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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/MicroscopyTechnology.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/MicroscopyTechnology.js
index bb9b5a7d4e2f5bd94e1e4dcd281de83f91ba9fbd..f1b730828af9bf373b7dd4cf152e5cf9d6fbe061 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
@@ -3,103 +3,366 @@ function MicroscopyTechnology() {
}
$.extend(MicroscopyTechnology.prototype, ELNLIMSPlugin.prototype, {
- init: function() {
-
+ 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" : []
- }]
- }
+ 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 }
- }
+ 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) {
+ 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)) {
+ 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) {
+
+ 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) {
-
+ 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) {
+ 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());
- });
+
+ // 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) {
-
+ dataSetFormBottom: function ($container, model) {
+
+ },
+
+ displayExperimentThumbnails: function ($container, model, microscopyExperimentSample) {
+ if (microscopyExperimentSample.sampleTypeCode !== "MICROSCOPY_EXPERIMENT") {
+ return;
+ }
+
+ if (microscopyExperimentSample.children.length === 0) {
+ return;
+ }
+
+ // Clear the container
+ $container.empty();
+
+ // 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 % 3 === 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-4",
+ 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 = $("<a>").text(displayName).attr("href", "#").attr("title", name).click(
+ function () {
+ window.top.location.hash = "#" + (new Date().getTime());
+ return false;
+ });
+
+ // Actual thumbnail. Initially we display a place holder. Later,
+ // we will replace it asynchronously.
+ var thumbnailImage = $("<img />",
+ {
+ src: "./img/wait.png",
+ id: "image_" + sample.code,
+ title: name
+ });
+
+ // Build the thumbnail viewer
+ thumbnailView.append(thumbnailImage);
+ thumbnailView.append($("<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) {
+
+ // Get the datasets with type "MICROSCOPY_IMG_THUMBNAIL" for current sample
+ this.getMicroscopyImgThumbnailDataSetsForMicroscopySample(
+ model,
+ sample.experimentIdentifierOrNull,
+ sample.code, function(dataset) {
+
+ // Get the containers
+ if (dataset == null) {
+ return;
+ }
+
+ // Retrieve the file for the dataset and the associated URL
+ mainController.openbisV1.listFilesForDataSet(dataset.code, '/', true,
+ function(response) {
+
+ // Make sure that we got some results from the DSS to process
+ if (response.error) {
+
+ // Thumbnail not found!
+ var imD = $("#" + img_id);
+ imD.attr("src", "./img/error.png");
+ imD.attr("title", "Could not find any files associated to this dataset!");
+
+ return;
+
+ }
+
+ // Find the thumbnail.png file
+ response.result.forEach(function(f) {
+
+ if (!f.isDirectory && f.pathInDataSet.toLowerCase() === "thumbnail.png") {
+
+ // Retrieve the file URL
+ mainController.openbisV1.getDownloadUrlForFileForDataSetInSession(
+ dataset.code, f.pathInDataSet, function(url){
+
+ // Replace the image
+ var eUrl = encodeURI(url);
+ eUrl = eUrl.replace('+', '%2B');
+ $("#" + img_id).attr("src", eUrl);
+
+ });
+ } else {
+
+ // Thumbnail not found!
+ var imD = $("#" + img_id);
+ imD.attr("src", "./img/error.png");
+ imD.attr("title", "Could not find a thumbnail for this dataset!");
+
+ }
+ });
+
+ });
+
+ });
+
+ },
+
+ getMicroscopyImgThumbnailDataSetsForMicroscopySample : function (model, expCode, sampleCode, action) {
+
+ // Experiment criteria (experiment of type "COLLECTION" and code expCode)
+ var experimentCriteria = new SearchCriteria();
+ experimentCriteria.addMatchClause(
+ SearchCriteriaMatchClause.createAttributeMatch(
+ "CODE", expCode)
+ );
+ experimentCriteria.addMatchClause(
+ SearchCriteriaMatchClause.createAttributeMatch(
+ "TYPE", "COLLECTION")
+ );
+
+ // Sample criteria (sample of type "MICROSCOPY_SAMPLE_TYPE" and code sampleCode)
+ var sampleCriteria = new SearchCriteria();
+ sampleCriteria.addMatchClause(
+ SearchCriteriaMatchClause.createAttributeMatch(
+ "CODE", sampleCode)
+ );
+ sampleCriteria.addMatchClause(
+ SearchCriteriaMatchClause.createAttributeMatch(
+ "TYPE", "MICROSCOPY_SAMPLE_TYPE")
+ );
+
+ // Dataset criteria
+ var datasetCriteria = new SearchCriteria();
+ datasetCriteria.addMatchClause(
+ SearchCriteriaMatchClause.createAttributeMatch(
+ "TYPE", "MICROSCOPY_IMG_CONTAINER")
+ );
+
+ // Add sample and experiment search criteria as subcriteria
+ datasetCriteria.addSubCriteria(
+ SearchSubCriteria.createSampleCriteria(sampleCriteria)
+ );
+ datasetCriteria.addSubCriteria(
+ SearchSubCriteria.createExperimentCriteria(experimentCriteria)
+ );
+
+ // Search
+ mainController.openbisV1.searchForDataSets(datasetCriteria, function (response) {
+
+ // Get the containers
+ if (response.error || response.result.length === 0) {
+ return null;
+ }
+
+ // All MICROSCOPY_IMG_CONTAINER datasets (i.e. a file series) contain a MICROSCOPY_IMG_OVERVIEW
+ // and a MICROSCOPY_IMG dataset; one of the series will also contain a MICROSCOPY_IMG_THUMBNAIL,
+ // which is what we are looking for here.
+ // Even though the MICROSCOPY_IMG_THUMBNAIL is always created for series 0, we cannot guarantee
+ // here that series zero will be returned as the first. We quickly scan through the returned
+ // results for the MICROSCOPY_IMG_CONTAINER that has three contained datasets.
+ // From there we can then quickly retrieve the MICROSCOPY_IMG_THUMBNAIL.
+ for (var i = 0; i < response.result.length; i++) {
+ var series = response.result[i];
+ for (var j = 0; j < series.containedDataSets.length; j++) {
+ if (series.containedDataSets[j].dataSetTypeCode === "MICROSCOPY_IMG_THUMBNAIL") {
+ action(series.containedDataSets[j]);
+ return;
+ }
+ }
+ }
+ });
+
}
});