From b8be8adb580932d4d51b286b377d2ed2349eb919 Mon Sep 17 00:00:00 2001
From: felmer <franz-josef.elmer@id.ethz.ch>
Date: Thu, 5 Jul 2018 14:56:03 +0200
Subject: [PATCH] SSDM-6881: introduce 'createSampleIdentifier' and use it in
ELN-LIMS-API
---
.../reporting-plugins/eln-lims-api/script.py | 22 ++++++++++++-------
1 file changed, 14 insertions(+), 8 deletions(-)
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/eln-lims-api/script.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/eln-lims-api/script.py
index a81b5551451..84980ec570c 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/eln-lims-api/script.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/eln-lims-api/script.py
@@ -103,7 +103,10 @@ def getDirectLinkURL():
"sftp" : sftpConfig
});
-
+def createSampleIdentifier(sampleSpace, sampleProject, sampleCode, projectSamplesEnabled):
+ template = '/%(sampleSpace)s/%(sampleProject)s/%(sampleCode)s' if projectSamplesEnabled else '/%(sampleSpace)s/%(sampleCode)s'
+ return template % vars()
+
def isSampleTypeAvailable(sampleTypes, sampleTypeCode):
for sampleType in sampleTypes:
if sampleType.getCode() == sampleTypeCode:
@@ -199,7 +202,7 @@ def process(tr, parameters, tableBuilder):
projectSamplesEnabled = v3.getServerInformation(sessionToken)['project-samples-enabled'] == 'true'
if method == "init":
- isOk = init(tr, parameters, tableBuilder);
+ isOk = init(tr, projectSamplesEnabled, parameters, tableBuilder);
if method == "isFileAuthUser":
result = isFileAuthUser(tr, parameters, tableBuilder);
isOk = True;
@@ -431,7 +434,7 @@ def insertSampleIfMissing(tr, sampleIdentifier, experiment, sampleType, properti
sample.setPropertyValue(key, properties[key]);
return sample;
-def init(tr, parameters, tableBuilder):
+def init(tr, projectSamplesEnabled, parameters, tableBuilder):
projectsCache = {};
installedTypes = getSampleTypes(tr, parameters);
inventorySpace = tr.getSpace("DEFAULT_LAB_NOTEBOOK");
@@ -470,7 +473,8 @@ def init(tr, parameters, tableBuilder):
if isFirstTimeInstallingStorage:
insertProjectIfMissing(tr, "/ELN_SETTINGS/STORAGES", projectsCache);
storageCollection = insertExperimentIfMissing(tr, "/ELN_SETTINGS/STORAGES/STORAGES_COLLECTION", "COLLECTION", "Storages Collection");
- bench = insertSampleIfMissing(tr, "/ELN_SETTINGS/BENCH", storageCollection, "STORAGE", None);
+ benchIdentifier = createSampleIdentifier("ELN_SETTINGS", "STORAGES", "BENCH", projectSamplesEnabled)
+ bench = insertSampleIfMissing(tr, benchIdentifier, storageCollection, "STORAGE", None);
bench.setPropertyValue("NAME", "Bench");
bench.setPropertyValue("ROW_NUM", "1");
bench.setPropertyValue("COLUMN_NUM", "1");
@@ -479,7 +483,8 @@ def init(tr, parameters, tableBuilder):
bench.setPropertyValue("BOX_SPACE_WARNING", "80");
bench.setPropertyValue("STORAGE_VALIDATION_LEVEL", "BOX_POSITION");
- defaultStorage = insertSampleIfMissing(tr, "/ELN_SETTINGS/DEFAULT_STORAGE", storageCollection, "STORAGE", None);
+ defaultStorageIdentifier = createSampleIdentifier("ELN_SETTINGS", "STORAGES", "DEFAULT_STORAGE", projectSamplesEnabled)
+ defaultStorage = insertSampleIfMissing(tr, defaultStorageIdentifier, storageCollection, "STORAGE", None);
defaultStorage.setPropertyValue("NAME", "Default Storage");
defaultStorage.setPropertyValue("ROW_NUM", "4");
defaultStorage.setPropertyValue("COLUMN_NUM", "4");
@@ -747,8 +752,9 @@ def copyAndLinkAsParent(tr, parameters, tableBuilder):
def copySample(tr, projectSamplesEnabled, parameters, tableBuilder):
#Store Children to copy later
sampleSpace = parameters.get("sampleSpace"); #String
+ sampleProject = parameters.get("sampleProject"); #String
sampleCode = parameters.get("sampleCode"); #String
- sampleIdentifier = '/' + sampleSpace + '/' + sampleCode;
+ sampleIdentifier = createSampleIdentifier(sampleSpace, sampleProject, sampleCode, projectSamplesEnabled)
sampleChildren = parameters.get("sampleChildren"); #List<String> Identifiers are in SPACE/CODE format
parameters.put("sampleChildren", []); #List<String> Identifiers are in SPACE/CODE format
@@ -769,7 +775,7 @@ def copySample(tr, projectSamplesEnabled, parameters, tableBuilder):
except: #For all other children
copyChildCode = parameters.get("sampleCode") + "_" + child.getCode();
- copyChildIdentifier = "/" + parameters.get("sampleSpace") + "/" + copyChildCode;
+ copyChildIdentifier = createSampleIdentifier(sampleSpace, sampleProject, copyChildCode, projectSamplesEnabled)
# Create new sample children
childCopy = tr.createNewSample(copyChildIdentifier, child.getSampleType()); #Create Sample given his id
@@ -832,7 +838,7 @@ def insertUpdateSample(tr, projectSamplesEnabled, parameters, tableBuilder):
sampleParentsNew = parameters.get("sampleParentsNew");
#Create/Get for update sample
- sampleIdentifier = ('/%(sampleSpace)s/%(sampleProject)s/%(sampleCode)s' if projectSamplesEnabled else '/%(sampleSpace)s/%(sampleCode)s') % vars()
+ sampleIdentifier = createSampleIdentifier(sampleSpace, sampleProject, sampleCode, projectSamplesEnabled)
method = parameters.get("method");
if method == "insertSample":
--
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