From ed3a13109499a6b9aa4de3dd313f5f096e1a09b7 Mon Sep 17 00:00:00 2001
From: juanf <juanf@ethz.ch>
Date: Mon, 27 Nov 2023 16:15:18 +0100
Subject: [PATCH] SSDM-14137: make storage positions be inside a collection
---
.../generic/server/hotfix/ELNFixes.java | 140 ++++++++++++++++++
.../1/as/master-data/common-data-model.xls | Bin 75776 -> 75776 bytes
.../SampleForm/widgets/StorageListView.js | 6 +
3 files changed, 146 insertions(+)
diff --git a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/hotfix/ELNFixes.java b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/hotfix/ELNFixes.java
index 72a91ed2c67..b9ba0f449a6 100644
--- a/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/hotfix/ELNFixes.java
+++ b/server-application-server/source/java/ch/systemsx/cisd/openbis/generic/server/hotfix/ELNFixes.java
@@ -18,8 +18,25 @@ package ch.systemsx.cisd.openbis.generic.server.hotfix;
import static ch.systemsx.cisd.common.spring.ExposablePropertyPlaceholderConfigurer.PROPERTY_CONFIGURER_BEAN_NAME;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.EntityKind;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create.ExperimentCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.IExperimentId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.create.ProjectCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions.ProjectFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.IProjectId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.Space;
import org.apache.log4j.Logger;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
@@ -43,6 +60,7 @@ public class ELNFixes {
public static void beforeUpgrade(String sessionToken) throws Exception {
operationLog.info("ELNFixes beforeUpgrade START");
IApplicationServerInternalApi api = CommonServiceProvider.getApplicationServerApi();
+ storageCollectionIntroduction(sessionToken, api);
storageValidationLevelFix(sessionToken, api);
nameNoRTFFix(sessionToken, api);
// TODO(alaskowski): SSDM-13831: Do migration here!!!
@@ -155,4 +173,126 @@ public class ELNFixes {
operationLog.info(String.format("ELNFixes fixProperties for propertiesTable %s", propertiesTable));
}
+ private static void storageCollectionIntroduction(String sessionToken,
+ IApplicationServerInternalApi api)
+ {
+ SampleSearchCriteria criteria = new SampleSearchCriteria();
+ criteria.withType().withCode().thatEquals("STORAGE_POSITION");
+
+ SampleFetchOptions options = new SampleFetchOptions();
+ options.withSpace();
+ options.withExperiment();
+ options.withProject();
+
+ SearchResult<Sample> storagePositionResults = api.searchSamples(sessionToken, criteria, options);
+
+ Set<ProjectIdentifier> createdProjects = new HashSet<>();
+ Set<ExperimentIdentifier> createdExperiments = new HashSet<>();
+
+ List<SampleUpdate> storagePositionUpdates = new ArrayList<>();
+
+ for (Sample storagePosition:storagePositionResults.getObjects()) {
+ Space space = storagePosition.getSpace();
+ String spaceCode = space.getCode();
+ String postFix = "";
+
+ if (spaceCode.startsWith("STORAGE") && spaceCode.length() > "STORAGE".length())
+ {
+ int start = spaceCode.indexOf("_");
+ postFix = spaceCode.substring(start + 1);
+ }
+
+ ProjectIdentifier projectIdentifier = null;
+
+ if (storagePosition.getProject() == null)
+ {
+ String projectCode = "STORAGE_POSITIONS";
+ if (!postFix.isBlank()) {
+ projectCode += "_" + postFix;
+ }
+ projectIdentifier = new ProjectIdentifier(spaceCode, projectCode);
+
+ if (createdProjects.contains(projectIdentifier) == false)
+ {
+ Map<IProjectId, Project> projects =
+ api.getProjects(sessionToken, Arrays.asList(projectIdentifier),
+ new ProjectFetchOptions());
+
+ System.out.println("PROJECT [FETCH]: " + projectIdentifier + " " + projects.size() + " " + Thread.currentThread().getName());
+
+ if (projects.size() == 1) {
+ createdProjects.add(projectIdentifier);
+ }
+ }
+
+ if (createdProjects.contains(projectIdentifier) == false)
+ {
+ ProjectCreation creation = new ProjectCreation();
+ creation.setSpaceId(space.getPermId());
