diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/error.png b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/error.png
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diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/wait.png b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/img/wait.png
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diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/FlowCytometryTechnology.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/FlowCytometryTechnology.js
index deffccd1f660a2758d8b84559276f18e4d8429f4..bd6a377e9d0a6ad004ad133e75c57b232bd3b8bd 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/FlowCytometryTechnology.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/FlowCytometryTechnology.js
@@ -174,14 +174,14 @@ $.extend(FlowCytometryTechnology.prototype, ELNLIMSPlugin.prototype, {
// Additional functionality
renderParameterSelectionWidget: function ($container, model) {
- // Clear the container
- $container.empty();
-
// Check that we ave the correct dataset type
if (!model.dataSetV3.type.code.endsWith("_FCSFILE")) {
return;
}
+ // Clear the container
+ $container.empty();
+
//
// Retrieve the parameter info
//
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js
index bb9b5a7d4e2f5bd94e1e4dcd281de83f91ba9fbd..d0d3d304695147ff5716ba69fbf0b767dc535f28 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js
@@ -1,105 +1,327 @@
function MicroscopyTechnology() {
- this.init();
+ this.init();
}
$.extend(MicroscopyTechnology.prototype, ELNLIMSPlugin.prototype, {
- init: function() {
-
- },
- forcedDisableRTF : [],
- forceMonospaceFont : [],
- sampleTypeDefinitionsExtension : {
- "MICROSCOPY_SAMPLE_TYPE" : {
- "SHOW_ON_NAV" : true,
- "SHOW" : false,
- "SAMPLE_CHILDREN_DISABLED" : true,
- "SAMPLE_PARENTS_DISABLED" : true,
- "TOOLBAR" : { CREATE : false, EDIT : true, MOVE : false, COPY : false, DELETE : false, PRINT : true, HIERARCHY_GRAPH : true, HIERARCHY_TABLE : true, UPLOAD_DATASET : false, UPLOAD_DATASET_HELPER : false, EXPORT_ALL : true, EXPORT_METADATA : true }
- },
- "MICROSCOPY_EXPERIMENT" : {
- "SHOW" : false,
- "SAMPLE_CHILDREN_DISABLED" : false,
- "SAMPLE_PARENTS_DISABLED" : false,
- "SAMPLE_PARENTS_ANY_TYPE_DISABLED" : true,
- "TOOLBAR" : { CREATE : false, EDIT : true, MOVE : false, COPY : false, DELETE : false, PRINT : true, HIERARCHY_GRAPH : true, HIERARCHY_TABLE : true, UPLOAD_DATASET : false, UPLOAD_DATASET_HELPER : false, EXPORT_ALL : true, EXPORT_METADATA : true },
- "SAMPLE_PARENTS_HINT" : [{
- "LABEL" : "Organization Units",
- "TYPE": "ORGANIZATION_UNIT",
- "ANNOTATION_PROPERTIES" : []
- }]
- }
- },
- dataSetTypeDefinitionsExtension : {
- "MICROSCOPY_ACCESSORY_FILE" : {
- "DATASET_PARENTS_DISABLED" : true,
- "TOOLBAR" : { EDIT : true, MOVE : false, ARCHIVE : true, DELETE : false, HIERARCHY_TABLE : true, EXPORT_ALL : true, EXPORT_METADATA : true }
- },
- "MICROSCOPY_IMG" : {
- "DATASET_PARENTS_DISABLED" : true,
- "TOOLBAR" : { EDIT : true, MOVE : false, ARCHIVE : true, DELETE : false, HIERARCHY_TABLE : true, EXPORT_ALL : true, EXPORT_METADATA : true }
- },
- "MICROSCOPY_IMG_OVERVIEW" : {
- "DATASET_PARENTS_DISABLED" : true,
- "TOOLBAR" : { EDIT : true, MOVE : false, ARCHIVE : true, DELETE : false, HIERARCHY_TABLE : true, EXPORT_ALL : true, EXPORT_METADATA : true }
- },
- "MICROSCOPY_IMG_THUMBNAIL" : {
- "DATASET_PARENTS_DISABLED" : true,
- "TOOLBAR" : { EDIT : true, MOVE : false, ARCHIVE : true, DELETE : false, HIERARCHY_TABLE : true, EXPORT_ALL : true, EXPORT_METADATA : true }
- },
- "MICROSCOPY_IMG_CONTAINER" : {
- "DATASET_PARENTS_DISABLED" : true,
- "TOOLBAR" : { EDIT : true, MOVE : false, ARCHIVE : true, DELETE : false, HIERARCHY_TABLE : true, EXPORT_ALL : true, EXPORT_METADATA : true }
- }
- },
- sampleFormTop : function($container, model) {
- if(model.datasets && model.datasets.length > 0) {
- var imageViewerDataSets = [];
- for(var dsIdx = 0; dsIdx < model.datasets.length; dsIdx++) {
