyter notebook title, modify me!"
]
}
content.push(mainTitle);
+ var openbisCell = {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": ["# Mark : Autogenerated with openBIS-ELN/LIMS (System Cell, Don't delete!)"]
+ };
+ content.push(openbisCell);
+ var fileNameCell = {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": ["# Variable - File Name (System Cell, Don't delete!)\n",
+ "fileName='" + fileName + "'"]
+ };
+ content.push(fileNameCell);
+ var parentsCell = {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": ["# Variable : Parents used by the automaticaly generated result dataset (System Cell, Don't delete!)\n",
+ "resultDatasetParents=" + JSON.stringify(dataSetIds)]
+ };
+ content.push(parentsCell);
+
var connectTitle = {
"cell_type": "markdown",
"metadata": {},
@@ -178,18 +241,19 @@ var JupyterUtil = new function() {
"cell_type": "markdown",
"metadata": {},
"source": [
- "### Create Result Dataset with current notebook and HTML version with the output (save the notebook first!)"
+ "### Result Dataset, it will hold the current notebook and HTML version with the output (press save before executing this!)"
]
}
content.push(saveTitle);
+
var createHTML = [
"from nbconvert import HTMLExporter\n",
"import codecs\n",
"import nbformat\n",
"exporter = HTMLExporter()\n",
- "output_notebook = nbformat.read('" + fileName + "', as_version=4)\n",
+ "output_notebook = nbformat.read(fileName, as_version=4)\n",
"output, resources = exporter.from_notebook_node(output_notebook)\n",
- "codecs.open('" + fileName + ".html', 'w', encoding='utf-8').write(output)\n",
+ "codecs.open(fileName + '.html', 'w', encoding='utf-8').write(output)\n",
"\n"
];
@@ -204,14 +268,13 @@ var JupyterUtil = new function() {
break;
}
- var parents = JSON.stringify(dataSetIds);
var createDataset = [
"ds_new = o.new_dataset(\n",
"type='ANALYZED_DATA',\n",
ownerSettings,
- "parents=" + parents + ",\n",
- "files = ['" + fileName + "', '" + fileName + ".html'],\n",
+ "parents=resultDatasetParents,\n",
+ "files = [fileName, fileName + '.html'],\n",
"props={'name': 'Name your dataset!', 'notes': 'Write some notes or delete this property!'}\n",
")\n",
"ds_new.save()"
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/JupyterCopyNotebookController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/JupyterCopyNotebookController.js
index 2b096a86d09..5895631461c 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/JupyterCopyNotebookController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/JupyterCopyNotebookController.js
@@ -22,8 +22,8 @@ function JupyterCopyNotebookController(datasetCode, existingNotebookURL) {
this._jupyterNotebookView.repaint();
}
- this.create = function(workspace, notebook, existingNotebookURL) {
- JupyterUtil.openJupyterNotebookFromTemplate(workspace, notebook, existingNotebookURL);
+ this.create = function(workspace, notebook, existingNotebookURL, datasetCode) {
+ JupyterUtil.openJupyterNotebookFromTemplate(workspace, notebook, existingNotebookURL, datasetCode);
Util.unblockUI();
}
}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/JupyterCopyNotebookView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/JupyterCopyNotebookView.js
index b55edfbc0e6..81de70bb1ce 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/JupyterCopyNotebookView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/JupyterCopyNotebookView.js
@@ -32,7 +32,7 @@ function JupyterCopyNotebookView(jupyterNotebookController, jupyterNotebookModel
var $btnAccept = $('<input>', { 'type': 'submit', 'class' : 'btn btn-primary', 'value' : 'Accept' });
$window.submit(function() {
$.get(_this._jupyterNotebookModel.existingNotebookURL, function( data ) {
- _this._jupyterNotebookController.create($workspace.val(), $notebookName.val(), data);
+ _this._jupyterNotebookController.create($workspace.val(), $notebookName.val(), data, _this._jupyterNotebookModel.datasetCode);
});
});
var $btnCancel = $('<a>', { 'class' : 'btn btn-default' }).append('Cancel');
--
GitLab