From 47be72e969344a494b01b759575d390275d911dc Mon Sep 17 00:00:00 2001
From: Mariia Pukhliakova <mariia.pukhliakova@id.ethz.ch>
Date: Mon, 10 Feb 2020 13:05:43 +0100
Subject: [PATCH] SSDM-9301 Move BBB-HUB in ELN
---
.../1/as/webapps/eln-lims/html/etc/config.js | 2 +-
.../html/plugins/bbb-hub/BBBServerFacade.js | 142 +++++++++++++++
.../html/plugins/bbb-hub/UiComponents.js | 104 +++++++++++
.../eln-lims/html/plugins/bbb-hub/plugin.js | 37 ++++
.../html/plugins/bbb-hub/snakemake-table.js | 169 ++++++++++++++++++
.../html/plugins/bbb-hub/snakemake-trigger.js | 161 +++++++++++++++++
6 files changed, 614 insertions(+), 1 deletion(-)
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/BBBServerFacade.js
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/UiComponents.js
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/plugin.js
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-table.js
create mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-trigger.js
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/etc/config.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/etc/config.js
index 589cda418e5..549b910bf1c 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/etc/config.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/etc/config.js
@@ -30,7 +30,7 @@ loadJSResorce("./etc/InstanceProfile.js", onLoadInstanceProfileResorceFunc);
//</PROFILE_PLACEHOLDER>
var PLUGINS_CONFIGURATION = {
- extraPlugins : ["life-sciences", "flow", "microscopy"]
+ extraPlugins : ["life-sciences", "flow", "microscopy", "bbb-hub"]
};
var options = {
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/BBBServerFacade.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/BBBServerFacade.js
new file mode 100644
index 00000000000..32c4989cf99
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/BBBServerFacade.js
@@ -0,0 +1,142 @@
+var BBBServerFacade = new function() {
+ this.getExperiment = function($container, model) {
+ require(["openbis",
+ "as/dto/sample/fetchoptions/SampleFetchOptions",
+ "as/dto/experiment/fetchoptions/ExperimentFetchOptions",
+ "as/dto/experiment/id/ExperimentIdentifier",
+ "as/dto/dataset/fetchoptions/DataSetFetchOptions"],
+ function(openbis, SampleFetchOptions,
+ ExperimentFetchOptions,
+ ExperimentIdentifier,
+ DataSetFetchOptions) {
+
+ var v3 = new openbis(null);
+ v3._private.sessionToken = mainController.openbisV1._internal.sessionToken;
+
+ var webAppContext = v3.getWebAppContext();
+
+ var dataSetFetchOptions = new DataSetFetchOptions();
+ dataSetFetchOptions.withType();
+ dataSetFetchOptions.withPhysicalData();
+
+ var experimentId = new ExperimentIdentifier(model.experiment.identifier);
+ var fetchOptions = new ExperimentFetchOptions();
+ fetchOptions.withDataSetsUsing(dataSetFetchOptions);
+ fetchOptions.withType();
+
+ var sampleFetchOptions = new SampleFetchOptions();
+ sampleFetchOptions.withType().withPropertyAssignments().withPropertyType();
+ sampleFetchOptions.withProperties();
+ fetchOptions.withSamplesUsing(sampleFetchOptions);
+ v3.getExperiments([experimentId], fetchOptions).done(function(result) {
+ var experiment = result[model.experiment.identifier];
+ if (experiment.type.code == "BBB") {
+ SnakemakeTrigger.paintTriggerContainers($container, model, experiment);
+ }
+ });
+ });
+ }
+
+ this.getExperiments = function($content) {
+ require(["openbis", "as/dto/sample/fetchoptions/SampleFetchOptions",
+ "as/dto/experiment/fetchoptions/ExperimentFetchOptions",