- if(profile.isImageViewerDataSetCode(model.datasets[dsIdx].dataSetTypeCode)) {
- imageViewerDataSets.push(model.datasets[dsIdx].code);
- }
- }
-
- if(imageViewerDataSets.length > 0) {
- require(["openbis-screening", "components/imageviewer/ImageViewerWidget" ], function(openbis, ImageViewerWidget) {
- var screningFacade = new openbis(null);
- screningFacade._internal.sessionToken = mainController.openbisV1._internal.sessionToken;
-
- // Create the image viewer component for the specific data sets
- var widget = new ImageViewerWidget(screningFacade, imageViewerDataSets);
-
- // Render the component and add it to the page
- $container.append($('<legend>').text('Microscopy Viewer'));
- var $imageWidgetContainer = new $('<div>');
- $imageWidgetContainer.css("margin", "20px");
- $container.append($imageWidgetContainer);
- $imageWidgetContainer.append(widget.render());
- });
- }
- }
- },
- sampleFormBottom : function($container, model) {
-
- },
- dataSetFormTop : function($container, model) {
- if(model.dataSetV3 && profile.isImageViewerDataSetCode(model.dataSetV3.type.code)) {
- require(["openbis-screening", "components/imageviewer/ImageViewerWidget" ], function(openbis, ImageViewerWidget) {
- var screningFacade = new openbis(null);
- screningFacade._internal.sessionToken = mainController.openbisV1._internal.sessionToken;
-
- // Create the image viewer component for the specific data sets
- var widget = new ImageViewerWidget(screningFacade, [model.dataSetV3.permId.permId]);
-
- // Render the component and add it to the page
- $container.append($('<legend>').text('Microscopy Viewer'));
- var $imageWidgetContainer = new $('<div>');
- $imageWidgetContainer.css("margin", "20px");
- $container.append($imageWidgetContainer);
- $imageWidgetContainer.append(widget.render());
- });
- }
- },
- dataSetFormBottom : function($container, model) {
-
- }
-});
+ init: function () {
+
+ },
+ forcedDisableRTF: [],
+ forceMonospaceFont: [],
+ sampleTypeDefinitionsExtension: {
+ "MICROSCOPY_SAMPLE_TYPE": {
+ "SHOW_ON_NAV": true,
+ "SHOW": false,
+ "SAMPLE_CHILDREN_DISABLED": true,
+ "SAMPLE_PARENTS_DISABLED": true,
+ "TOOLBAR": { CREATE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true }
+ },
+ "MICROSCOPY_EXPERIMENT": {
+ "SHOW": false,
+ "SAMPLE_CHILDREN_DISABLED": false,
+ "SAMPLE_PARENTS_DISABLED": false,
+ "SAMPLE_PARENTS_ANY_TYPE_DISABLED": true,
+ "TOOLBAR": { CREATE: false, EDIT: true, MOVE: false, COPY: false, DELETE: false, PRINT: true, HIERARCHY_GRAPH: true, HIERARCHY_TABLE: true, UPLOAD_DATASET: false, UPLOAD_DATASET_HELPER: false, EXPORT_ALL: true, EXPORT_METADATA: true },
+ "SAMPLE_PARENTS_HINT": [{
+ "LABEL": "Organization Units",
+ "TYPE": "ORGANIZATION_UNIT",
+ "ANNOTATION_PROPERTIES": []
+ }]
+ }
+ },
+ dataSetTypeDefinitionsExtension: {
+ "MICROSCOPY_ACCESSORY_FILE": {
+ "DATASET_PARENTS_DISABLED": true,
+ "TOOLBAR": { EDIT: true, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ },
+ "MICROSCOPY_IMG": {
+ "DATASET_PARENTS_DISABLED": true,
+ "TOOLBAR": { EDIT: true, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ },
+ "MICROSCOPY_IMG_OVERVIEW": {
+ "DATASET_PARENTS_DISABLED": true,
+ "TOOLBAR": { EDIT: true, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ },
+ "MICROSCOPY_IMG_THUMBNAIL": {
+ "DATASET_PARENTS_DISABLED": true,
+ "TOOLBAR": { EDIT: true, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ },
+ "MICROSCOPY_IMG_CONTAINER": {
+ "DATASET_PARENTS_DISABLED": true,
+ "TOOLBAR": { EDIT: true, MOVE: false, ARCHIVE: true, DELETE: false, HIERARCHY_TABLE: true, EXPORT_ALL: true, EXPORT_METADATA: true }
+ }
+ },
+ sampleFormTop: function ($container, model) {
+ if (model.sample && model.sample.sampleTypeCode == "MICROSCOPY_EXPERIMENT") {
+ this.displayExperimentThumbnails($container, model, model.sample);
+ }
+ if (model.datasets && model.datasets.length > 0) {
+ var imageViewerDataSets = [];
+ for (var dsIdx = 0; dsIdx < model.datasets.length; dsIdx++) {
