From f4b301d5bdeebdfe3c747b1732dfb2c2a475e4b8 Mon Sep 17 00:00:00 2001
From: felmer <franz-josef.elmer@id.ethz.ch>
Date: Fri, 31 Mar 2023 09:54:03 +0200
Subject: [PATCH] SSDM-13489: wrapping data sets in hierarchical content:
instead of calling AS for each data set only one call for all data sets is
invoked
---
.../eln-tree/resolver-plugins/flow.py | 14 +++--
.../eln-tree/resolver-plugins/microscopy.py | 7 ++-
.../file-system-plugins/eln-tree/script.py | 53 ++++++++++++++++++-
3 files changed, 60 insertions(+), 14 deletions(-)
diff --git a/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/resolver-plugins/flow.py b/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/resolver-plugins/flow.py
index 5e1141655e9..32ffa0c8dae 100644
--- a/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/resolver-plugins/flow.py
+++ b/ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/resolver-plugins/flow.py
@@ -2,22 +2,20 @@ import script
def addSampleChildNodes(path, samplePermId, sampleType, response, acceptor, context):
dataSets = script.getDataSetsOfSampleAndItsChildren(samplePermId, context)
+ filteredDataSets = []
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)
+ filteredDataSets.append(dataSet)
+ script.addDataSetFileNodesFor(path, filteredDataSets, response, acceptor, context)
def addSampleChildNodesWithPlates(path, samplePermId, sampleType, response, acceptor, context):
dataSets = script.getDataSetsOfSampleAndItsChildren(samplePermId, context)
+ filteredDataSets = []
for dataSet in dataSets:
sampleTypeCode = dataSet.getSample().getType().getCode()
if not sampleTypeCode.endswith("_WELL"):
- dataSetCode = dataSet.getCode()
- content = context.getContentProvider().asContent(dataSetCode)
- contentNode = content.getRootNode()
- script.addDataSetFileNodes(path, dataSetCode, contentNode, response, acceptor, context)
+ filteredDataSets.append(dataSet)
+ script.addDataSetFileNodesFor(path, filteredDataSets, response, acceptor, context)
script.addSampleSampleChildNodes(path, samplePermId, response, acceptor, context)
for t in ["FACS_ARIA", "INFLUX", "MOFLO_XDP", "S3E", "SONY_SH800S", "SONY_MA900"]:
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 7429a9d6a6d..272ec466926 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
@@ -7,11 +7,10 @@ acceptor.hideDataSetType("MICROSCOPY_IMG_THUMBNAIL")
def addSampleChildNodes(path, samplePermId, sampleType, response, acceptor, context):
dataSets = script.getDataSetsOfSampleAndItsChildren(samplePermId, context)
+ filteredDataSets = []
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)
+ filteredDataSets.append(dataSet)
+ script.addDataSetFileNodesFor(path, filteredDataSets, 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 c94b6c7577d..fa1a17da033 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
@@ -15,6 +15,10 @@ from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search import SampleSearchC
from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions import SampleFetchOptions
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
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id import DataSetPermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset import DataSetKind
+from ch.systemsx.cisd.openbis.generic.shared.basic.dto import PhysicalDataSet
+from ch.systemsx.cisd.openbis.generic.shared.basic.dto import DataStore
from ch.systemsx.cisd.openbis.dss.generic.server.ftp import Node
class NodeWithEntityType(Node):
@@ -233,8 +237,8 @@ def listChildren(subPath, acceptor, context):
permId = node.getPermId()
if nodeType == "DATASET":
response = None
- for permId in node.permIds:
- dataSetCode, contentNode, content = getContentNode(permId, context)
+ contentNodes = getContentNodes(node.permIds, context)
+ for dataSetCode, contentNode, content in contentNodes:
if contentNode.isDirectory():
if response is None:
response = context.createDirectoryResponse()
@@ -352,6 +356,49 @@ def addDataSetFileNodes(path, dataSetCode, contentNode, response, acceptor, cont
else:
response.addFile(nodeName, childNode)
+def addDataSetFileNodesFor(path, dataSets, response, acceptor, context):
+ contentNodes = asContentNodes(dataSets, context)
+ for dataSetCode, contentNode, _ in contentNodes:
+ addDataSetFileNodes(path, dataSetCode, contentNode, response, acceptor, context)
+
+def getContentNodes(permIds, context):
+ ids = []
+ paths = []
+ for permId in permIds:
+ splittedId = permId.split("::")
+ ids.append(DataSetPermId(splittedId[0]))
+ paths.append(splittedId[1] if len(splittedId) > 1 else None)
+
+ fetchOptions = DataSetFetchOptions()
+ fetchOptions.withDataStore()
+ fetchOptions.withPhysicalData()
+ dataSets = context.getApi().getDataSets(context.getSessionToken(), ids, fetchOptions).values()
+ return asContentNodes(dataSets, context, paths)
+
+def asContentNodes(dataSets, context, paths=None):
+ result = []
+ contentProvider = context.getContentProvider()
+ for i in range(len(dataSets)):
+ dataSet = dataSets[i]
+ dataSetCode = dataSet.getCode()
+ dataStore = DataStore()
+ dataStore.setCode(dataSet.getDataStore().getCode())
+ dataStore.setHostUrl(dataSet.getDataStore().getDownloadUrl())
+ kind = dataSet.getKind()
+ if kind == DataSetKind.PHYSICAL:
+ physicalData = dataSet.getPhysicalData()
+ physicalDataSet = PhysicalDataSet()
+ physicalDataSet.setCode(dataSetCode)
+ physicalDataSet.setLocation(physicalData.getLocation())
+ physicalDataSet.setDataStore(dataStore)
+ physicalDataSet.setShareId(physicalData.getShareId())
+ content = contentProvider.asContentWithoutModifyingAccessTimestamp(physicalDataSet)
+ contentNode = content.getRootNode() if paths is None or paths[i] is None else content.tryGetNode(paths[i])
+ result.append((dataSetCode, contentNode, content))
+ else:
+ raise Exception("Not supported data set kind: %s" % kind)
+ return result
+
def getContentNode(permId, context):
splittedId = permId.split("::")
dataSetCode = splittedId[0]
@@ -366,6 +413,8 @@ def getDataSetsOfSampleAndItsChildren(samplePermId, context):
parentsSearchCriteria = dataSetSearchCriteria.withSample().withParents()
parentsSearchCriteria.withPermId().thatEquals(samplePermId)
fetchOptions = DataSetFetchOptions()
+ fetchOptions.withDataStore()
+ fetchOptions.withPhysicalData()
fetchOptions.withType()
fetchOptions.withProperties()
fetchOptions.withSample().withType()
--
GitLab