+ "as/dto/experiment/id/ExperimentIdentifier",
+ "as/dto/dataset/fetchoptions/DataSetFetchOptions",
+ "as/dto/experiment/search/ExperimentSearchCriteria",
+ "as/dto/project/fetchoptions/ProjectFetchOptions"],
+ function(openbis, SampleFetchOptions,
+ ExperimentFetchOptions,
+ ExperimentIdentifier,
+ DataSetFetchOptions,
+ ExperimentSearchCriteria,
+ ProjectFetchOptions) {
+
+ var v3 = new openbis();
+
+ v3.loginAsAnonymousUser().done(function(sessionToken) {
+ v3._private.sessionToken = sessionToken;
+ var webAppContext = v3.getWebAppContext();
+
+ var fetchOptions = new ExperimentFetchOptions();
+ fetchOptions.withType();
+ fetchOptions.withProperties();
+ fetchOptions.withRegistrator();
+
+ var projectFetchOptions = new ProjectFetchOptions();
+ projectFetchOptions.withSpace();
+
+ fetchOptions.withProjectUsing(projectFetchOptions);
+
+ var searchCriteria = new ExperimentSearchCriteria();
+ searchCriteria.withType();
+
+ v3.searchExperiments(searchCriteria, fetchOptions).done(function(result) {
+ BBBServerFacade.getRoleAssignment($content, result.objects);
+ });
+ }).fail(function(result) {
+ console.log("Call failed to server: " + JSON.stringify(result));
+ });
+ });
+ }
+
+ this.getRoleAssignment = function ($content, experiments) {
+ require(["openbis", "as/dto/roleassignment/fetchoptions/RoleAssignmentFetchOptions",
+ "as/dto/roleassignment/search/RoleAssignmentSearchCriteria"],
+ function(openbis, RoleAssignmentFetchOptions, RoleAssignmentSearchCriteria) {
+
+ var v3 = new openbis();
+
+ v3.loginAsAnonymousUser().done(function(sessionToken) {
+ v3._private.sessionToken = sessionToken;
+ var webAppContext = v3.getWebAppContext();
+
+ var criteria = new RoleAssignmentSearchCriteria();
+ criteria.withOrOperator();
+ criteria.withProject();
+ criteria.withSpace();
+
+ var fetchOptions = new RoleAssignmentFetchOptions();
+ fetchOptions.withSpace();
+ fetchOptions.withProject();
+ fetchOptions.withUser();
+ fetchOptions.withAuthorizationGroup();
+
+ v3.searchRoleAssignments(criteria, fetchOptions).done(function(result) {
+ SnakemakeTable.paintTable($content, experiments, result.objects);
+ });
+ }).fail(function(result) {
+ console.log("Call failed to server: " + JSON.stringify(result));
+ });
+ });
+ }
+
+ this.callCustomASService = function(params, $model, action) {
+ var result_div = $('#callback_message');
+
+ require(["openbis",
+ "as/dto/service/id/CustomASServiceCode",
+ "as/dto/service/CustomASServiceExecutionOptions",
+ "as/dto/experiment/id/ExperimentIdentifier"],
+ function(openbis, CustomASServiceCode, CustomASServiceExecutionOptions, ExperimentIdentifier) {
+
+ var v3 = new openbis(null);
+ v3._private.sessionToken = mainController.openbisV1._internal.sessionToken;
+ var webAppContext = mainController.openbisV3.getWebAppContext();
+ webAppContext['entityIdentifier'] = $model.experiment.identifier;
+
+ var serviceCode = new CustomASServiceCode("snakemake_service");
+ var options = new CustomASServiceExecutionOptions();
+
+ options.withParameter("webapp_context", webAppContext)
+ Object.keys(params).forEach(function(key) {
+ options.withParameter(key, params[key]);
+ });
+
+ v3.executeCustomASService(serviceCode, options).done(function(result) {
+ result_json = JSON.parse(result);
+ action(result_json)
+ });
+ });
+ return false;
+ }
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/UiComponents.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/UiComponents.js
