Merge remote-tracking branch 'origin/master'

README.md

@@ -62,9 +62,10 @@ openbis.bundle.min.js
 
 ## Requirements
 
+- Software Requirements
 - IntelliJ IDEA CE
 
-## Step By Step:
+## Step By Step
 
 ```
 File -> New -> Project From Existing Sources
@@ -76,6 +77,50 @@ openBISDevelopementEnvironmentASStart
 openBISDevelopementEnvironmentDSSStart
 ```
 
+## Source Code Auto Formatting
+
+OpenBIS source code uses a particular style preset that guarantees all code is formatted uniformly.
+
+To make use of the preset go to File/Settings or IntelliJIDEA/Preferences depending on your OS.
+
+Then import the XML file under 'docs/codestyle/SIS_Conventions_IntelliJ_V3.xml'. See images below:
+
+!["IntelliJ Code Style Configuration 1"](./docs/readme/intellij-codestyle-config-1.png "IntelliJ Code Style Configuration 1")
+!["IntelliJ Code Style Configuration 2"](./docs/readme/intellij-codestyle-config-2.png "IntelliJ Code Style Configuration 2")
+!["IntelliJ Code Style Configuration 3"](./docs/readme/intellij-codestyle-config-3.png "IntelliJ Code Style Configuration 3")
+!["IntelliJ Code Style Configuration 4"](./docs/readme/intellij-codestyle-config-4.png "IntelliJ Code Style Configuration 4")
+
+## Commit Messages Formatting
+
+OpenBIS source code commit messages use a particular formatting.
+
+This formatting guarantees that there is a User Story behind it.
+
+To ensure commits follow the formatting 'Git Hooks' are provided.
+
+Just copy them from the root folder of this repo run the next command:
+````
+%/> cp ./docs/hooks/* ./.git/hooks/   
+%/> git add README.md
+%/> git commit -m "Test incorrectly formatted message"
+Aborting commit. Your commit message is missing an issue number ('SSDM-XXXXX:')
+````
+
+## Source Code Copyright Header
+
+OpenBIS source code is licensed under SIS copyright and licensed under 'Apache 2 License':
+````
+http://www.apache.org/licenses/LICENSE-2.0
+````
+To guarantee all new source files contain the appropriate license a preset is provided.
+
+To make use of the preset go to File/Settings or IntelliJIDEA/Preferences depending on your OS.
+
+Then import the XML file under 'docs/copyright/Copyright_IntelliJ.xml' under the copyright section as the image below indicate.
+!["IntelliJ Copyright Configuration 1"](./docs/readme/intellij-copyright-config-1.png "IntelliJ Copyright Configuration 1")
+Last, set the Copyright Profile under the Copyright section as the image below indicate:
+!["IntelliJ Copyright Configuration 2"](./docs/readme/intellij-copyright-config-2.png "IntelliJ Copyright Configuration 2")
+
 ## Typical Errors
 
 # IntelliJ can't find package com.sun.*, but I can compile the project using the command line!
@@ -83,22 +128,19 @@ openBISDevelopementEnvironmentDSSStart
 Turn off "File | Settings | Build, Execution, Deployment | Compiler | Java Compiler | Use --release
 option for cross-compilation".
 
-# IntelliJ can't find a particular method:
+# IntelliJ can't find a particular method
 
 Code compatiblity 1.8 is set by default to work well with our javadoc tools but it can be set to 17 on IntelliJ. See image below.
-
 !["IntelliJ Configuration 1"](./docs/readme/intellij-config-1.png "IntelliJ Configuration 1")
 
-# Test seem to run through Gradle and fail:
+# Test seem to run through Gradle and fail
 
 They need to be set to run using IntelliJ.
-
 !["IntelliJ Configuration 2"](./docs/readme/intellij-config-2.png "IntelliJ Configuration 2")
 
-# Test seem to run through intelliJ but throw a package not open error:
+# Test seem to run through intelliJ but throw a package not open error
 
 The project does not uses modules yet. Add '--add-opens' statements manually when launching the tests as shown below.
-
 !["IntelliJ Configuration 3"](./docs/readme/intellij-config-3.png "IntelliJ Configuration 3")
 