+ if (profile.isImageViewerDataSetCode(model.datasets[dsIdx].dataSetTypeCode)) {
+ imageViewerDataSets.push(model.datasets[dsIdx].code);
+ }
+ }
+
+ if (imageViewerDataSets.length > 0) {
+ require(["openbis-screening", "components/imageviewer/ImageViewerWidget"], function (openbis, ImageViewerWidget) {
+ var screningFacade = new openbis(null);
+ screningFacade._internal.sessionToken = mainController.openbisV1._internal.sessionToken;
+
+ // Create the image viewer component for the specific data sets
+ var widget = new ImageViewerWidget(screningFacade, imageViewerDataSets);
+
+ // Render the component and add it to the page
+ $container.append($('<legend>').text('Microscopy Viewer'));
+ var $imageWidgetContainer = new $('<div>');
+ $imageWidgetContainer.css("margin", "20px");
+ $container.append($imageWidgetContainer);
+ $imageWidgetContainer.append(widget.render());
+ });
+ }
+ }
+ },
+ sampleFormBottom: function ($container, model) {
+
+ },
+ dataSetFormTop: function ($container, model) {
+ if (model.dataSetV3 && profile.isImageViewerDataSetCode(model.dataSetV3.type.code)) {
+ require(["openbis-screening", "components/imageviewer/ImageViewerWidget"], function (openbis, ImageViewerWidget) {
+ var screningFacade = new openbis(null);
+ screningFacade._internal.sessionToken = mainController.openbisV1._internal.sessionToken;
+
+ // Create the image viewer component for the specific data sets
+ var widget = new ImageViewerWidget(screningFacade, [model.dataSetV3.permId.permId]);
+
+ // Render the component and add it to the page
+ $container.append($('<legend>').text('Microscopy Viewer'));
+ var $imageWidgetContainer = new $('<div>');
+ $imageWidgetContainer.css("margin", "20px");
+ $container.append($imageWidgetContainer);
+ $imageWidgetContainer.append(widget.render());
+ });
+ }
+ },
+ dataSetFormBottom: function ($container, model) {
+
+ },
+
+ displayExperimentThumbnails: function ($container, model, microscopyExperimentSample) {
+ if (microscopyExperimentSample.sampleTypeCode !== "MICROSCOPY_EXPERIMENT") {
+ return;
+ }
+
+ // Clear the container
+ $container.empty();
+
+ if (microscopyExperimentSample.children.length === 0) {
+ return;
+ }
+
+ // Add legend
+ var legend = $("<legend>")
+ .text("File previews");
+ $container.append(legend);
+
+ // Prepare a div to host the thumbnails
+ var sampleView_div = $("<div>");
+ $container.append(sampleView_div);
+
+ var newThumbRow = null;
+ var numSample = 0;
+
+ var thisObj = this;
+
+ // Prepare the display
+ microscopyExperimentSample.children.forEach(function (sample) {
+
+ // Keep track of the number of the sample
+ numSample++;
+
+ // Add a new row for the next three thumbnails
+ if (numSample % 4 === 1) {
+ newThumbRow = $("<div />", { class: "row" });
+ sampleView_div.append(newThumbRow);
+ }
+
+ // Prepare the name to be shown
+ var name;
+ if (sample.properties.MICROSCOPY_SAMPLE_NAME) {
+ name = sample.properties.MICROSCOPY_SAMPLE_NAME;
+ } else {
+ name = sample.code;
+ }
+
+ // Make sure it is not too long
+ var displayName;
+ var l = name.length;
+ if (l > 40) {
+ displayName = name.substring(0, 18) + "..." + name.substring(l - 18);
+ } else {
+ displayName = name;
+ }
+
+ // If the size property exists (this was added later), retrieve it and display it as well
+ var datasetSize;
+ if (sample.properties.MICROSCOPY_SAMPLE_SIZE_IN_BYTES) {
+ datasetSize = thisObj.formatSizeForDisplay(sample.properties.MICROSCOPY_SAMPLE_SIZE_IN_BYTES);
+ } else {
+ datasetSize = "";
+ }
+
+ // A column to be added to current row that will store all
+ // elements related to current sample
+ var newThumbCol = $("<div />",
+ {
+ class: "col-md-3",
+ display: "inline",
+ "text-align": "center",
+ id: sample.code
+ });
+
+ // A div element to contain the thumbnail and its info
+ var thumbnailView = $("<div />")
+ .css("min-height", "320px")
+ .css("text-align", "center")
+ .css("padding-top", "10px")
+ .css("padding-bottom", "10px")
+
+ // Link to the dataset (sample) viewer.