new file mode 100644
index 00000000000..36e1f12a640
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/UiComponents.js
@@ -0,0 +1,104 @@
+var UiComponents = new function() {
+
+ this.addDropdown = function(label, options, $container, selectAction) {
+ var $dropdown = UiComponents.getDropdown(options);
+ $inputGroup = UiComponents.getInputGroup($dropdown, label);
+ $inputGroup.css("margin-top", "3px");
+ $container.append($inputGroup);
+ $dropdown.select2({ width : "100%", theme : "bootstrap", minimumResultsForSearch: 10 });
+ if (selectAction) {
+ $dropdown.on('select2:select', function (e) {
+ selectAction(e.params.data.id);
+ });
+ }
+ $inputGroup.getValue = function() {
+ return $dropdown.val();
+ }
+ return $inputGroup;
+ }
+
+ this.getDropdown = function(options, value) {
+ var $input = $("<select>", { class : "form-control", type : "text" });
+ $input.append($("<option>", { "disabled" : true, "selected" : true, "value" : true }).text(" -- select an option -- "));
+ for (option of options) {
+ var $option = $("<option>");
+ $option.text(option.label);
+ $option.attr("value", option.value);
+ $input.append($option);
+ }
+ if (value) {
+ $input.val(value);
+ }
+ return $input;
+ }
+
+ this.getInputGroup = function($input, label) {
+ var $inputGroup = $("<div>", { class : "input-group" });
+ $inputGroup.append($("<span>", { class : "input-group-addon" }).text(label).css({ 'min-width' : '150px' }));
+ $inputGroup.append($input);
+ return $inputGroup;
+ }
+
+ this.getButton = function($html, action, size, icon) {
+ var buttonSize = size ? size : 'md';
+ var $button = $('<button>', {
+ type : 'button',
+ class : 'btn btn-default btn-' + buttonSize,
+ 'aria-label' : 'Left Align'
+ });
+ if(icon) {
+ var $icon = $('<span>', { class : 'glyphicon ' + icon });
+ $icon.css("margin-right", "0.5rem");
+ $button.append($icon);
+ }
+ if($html) {
+ $button.append($("<span>").text($html));
+ }
+ if(action) {
+ $button.click(action);
+ }
+ return $button;
+ }
+
+ this.getFieldset = function(legendText) {
+ var $fieldset = $('<fieldset>');
+ if (legendText) {
+ var $legend = $('<legend>', { class : 'section-legend' }).append(legendText)
+ $fieldset.append($legend);
+ }
+ return $fieldset;
+ }
+
+ this.getLoader = function() {
+ return $('<div>').attr('class', 'loader col-centered');
+ }
+
+ // blocks given $component or whole screen of none given
+ this.startLoading = function($component) {
+ var params = {
+ message : this.getLoader(),
+ css: {
+ border: 'none',
+ padding: '15px',
+ backgroundColor: 'transparent',
+ },
+ overlayCSS: {
+ opacity : 0.1,
+ }
+ };
+ if ($component) {
+ $component.block(params);
+ } else {
+ $.blockUI(params);
+ }
+ }
+
+ // unblocks given $component or whole screen of none given
+ this.stopLoading = function($component) {
+ if ($component) {
+ $component.unblock();
+ } else {
+ $.unblockUI();
+ }
+ }
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/plugin.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/plugin.js
new file mode 100644
index 00000000000..b6803e35362
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/plugin.js
@@ -0,0 +1,37 @@
+function BBBHubTechnology() {
+ this.init();
+}
+
+$.extend(BBBHubTechnology.prototype, ELNLIMSPlugin.prototype, {
+ // This code is copy of openBis plugin. It was taken from here:
+ // https://sissource.ethz.ch/sis/bbb-hub/tree/master/openbis/core-plugins/bbb-hub/1/as/webapps/snakemake/html/js
+ // Now it is a ELN plugin.
