From 82395b5a30893787564bdb700f96df3dc8419bae Mon Sep 17 00:00:00 2001
From: felmer <franz-josef.elmer@id.ethz.ch>
Date: Sat, 18 Feb 2023 08:08:35 +0100
Subject: [PATCH] SSDM-12929: SFTP resolver for microscopy
---
.../eln-tree/resolver-plugins/microscopy.py | 24 ++++++++++
.../file-system-plugins/eln-tree/script.py | 44 +++++++++++++------
2 files changed, 55 insertions(+), 13 deletions(-)
diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/resolver-plugins/microscopy.py b/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/resolver-plugins/microscopy.py
index 36571d8a4e6..e2d4f56fde2 100644
--- a/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/resolver-plugins/microscopy.py
+++ b/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/resolver-plugins/microscopy.py
@@ -1,3 +1,27 @@
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search import DataSetSearchCriteria
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions import DataSetFetchOptions
+
+import script
+
acceptor.hideDataSetType("MICROSCOPY_IMG_CONTAINER")
acceptor.hideDataSetType("MICROSCOPY_IMG_OVERVIEW")
acceptor.hideDataSetType("MICROSCOPY_IMG_THUMBNAIL")
+#acceptor.hideSampleType("MICROSCOPY_SAMPLE_TYPE")
+
+def addSampleChildNodes(path, samplePermId, sampleType, response, acceptor, context):
+ dataSetSearchCriteria = DataSetSearchCriteria()
+ parentsSearchCriteria = dataSetSearchCriteria.withSample().withParents()
+ parentsSearchCriteria.withPermId().thatEquals(samplePermId)
+ fetchOptions = DataSetFetchOptions()
+ fetchOptions.withType()
+ fetchOptions.withProperties()
+ fetchOptions.withSample()
+ dataSets = context.getApi().searchDataSets(context.getSessionToken(), dataSetSearchCriteria, fetchOptions).getObjects()
+ for dataSet in dataSets:
+ if acceptor.acceptDataSet(dataSet):
+ dataSetCode = dataSet.getCode()
+ content = context.getContentProvider().asContent(dataSetCode)
+ contentNode = content.getRootNode()
+ script.addDataSetFileNodes(path, dataSetCode, contentNode, response, acceptor, context)
+
+acceptor.sampleChildrenHandlers["MICROSCOPY_EXPERIMENT"] = addSampleChildNodes
diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/script.py b/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/script.py
index c4d8881db88..f3eb85b9711 100644
--- a/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/script.py
+++ b/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/script.py
@@ -21,10 +21,15 @@ class NodeWithEntityType(Node):
def __init__(self, type, permId, entityType):
super(NodeWithEntityType, self).__init__(type, permId)
self.entityType = entityType
+ self.permIds = set()
+ self.addPermId(permId)
def getEntityType(self):
return self.entityType
+ def addPermId(self, permId):
+ self.permIds.add(permId)
+
class Acceptor(object):
def __init__(self, settings):
self.sections = ["Lab Notebook", "Inventory", "Stock"]
@@ -38,6 +43,7 @@ class Acceptor(object):
self.hiddenExperimentTypes = {}
self.hiddenSampleTypes = {}
self.hiddenDataSetTypes = {}
+ self.sampleChildrenHandlers = {}
def assertValidSection(self, section):
if section not in self.sections:
@@ -234,13 +240,16 @@ def listChildren(subPath, acceptor, context):
nodeType = node.getType()
permId = node.getPermId()
if nodeType == "DATASET":
- dataSetCode, contentNode, content = getContentNode(permId, context)
- if contentNode.isDirectory():
- response = context.createDirectoryResponse()
- addDataSetFileNodes(path, dataSetCode, contentNode, response, acceptor, context)
- return response
- else:
- return context.createFileResponse(contentNode, content)
+ response = None
+ for permId in node.permIds:
+ dataSetCode, contentNode, content = getContentNode(permId, context)
+ if contentNode.isDirectory():
+ if response is None:
+ response = context.createDirectoryResponse()
+ addDataSetFileNodes(path, dataSetCode, contentNode, response, acceptor, context)
+ else:
+ response = context.createFileResponse(contentNode, content)
+ return response
elif nodeType == "SAMPLE":
response = context.createDirectoryResponse()
addSampleChildNodes(path, permId, node.getEntityType(), response, acceptor, context)
@@ -259,11 +268,13 @@ def getNode(subPath, acceptor, context):
nodeType = parentNode.getType()
entityType = parentNode.getEntityType()
permId = parentNode.getPermId()
+ print(">>>>>>>>>> GET NODE: %s, %s, %s" % (path, nodeType, parentNode.permIds))
if nodeType == "EXPERIMENT":
addExperimentChildNodes(parentPathString, permId, entityType, None, acceptor, context)
elif nodeType == "SAMPLE":
addSampleChildNodes(parentPathString, permId, entityType, None, acceptor, context)
elif nodeType == "DATASET":
+ print("====== GET DATASET NODE: %s, %s" % (path, parentNode.permIds))
dataSetCode, contentNode, _ = getContentNode(parentNode.getPermId(), context)
addDataSetFileNodes(parentPathString, dataSetCode, contentNode, None, acceptor, context)
else:
@@ -307,6 +318,9 @@ def addExperimentChildNodes(path, experimentPermId, experimentType, response, ac
addNodes("SAMPLE", entitiesByName, path, response, context)
def addSampleChildNodes(path, samplePermId, sampleType, response, acceptor, context):
+ if sampleType in acceptor.sampleChildrenHandlers:
+ acceptor.sampleChildrenHandlers[sampleType](path, samplePermId, sampleType, response, acceptor, context)
+ return
dataSetSearchCriteria = DataSetSearchCriteria()
dataSetSearchCriteria.withSample().withPermId().thatEquals(samplePermId)
@@ -335,12 +349,16 @@ def addDataSetFileNodes(path, dataSetCode, contentNode, response, acceptor, cont
nodeName = childNode.getName()
filePath = "%s/%s" % (path, nodeName)
filePermId = "%s::%s" % (dataSetCode, childNode.getRelativePath())
- context.getCache().putNode(NodeWithEntityType("DATASET", filePermId, None), filePath)
- if response is not None:
- if childNode.isDirectory():
- response.addDirectory(nodeName, childNode.getLastModified())
- else:
- response.addFile(nodeName, childNode)
+ cachedNode = context.getCache().getNode(filePath)
+ if cachedNode is not None:
+ cachedNode.addPermId(filePermId)
+ else:
+ context.getCache().putNode(NodeWithEntityType("DATASET", filePermId, None), filePath)
+ if response is not None:
+ if childNode.isDirectory():
+ response.addDirectory(nodeName, childNode.getLastModified())
+ else:
+ response.addFile(nodeName, childNode)
def getContentNode(permId, context):
splittedId = permId.split("::")
--
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