 ## Development of NG UI
@@ -119,33 +161,4 @@ The project does not uses modules yet. Add '--add-opens' statements manually whe
 ## Setting up IntelliJ Idea
 
 1. Under "IntelliJ IDEA" -> "Preferences" -> "Languages and Frameworks" -> Javascript, set the
-   language version to ECMAScript 6.
-
-## Coding Style
-
-openBIS source code uses a particular style preset that guarantees all code is formatted uniformly.
-
-To make use of the preset go to File/Settings or IntelliJIDEA/Preferences depending on your OS.
-
-Then import the XML file under 'docs/CISD_Conventions_IntelliJ_V2.xml'. See images below.
-
-!["IntelliJ Code Style Configuration 1"](./docs/readme/intellij-codestyle-config-1.png "IntelliJ Code Style Configuration 1")
-!["IntelliJ Code Style Configuration 2"](./docs/readme/intellij-codestyle-config-2.png "IntelliJ Code Style Configuration 2")
-!["IntelliJ Code Style Configuration 3"](./docs/readme/intellij-codestyle-config-3.png "IntelliJ Code Style Configuration 3")
-!["IntelliJ Code Style Configuration 4"](./docs/readme/intellij-codestyle-config-4.png "IntelliJ Code Style Configuration 4")
-
-## Git Hooks
-
-openBIS source code commit messages use a particular formatting.
-
-This formatting guarantees that there is a User Story behind it.
-
-To ensure commits follow the formatting 'Git Hooks' are provided.
-
-Just copy them from the root folder of this repo run the next command:
-````
-%/> cp ./docs/hooks/* ./.git/hooks/   
-%/> git add README.md
-%/> git commit -m "Test incorrectly formatted message"
-Aborting commit. Your commit message is missing an issue number ('SSDM-XXXXX:')
-````
\ No newline at end of file
+   language version to ECMAScript 6.
\ No newline at end of file

docs/copyright/Copyright_IntelliJ.xml

 <component name="CopyrightManager">
   <copyright>
     <option name="notice" value=" Copyright ETH &amp;#36;originalComment.match(&quot;Copyright ETH (\d+)&quot;, 1, &quot; - &quot;, &quot;&amp;#36;today.year&quot;)&amp;#36;today.year Zürich, Scientific IT Services&#10; &#10; Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);&#10; you may not use this file except in compliance with the License.&#10; You may obtain a copy of the License at&#10; &#10;      http://www.apache.org/licenses/LICENSE-2.0&#10;  &#10; Unless required by applicable law or agreed to in writing, software&#10; distributed under the License is distributed on an &quot;AS IS&quot; BASIS,&#10; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.&#10; See the License for the specific language governing permissions and&#10; limitations under the License.&#10;" />
-    <option name="myName" value="Copyright" />
+    <option name="myName" value="Copyright SIS - License Apache 2" />
   </copyright>
 </component>
\ No newline at end of file

ui-eln-lims/src/core-plugins/eln-lims/1/dss/file-system-plugins/eln-tree/resolver-plugins/microscopy.py

+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

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:
@@ -93,15 +99,7 @@ class Acceptor(object):
         self.hiddenSampleTypes[typeCode] = True
 
     def acceptSample(self, sample):
-        group = self._getGroupPrefix(sample.getSpace().getCode())
-        attributes = self.sampleTypeViewAttributes[group]
-        sampleTypeCode = sample.getType().getCode()
-        if sampleTypeCode in self.hiddenSampleTypes:
-            return False
-        if sampleTypeCode in attributes:
-            attr = attributes[sampleTypeCode]
-            return "SHOW_ON_NAV" in attr and attr["SHOW_ON_NAV"]
-        return False
+        return sample.getType().getCode() not in self.hiddenSampleTypes
 
     def hideDataSetType(self, typeCode):
         self.hiddenDataSetTypes[typeCode] = True
@@ -234,13 +232,16 @@ 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 +260,13 @@ 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 +310,9 @@ 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 +341,16 @@ 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("::")