+
+ init: function() {
+ loadJSResorce("./plugins/bbb-hub/UiComponents.js");
+ loadJSResorce("./plugins/bbb-hub/BBBServerFacade.js");
+ loadJSResorce("./plugins/bbb-hub/snakemake-table.js");
+ loadJSResorce("./plugins/bbb-hub/snakemake-trigger.js");
+ },
+
+ experimentFormTop : function($container, model) {
+ BBBServerFacade.getExperiment($container, model);
+ },
+
+ experimentFormBottom : function($container, model) {
+ },
+
+ getExtraUtilities : function() {
+ return [{
+ icon : "fa fa-table",
+ uniqueViewName : "BBB_VIEW_NAME_TEST",
+ label : "Snakemake",
+ paintView : function($header, $content) {
+ $header.append($("<h1>").append("Public Index Page"));
+ BBBServerFacade.getExperiments($content);
+ }
+ }];
+ }
+});
+
+profile.plugins.push(new BBBHubTechnology());
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-table.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-table.js
new file mode 100644
index 00000000000..a6add5714f1
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-table.js
@@ -0,0 +1,169 @@
+var SnakemakeTable = new function() {
+
+ this.paintTable = function(container, experiments, roles) {
+ var columns = [];
+
+ columns.push({
+ label : 'Code',
+ property : 'code',
+ isExportable: false,
+ sortable : true
+ });
+
+ columns.push({
+ label : 'Description',
+ property : 'description',
+ isExportable: false,
+ sortable : true
+ });
+
+ columns.push({
+ label : 'Group',
+ property : 'group',
+ isExportable: false,
+ sortable : true
+ });
+
+ columns.push({
+ label : 'E-mail',
+ property : 'email',
+ isExportable: false,
+ sortable : true
+ });
+
+ columns.push({
+ label : 'Special access',
+ property : 'specialAccess',
+ isExportable: false,
+ sortable : true
+ });
+
+ var getDataList = function(callback) {
+ var entities = [];
+
+ var rolesMap = SnakemakeTable.rolesMap(roles);
+
+ var dataList = [];
+
+ for (i = 0; i < experiments.length; i++) {
+ if (experiments[i].type === undefined || experiments[i].type.code !== "BBB") {
+ continue;
+ }
+
+ var desc = experiments[i].properties["BBB.DESCRIPTION"];
+ var group = experiments[i].properties["BBB.GROUP"];
+ var registrator = experiments[i].registrator;
+ var projectCode = experiments[i].project.code;
+ var spaceCode = experiments[i].project.space.code;
+
+ var model = { 'code' : experiments[i].code,
+ 'description' : desc === undefined ? "" : desc,
+ 'group' : group === undefined ? "" : group,
+ 'email' : registrator === null ? "" : registrator.email,
+ 'specialAccess' : SnakemakeTable.getSpecialAccess(rolesMap, projectCode, spaceCode)
+ };
+
+ dataList.push(model);
+ }
+ callback(dataList);
+ };
+
+ var dataGridController = new DataGridController(null, columns, [], null, getDataList, null, true, "ENTITY_TABLE_BBB", null, 90);
+ dataGridController.init(container);
+ }
+
+ this.prepareData = function(experiments, roles) {
+ var data = [];
+
+ var rolesMap = SnakemakeTable.rolesMap(roles);
+
+ for (i = 0; i < experiments.length; i++) {
+ var row = [];
+
+ if (experiments[i].type === undefined || experiments[i].type.code !== "BBB") {
+ continue;
+ }
+
+ var desc = experiments[i].properties["BBB.DESCRIPTION"];
+ var group = experiments[i].properties["BBB.GROUP"];
+ var registrator = experiments[i].registrator;
+ var projectCode = experiments[i].project.code;
+ var spaceCode = experiments[i].project.space.code;
+
+ row.push(experiments[i].code);
+ row.push(desc === undefined ? "" : desc);
+ row.push(group === undefined ? "" : group);
+ row.push(registrator === null ? "" : registrator.email);
+ row.push(SnakemakeTable.getSpecialAccess(rolesMap, projectCode, spaceCode));
+
+ data.push(row);