+ var link = FormUtil.getFormLink(displayName, "Sample", sample.permId, null);
+
+ // Actual thumbnail. Initially we display a place holder. Later,
+ // we will replace it asynchronously.
+ var thumbnailImage = $("<img />",
+ {
+ src: "./img/wait.png",
+ class: "img-responsive",
+ display: "inline",
+ "text-align": "center",
+ id: "image_" + sample.code,
+ title: name
+ });
+
+ // Build the thumbnail viewer
+ thumbnailView.append(thumbnailImage);
+ thumbnailView.append($("<br />"));
+ thumbnailView.append(link);
+ if (datasetSize !== "") {
+ thumbnailView.append($("<br />"));
+ var spanSz = $("<span>").text(datasetSize);
+ thumbnailView.append(spanSz);
+ }
+
+ // Add the thumbnail to the column and the row
+ newThumbCol.append(thumbnailView);
+ newThumbRow.append(newThumbCol);
+
+ // Now retrieve the link to the thumbnail image asynchronously and update the <img>
+ thisObj.displayThumbnailForSample(model, sample, "image_" + sample.code);
+
+ });
+ },
+
+ formatSizeForDisplay: function (datasetSize) {
+
+ // Output
+ var formattedDatasetSize = "";
+
+ // Cast datasetSize to float
+ var datasetSizeF = parseFloat(datasetSize);
+
+ var sMB = datasetSizeF / 1024.0 / 1024.0;
+ if (sMB < 1024.0) {
+ formattedDatasetSize = sMB.toFixed(2) + " MiB";
+ } else {
+ var sGB = sMB / 1024.0;
+ formattedDatasetSize = sGB.toFixed(2) + " GiB";
+ }
+
+ return formattedDatasetSize;
+ },
+
+ displayThumbnailForSample: function (model, sample, img_id) {
+
+ require([
+ "as/dto/sample/search/SampleSearchCriteria",
+ "as/dto/sample/fetchoptions/SampleFetchOptions",
+ "as/dto/dataset/search/DataSetSearchCriteria",
+ "dss/dto/datasetfile/search/DataSetFileSearchCriteria",
+ "dss/dto/datasetfile/fetchoptions/DataSetFileFetchOptions",
+ ],
+
+ function (
+ SampleSearchCriteria,
+ SampleFetchOptions,
+ DataSetSearchCriteria,
+ DataSetFileSearchCriteria,
+ DataSetFileFetchOptions) {
+
+ // First retrieve the sample again but with the associated datasets
+ var criteria = new SampleSearchCriteria();
+ criteria.withType().withCode().thatEquals(sample.sampleTypeCode);
+ criteria.withPermId().thatEquals(sample.permId);
+ var fetchOptions = new SampleFetchOptions();
+ fetchOptions.withDataSets().withType();
+
+ // Query the server
+ mainController.openbisV3.searchSamples(criteria, fetchOptions).done(function (result) {
+ if (result.getTotalCount() == 0) {
+ return null;
+ }
+ var sample = result.getObjects()[0];
+ for (var i = 0; i < sample.getDataSets().length; i++) {
+ var dataSet = sample.getDataSets()[i];
+
+ if (dataSet.getType().code === "MICROSCOPY_IMG_THUMBNAIL") {
+
+ // Now retrieve the thumbnail and add display it
+
+ // Get the file
+ var criteria = new DataSetFileSearchCriteria();
+ var dataSetCriteria = criteria.withDataSet().withOrOperator();
+ dataSetCriteria.withPermId().thatEquals(dataSet.permId.permId);
+
+ var fetchOptions = new DataSetFileFetchOptions();
+
+ // Query the server
+ mainController.openbisV3.getDataStoreFacade().searchFiles(criteria, fetchOptions).done(function (result) {
+
+ // Thumbnail
+ var imD = $("#" + img_id);
+
+ // Make sure to reset the display attribute
+ imD.css("display", "inline");
+
+ if (result.getTotalCount() == 0) {
+
+ // Thumbnail not found!
+ imD.attr("src", "./img/error.png");
+ imD.attr("title", "Could not find a thumbnail for this dataset!");
+
+ return;
+ }
+
+ // Extract the files
+ var datasetFiles = result.getObjects();
+
+ // Find the only fcs file and add its name and URL to the DynaTree
+ datasetFiles.forEach(function (f) {
+
+ // Build the download URL
+ var url = f.getDataStore().getDownloadUrl() + "/datastore_server/" +
+ f.permId.dataSetId.permId + "/" + f.getPath() + "?sessionID=" +
+ mainController.serverFacade.openbisServer.getSession();
+
+ // Replace the image
+ var eUrl = encodeURI(url);
+ eUrl = eUrl.replace('+', '%2B');
+ imD.attr("src", eUrl);
+ });
+ });
+ }
+ }
+ });
+ });
+ }
+});
\ No newline at end of file