+ creation.setCode(projectCode);
+ System.out.println("PROJECT [CREATION]: " + creation.getSpaceId() + " " + projectCode + " " + Thread.currentThread().getName());
+ api.createProjects(sessionToken, Arrays.asList(creation));
+ createdProjects.add(projectIdentifier);
+ }
+ } else {
+ projectIdentifier = storagePosition.getProject().getIdentifier();
+ }
+
+ ExperimentIdentifier experimentIdentifier;
+
+ if (storagePosition.getExperiment() == null)
+ {
+ String experimentCode = "STORAGE_POSITIONS_COLLECTION";
+ if (!postFix.isBlank()) {
+ experimentCode += "_" + postFix;
+ }
+ String experimentType = "COLLECTION";
+
+ experimentIdentifier = new ExperimentIdentifier(spaceCode, projectIdentifier.getIdentifier().substring(projectIdentifier.getIdentifier().lastIndexOf('/') + 1), experimentCode);
+
+ if (createdExperiments.contains(experimentIdentifier) == false)
+ {
+ Map<IExperimentId, Experiment> experiments =
+ api.getExperiments(sessionToken, Arrays.asList(experimentIdentifier),
+ new ExperimentFetchOptions());
+
+ System.out.println("EXPERIMENT [FETCH]: " + experimentIdentifier + " " + experiments.size() + " " + Thread.currentThread().getName());
+
+ if (experiments.size() == 1) {
+ createdExperiments.add(experimentIdentifier);
+ }
+ }
+
+ if (createdExperiments.contains(experimentIdentifier) == false)
+ {
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setProjectId(projectIdentifier);
+ creation.setCode(experimentCode);
+ creation.setTypeId(new EntityTypePermId(experimentType, EntityKind.EXPERIMENT));
+ System.out.println("EXPERIMENT [CREATION]: " + creation.getProjectId() + " " + experimentCode + " " + Thread.currentThread().getName());
+ api.createExperiments(sessionToken, Arrays.asList(creation));
+ createdExperiments.add(experimentIdentifier);
+ }
+ } else {
+ experimentIdentifier = storagePosition.getExperiment().getIdentifier();
+ }
+
+ SampleUpdate sampleUpdate = new SampleUpdate();
+ sampleUpdate.setSampleId(storagePosition.getPermId());
+ sampleUpdate.setExperimentId(experimentIdentifier);
+
+ storagePositionUpdates.add(sampleUpdate);
+
+ if (storagePositionUpdates.size() > 1000) {
+ api.updateSamples(sessionToken, storagePositionUpdates);
+ storagePositionUpdates.clear();
+ }
+ }
+
+ if (storagePositionUpdates.isEmpty() == false) {
+ api.updateSamples(sessionToken, storagePositionUpdates);
+ storagePositionUpdates.clear();
+ }
+ }
+
}
diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/as/master-data/common-data-model.xls b/ui-eln-lims/src/core-plugins/eln-lims/1/as/master-data/common-data-model.xls
index 86a4612971080b10dfbf33ebaa8b30de2430e281..d00993ab3e5d6e2edf97a7eb5d7f79cab09d8828 100644
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diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/StorageListView.js b/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/StorageListView.js
index d1100528832..820132f2e90 100644
--- a/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/StorageListView.js
+++ b/ui-eln-lims/src/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/widgets/StorageListView.js
@@ -166,6 +166,7 @@ function StorageListView(storageListController, storageListModel) {
code : uuid,
identifier : null,
sampleTypeCode : "STORAGE_POSITION",
+ experimentIdentifier: null,
properties : {}
};
_this._storageListModel.sample.children.push(newChildSample);
@@ -244,6 +245,11 @@ function StorageListView(storageListController, storageListModel) {
if(sampleChild.newSampleJustCreated) {
sampleChild.identifier = IdentifierUtil.getSampleIdentifier(storageSpaceCode, null, sampleChild.code);
delete sampleChild.newSampleJustCreated;
+ var postFix = "";
+ if(storageSpaceCode.length > "STORAGE".length) {
+ postFix = storageSpaceCode.substring("STORAGE".length + 1);
+ }
+ sampleChild.experimentIdentifier = "/" + storageSpaceCode + "/STORAGE_POSITIONS" + postFix + "/STORAGE_POSITIONS_COLLECTION" + postFix;
} else {
// On update the identifier should be set, fail if not
}
--
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