diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/Cache.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/Cache.java
index 9b714f3b8895beee4bf4d9a3eae838f47122fa69..157e7b401d99576b876fb1d9f0d42aa5fd4f5ddb 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/Cache.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/Cache.java
@@ -50,6 +50,8 @@ public class Cache
}
}
+ private final Map<String, Node> nodesByPath = new HashMap<>();
+
private final Map<String, TimeStampedObject<FtpFile>> filesByPath = new HashMap<>();
private final Map<String, TimeStampedObject<DataSet>> dataSetsByCode = new HashMap<String, Cache.TimeStampedObject<DataSet>>();
@@ -74,6 +76,16 @@ public class Cache
this.timeProvider = timeProvider;
}
+ public void putNode(Node node, String path)
+ {
+ nodesByPath.put(path, node);
+ }
+
+ public Node getNode(String path)
+ {
+ return nodesByPath.get(path);
+ }
+
public void putFile(FtpFile file, String path)
{
filesByPath.put(path, timestamp(file));
@@ -162,9 +174,16 @@ public class Cache
private <T> T getObject(Map<String, TimeStampedObject<T>> map, String key)
{
TimeStampedObject<T> timeStampedObject = map.get(key);
- return timeStampedObject == null
- || timeProvider.getTimeInMilliseconds() - timeStampedObject.timestamp > LIVE_TIME ? null
- : timeStampedObject.object;
+ if (timeStampedObject == null)
+ {
+ return null;
+ }
+ if (timeProvider.getTimeInMilliseconds() - timeStampedObject.timestamp > LIVE_TIME)
+ {
+ map.remove(key);
+ return null;
+ }
+ return timeStampedObject.object;
}
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/Node.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/Node.java
new file mode 100644
index 0000000000000000000000000000000000000000..92fa3744325dd67c54ad99952be2848d2d4b5489
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/Node.java
@@ -0,0 +1,43 @@
+/*
+ * Copyright 2021 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.generic.server.ftp;
+
+/**
+ * @author Franz-Josef Elmer
+ *
+ */
+public class Node
+{
+ private final String type;
+ private final String permId;
+
+ public Node(String type, String permId)
+ {
+ this.type = type;
+ this.permId = permId;
+ }
+
+ public String getType()
+ {
+ return type;
+ }
+
+ public String getPermId()
+ {
+ return permId;
+ }
+}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/plugin.properties b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..108bd92e19d2d0517881b3a280daeece8970a539
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/plugin.properties
@@ -0,0 +1,3 @@
+resolver-class = ch.systemsx.cisd.openbis.dss.generic.server.fs.plugins.JythonResolver
+code = Lab Notebook
+script-file = script.py
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/script.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/script.py
new file mode 100644
index 0000000000000000000000000000000000000000..5a3a28e26c9fc7901f2c77f56f274b0688772d5f
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/script.py
@@ -0,0 +1,77 @@
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search import SpaceSearchCriteria
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions import SpaceFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.search import ProjectSearchCriteria
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions import ProjectFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search import ExperimentSearchCriteria
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions import ExperimentFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search import SampleSearchCriteria
+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.systemsx.cisd.openbis.dss.generic.server.ftp import Node
+
+def resolve(subPath, context):
+ path = "/".join(subPath)
+ if len(subPath) == 0:
+ return listSpaces(context)
+ space = subPath[0]
+ if len(subPath) == 1:
+ return listProjects(space, context)
+ project = subPath[1]
+ if len(subPath) == 2:
+ return listExperiments(space, project, context)
+ experiment = subPath[2]
+ if len(subPath) == 3:
+ return listExperimentContent(path, context)
+
+def listSpaces(context):
+ spaces = context.getApi().searchSpaces(context.getSessionToken(), SpaceSearchCriteria(), SpaceFetchOptions()).getObjects()
+ response = context.createDirectoryResponse()
+ for space in spaces:
+ response.addDirectory(space.getCode(), space.getModificationDate())
+ return response
+
+def listProjects(space, context):
+ projectSearchCriteria = ProjectSearchCriteria()
+ projectSearchCriteria.withSpace().withCode().thatEquals(space)
+ projects = context.getApi().searchProjects(context.getSessionToken(), projectSearchCriteria, ProjectFetchOptions()).getObjects()
+ response = context.createDirectoryResponse()
+ for project in projects:
+ response.addDirectory(project.getCode(), project.getModificationDate())
+ return response
+
+def listExperiments(space, project, context):
+ searchCriteria = ExperimentSearchCriteria()
+ searchCriteria.withProject().withCode().thatEquals(project)
+ searchCriteria.withProject().withSpace().withCode().thatEquals(space)
+ fetchOptions = ExperimentFetchOptions()
+ fetchOptions.withProperties()
+ experiments = context.getApi().searchExperiments(context.getSessionToken(), searchCriteria, fetchOptions).getObjects()
+ response = context.createDirectoryResponse()
+ for experiment in experiments:
+ nodeName = experiment.getProperties().get("$NAME")
+ if nodeName is None:
+ nodeName = experiment.getCode()
+ path = "%s/%s/%s" % (space, project, nodeName)
+ context.getCache().putNode(Node("EXP", experiment.getPermId().getPermId()), path)
+ response.addDirectory(nodeName, experiment.getModificationDate())
+ return response
+
+def listExperimentContent(path, context):
+ node = context.getCache().getNode(path)
+ experimentPermId = node.getPermId()
+ print("EXP:%s" % experimentPermId)
+ dataSetSearchCriteria = DataSetSearchCriteria()
+ dataSetSearchCriteria.withExperiment().withPermId().thatEquals(experimentPermId)
+ dataSets = context.getApi().searchDataSets(context.getSessionToken(), dataSetSearchCriteria, DataSetFetchOptions()).getObjects()
+ response = context.createDirectoryResponse()
+ for dataSet in dataSets:
+ response.addDirectory(dataSet.getCode(), dataSet.getModificationDate())
+
+ sampleSearchCriteria = SampleSearchCriteria()
+ sampleSearchCriteria.withExperiment().withPermId().thatEquals(experimentPermId)
+ samples = context.getApi().searchSamples(context.getSessionToken(), sampleSearchCriteria, SampleFetchOptions()).getObjects()
+ for sample in samples:
+ response.addDirectory(sample.getCode(), sample.getModificationDate())
+ return response
+
\ No newline at end of file