+ }
+
+ return data;
+ }
+
+ this.getSpecialAccess = function(rolesMap, projectCode, spaceCode) {
+ var projectUsers = rolesMap["projects"][projectCode] === undefined ? "" : rolesMap["projects"][projectCode]["users"].join(", ");
+ var projectGroups = rolesMap["projects"][projectCode] === undefined ? "" : rolesMap["projects"][projectCode]["groups"].join(", ");
+
+ var spaceUsers = rolesMap["space"][spaceCode] === undefined ? "" : rolesMap["space"][spaceCode]["users"].join(", ");
+ var spaceGroups = rolesMap["space"][spaceCode] === undefined ? "" : rolesMap["space"][spaceCode]["groups"].join(", ");
+
+ var users = projectUsers + (projectUsers !== "" && spaceUsers !== "" ? ", " : "") + spaceUsers;
+ var groups = projectGroups + (projectGroups !== "" && spaceGroups !== "" ? ", " : "") + spaceGroups;
+
+ var access = "";
+ if (users !== "") {
+ access += "<span style='font-weight:bold'>Users: </span>" + users;
+ }
+
+ if (groups !== "") {
+ if (access !== "") {
+ access += "<br/>";
+ }
+ access += "<span style='font-weight:bold'>Groups: </span>" + groups;
+ }
+
+ return access;
+ }
+
+ this.rolesMap = function(roles) {
+ var rolesMap = new Map();
+
+ var projects = new Map();
+ var spaces = new Map();
+
+ rolesMap["projects"] = projects;
+ rolesMap["space"] = spaces;
+
+ for (i = 0; i < roles.length; i++) {
+ var user = roles[i].user == null ? null : roles[i].user.userId;
+ var group = roles[i].authorizationGroup == null ? null : roles[i].authorizationGroup.code;
+
+ if (roles[i].project !== null) {
+ var value = projects[roles[i].project.code];
+ projects[roles[i].project.code] = SnakemakeTable.appendValue(value, user, group);
+ } else {
+ var value = spaces[roles[i].space.code];
+ spaces[roles[i].space.code] = SnakemakeTable.appendValue(value, user, group);
+ }
+ }
+
+ return rolesMap;
+ }
+
+ this.appendValue = function(value, user, group) {
+ if (value === undefined) {
+ value = new Map();
+ value["users"] = new Array();
+ value["groups"] = new Array();
+ }
+
+ if (user !== null) {
+ value["users"].push(user);
+ } else {
+ value["groups"].push(group);
+ }
+ return value;
+ }
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-trigger.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-trigger.js
new file mode 100644
index 00000000000..a3756fdfc4a
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/plugins/bbb-hub/snakemake-trigger.js
@@ -0,0 +1,161 @@
+var SnakemakeTrigger = new function() {
+
+ var groups;
+ var propTypeCodeToLabelMap = {};
+ var dataSetPaths;
+ var $formContainerAll;
+ var $formContainerGroups;
+ var $dropdownGroupBy;
+ var $dropdownGroup1;
+ var $dropdownGroup2;
+ var $button;
+ var $model;
+
+ this.paintTriggerContainers = function($container, model, experiment) {
+ $model = model;
+ SnakemakeTrigger.paintFormContainers($container);
+ SnakemakeTrigger.paintProcessAll();
+ SnakemakeTrigger.paintGroupBy(experiment);
+ SnakemakeTrigger.paintGroupValues();
+ groups = SnakemakeTrigger.getGroups(experiment);
+ files = SnakemakeTrigger.getFiles(experiment);
+ }
+
+ this.paintFormContainers = function($container) {
+ var $fieldsetAll = UiComponents.getFieldset("Process all comparisons");
+ var $fieldsetGroups = UiComponents.getFieldset("Pick groups to compare");
+ $formContainerAll = $('<div>').addClass('form-group');
+ $formContainerGroups = $('<div>').addClass('form-group');
+ $fieldsetAll.append($formContainerAll);
+ $fieldsetGroups.append($formContainerGroups);
+ $container.append($fieldsetAll).append($fieldsetGroups);
+ }
+
+ this.paintProcessAll = function() {
+ var $buttonAll = UiComponents.getButton("Start processing", SnakemakeTrigger.startProcessingAll);
