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 4f68c42e6d9229394f9ccdf3ae29dc9b5fd2fdd9..2db69a4ee9af6aaad9d74fe94086c6acf7ba4d13 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
@@ -174,7 +174,7 @@ $.extend(MicroscopyTechnology.prototype, ELNLIMSPlugin.prototype, {
var newThumbCol = $("<div />",
{
class: "col-md-3",
- display: "inline",
+ display: "inline",
"text-align": "center",
id: sample.code
});
@@ -246,133 +246,102 @@ $.extend(MicroscopyTechnology.prototype, ELNLIMSPlugin.prototype, {
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;
- }
+ 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
+ console.log("Processing microscopy sample " + sample.code);
+
+ // Search for the sample of type and given perm id
+ 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];
- // Retrieve the file for the dataset and the associated URL
- mainController.openbisV1.listFilesForDataSet(dataset.code, '/', true,
- function (response) {
+ if (dataSet.getType().code === "MICROSCOPY_IMG_THUMBNAIL") {
- // Make sure that we got some results from the DSS to process
- if (response.error) {
+ // Now retrieve the thumbnail and add display it
- // 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!");
+ // Get the file
+ var criteria = new DataSetFileSearchCriteria();
+ var dataSetCriteria = criteria.withDataSet().withOrOperator();
+ dataSetCriteria.withPermId().thatEquals(dataSet.permId.permId);
- return;
+ var fetchOptions = new DataSetFileFetchOptions();
- }
+ // Query the server
+ mainController.openbisV3.getDataStoreFacade().searchFiles(criteria, fetchOptions).done(function (result) {
- // Find the thumbnail.png file
- response.result.forEach(function (f) {
+ // Thumbnail
+ var imD = $("#" + img_id);
- // Thumbnail
- var imD = $("#" + img_id);
+ // Make sure to reset the display attribute
+ imD.css("display", "inline");
- if (!f.isDirectory && f.pathInDataSet.toLowerCase() === "thumbnail.png") {
+ if (result.getTotalCount() == 0) {
- // Retrieve the file URL
- mainController.openbisV1.getDownloadUrlForFileForDataSetInSession(
- dataset.code, f.pathInDataSet, function (url) {
+ // Thumbnail not found!
+ imD.attr("src", "./img/error.png");
+ imD.attr("title", "Could not find a thumbnail for this dataset!");
- // Replace the image
- var eUrl = encodeURI(url);
- eUrl = eUrl.replace('+', '%2B');
- imD.attr("src", eUrl);
+ return;
+ }
- });
- } else {
+ // Extract the files
+ var datasetFiles = result.getObjects();
- // Thumbnail not found!
- imD.attr("src", "./img/error.png");
- imD.attr("title", "Could not find a thumbnail for this dataset!");
+ // Find the only fcs file and add its name and URL to the DynaTree
+ datasetFiles.forEach(function (f) {
- }
+ // // Build the download URL
+ // let url = f.getDataStore().getDownloadUrl() + "/datastore_server/" +
+ // f.permId.dataSetId.permId + "/" + f.getPath() + "?sessionID=" +
+ // mainController.openbisV3.getWebAppContext().sessionId;
- // Make sure to reset the display attribute
- imD.css("display", "inline");
- });
+ if (!f.isDirectory() && f.getPath().toLowerCase() === "thumbnail.png") {
- });
+ // Still use the V1 API since the sessionId stored in the
+ // webapp context is null in V3.
+ mainController.openbisV1.getDownloadUrlForFileForDataSetInSession(
+ dataSet.code, f.getPath(), function (url) {
- });
+ // Replace the image
+ var eUrl = encodeURI(url);
+ eUrl = eUrl.replace('+', '%2B');
+ imD.attr("src", eUrl);
- },
+ console.log("Adding thumbnail " + eUrl + " to " + img_id);
- 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;
+ });
+ });
+ }
}
- }
- }
- });
-
+ });
+ });
}
-});
+});
\ No newline at end of file