+ $formContainerAll.append($buttonAll);
+ }
+
+ this.paintGroupBy = function(experiment) {
+ var groupByOptions = [];
+ if (experiment.samples.length > 0) {
+ var sample = experiment.samples[0];
+ for (var i = 0; i < sample.type.propertyAssignments.length; i++) {
+ var propertyAssignment = sample.type.propertyAssignments[i];
+ groupByOptions.push({
+ label: propertyAssignment.propertyType.label,
+ value: propertyAssignment.propertyType.code,
+ });
+ propTypeCodeToLabelMap[propertyAssignment.propertyType.code] = propertyAssignment.propertyType.label;
+ }
+ }
+
+ $dropdownGroupBy = UiComponents.addDropdown("Group by", groupByOptions, $formContainerGroups, SnakemakeTrigger.paintGroupValues);
+ }
+
+ this.paintGroupValues = function(propertyType) {
+ if (propertyType) {
+ var groupOptions = groups[propertyType].map(function(value) { return {
+ label: value,
+ value: value,
+ }});
+ } else {
+ var groupOptions = [];
+ }
+
+ if ($dropdownGroup1) {
+ $dropdownGroup1.remove();
+ }
+ if ($dropdownGroup2) {
+ $dropdownGroup2.remove();
+ }
+ if ($button) {
+ $button.remove();
+ }
+
+ $dropdownGroup1 = UiComponents.addDropdown("Group 1", groupOptions, $formContainerGroups);
+ $dropdownGroup2 = UiComponents.addDropdown("Group 2", groupOptions, $formContainerGroups);
+
+ $button = UiComponents.getButton("Start processing", SnakemakeTrigger.startProcessing);
+ $button.css("margin-top", "20px");
+ $formContainerGroups.append($button);
+ }
+
+ this.getGroups = function(experiment) {
+ var groups = {};
+ for (var i = 0; i < experiment.samples.length; i++) {
+ var sample = experiment.samples[i];
+ // collect groups
+ for (var propertyKey in sample.properties) {
+ if (sample.properties.hasOwnProperty(propertyKey)) {
+ var propertyValue = sample.properties[propertyKey];
+ if (groups.hasOwnProperty(propertyKey) == false) {
+ groups[propertyKey] = [];
+ }
+ if (groups[propertyKey].indexOf(propertyValue) == -1) {
+ groups[propertyKey].push(propertyValue);
+ }
+ }
+ }
+ }
+ return groups;
+ }
+
+ this.getFiles = function(experiment) {
+ dataSetPaths = [];
+ for (var i = 0; i < experiment.dataSets.length; i++) {
+ var dataSet = experiment.dataSets[i];
+ if (dataSet.type.code == "FASTQ" || dataSet.type.code == "METADATA") {
+ var path = dataSet.physicalData.shareId + "/" + dataSet.physicalData.location;
+ dataSetPaths.push(path);
+ }
+ }
+ }
+
+ this.startProcessingAll = function() {
+ UiComponents.startLoading();
+ var jsonrpc = {
+ "method": "start_processing_all",
+ "params": {
+ "data_set_paths": dataSetPaths
+ }
+ };
+ BBBServerFacade.callCustomASService(jsonrpc, $model, function(result) {
+ UiComponents.stopLoading();
+ if (result.success) {
+ alert("Processing started.");
+ } else {
+ alert("Error: " + result.data);
+ }
+ });
+ }
+
+ this.startProcessing = function() {
+ var groupSelection = {
+ groupBy: propTypeCodeToLabelMap[$dropdownGroupBy.getValue()],
+ group1: $dropdownGroup1.getValue(),
+ group2: $dropdownGroup2.getValue(),
+ }
+ if (!groupSelection.groupBy || !groupSelection.group1 || !groupSelection.group2) {
+ alert("Select both groups first.");
+ return;
+ }
+ UiComponents.startLoading();
+
+ var jsonrpc = {
+ "method": "start_processing",
+ "params": {
+ "group_selection": groupSelection,
+ "data_set_paths": dataSetPaths
+ }
+ };
+ BBBServerFacade.callCustomASService(jsonrpc, $model, function(result) {
+ UiComponents.stopLoading();
+ if (result.success) {
+ alert("Processing started.");
+ } else {
+ alert("Error: " + result.data);
+ }
+ });
+ }
+}
\ No newline at end of file
--
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