ENH: Add LIMS support (See #93)

This commit updates CellLocator and Slicer adding support for flags `--lims-specimen-id`
and `--lims-base-url`.

If `--lims-specimen-id` is provided, it is used:
* At application startup time to
   (1) retrieve the corresponding annotation from LIMS and load it by using the `/specimen_metadata/view` endpoint.
   (2) enable the "Upload Annotation" button
* After user initiate annotation upload to LIMS while using the `/specimen_metadata/store` endpoint.

The "kind" parameter for both  endpoints `/specimen_metadata/view` and `/specimen_metadata/store`
is set to "IVSCC cell locations"

IVSCC expected cell count is currently unsupported.

For testing this functionality, a mock server as been implemented. Relevant instructions
are available here: https://github.com/KitwareMedical/AllenInstituteMockLIMS

List of Slicer changes:

$ git shortlog 0661948e5..9b00dc521f --no-merges
David Allemang (1):
      [cell-locator] ENH: Add command line args --lims-specimen-id and --lims-base-url for LIMS integration.

CMakeLists.txt

@@ -13,7 +13,7 @@ if(NOT DEFINED slicersources_SOURCE_DIR)
   # Download Slicer sources and set variables slicersources_SOURCE_DIR and slicersources_BINARY_DIR
   FetchContent_Populate(slicersources
     GIT_REPOSITORY git://github.com/KitwareMedical/Slicer
-    GIT_TAG        0661948e52a7c809002954088bd3a8f847dc888d # cell-locator-v4.11.0-2018-12-19-0dc589ee5
+    GIT_TAG        9b00dc521fa993d0c3f266890fdae90c3c9945ca # cell-locator-v4.11.0-2018-12-19-0dc589ee5
     GIT_PROGRESS   1
     )
 else()

Modules/Scripted/Home/Home.py

@@ -1,7 +1,11 @@
 import os
 import json
 import logging
+import shutil
 import textwrap
+import urllib
+import urllib2
+import urlparse
 
 import vtk, qt, ctk, slicer
 
@@ -124,6 +128,10 @@ def postStartupInitialization():
       if annotationFilePath:
         self.loadAnnotationFile(annotationFilePath)
 
+      limsSpecimenID = slicer.app.commandOptions().limsSpecimenID
+      if limsSpecimenID:
+        self.loadLIMSSpecimen(limsSpecimenID)
+
     qt.QTimer.singleShot(0, lambda: postStartupInitialization())
 
   def isAnnotationSavingRequired(self):
@@ -271,6 +279,96 @@ def loadAnnotationFile(self, filename):
       self.onAnnotationLoaded(loadedNode)
     return success
 
+  def loadAnnotationJson(self, body):
+    tempdir = os.path.join(slicer.app.temporaryPath, 'json')
+    tempfile = os.path.join(tempdir, 'annotation.json')
+
+    if not (os.path.exists(tempdir) and os.path.isdir(tempdir)):
+      os.mkdir(tempdir)
+
+    with open(tempfile, 'w') as f:
+      json.dump(body, f)
+
+    self.loadAnnotationFile(tempfile)
+    self.MarkupsAnnotationNode.GetStorageNode().ResetFileNameList()
+    self.updateGUIFromMRML()
+
+    shutil.rmtree(tempdir)
+
+  def loadLIMSSpecimen(self, specimenID):
+    logging.info('Loading LIMS specimen id %s', specimenID)
+
+    base = slicer.app.commandOptions().limsBaseURL or 'http://localhost:5000/'
+    path = '/specimen_metadata/view'
+    url = urlparse.urljoin(base, path)
+
+    query = urllib.urlencode({
+      'kind': 'IVSCC cell locations',
+      'specimen_id': specimenID
+    })
+
+    try:
+      res = urllib2.urlopen('%s?%s' % (url, query))
+    except urllib2.URLError as e:
+      logging.error('Failed to connect to LIMS server.')
+      return
+
+    if res.getcode() != 200:
+      logging.error('Failed to load specimen ID %s from LIMS server.', specimenID)
+      return
+
+    body = json.loads(res.read())
+
+    self.loadAnnotationJson(body['data']['data'])
+
+  def onUploadAnnotationButtonClicked(self):
+    logging.info('Upload Annotation Button Clicked')
+
+    limsSpecimenID = slicer.app.commandOptions().limsSpecimenID
+    self.saveLIMSSpecimen(self.MarkupsAnnotationNode, limsSpecimenID)
+
+  def saveLIMSSpecimen(self, annotationNode, specimenID):
+    logging.info('Saving LIMS specimen id %s', specimenID)
+
+    data = self.saveAnnotationJson(annotationNode)
+
+    base = slicer.app.commandOptions().limsBaseURL or 'http://localhost:5000/'
+    path = '/specimen_metadata/store'
+    url = urlparse.urljoin(base, path)
+
+    body = json.dumps({
+      'kind': 'IVSCC cell locations',
+      'specimen_id': specimenID,
+      'data': data
+    })
+
+    try:
+      res = urllib2.urlopen(url, data=body)
+    except urllib2.URLError as e:
+      logging.error('Failed to connect to LIMS server')
+      return
+
+    if res.getcode() != 200:
+      logging.error('Failed to store specimen ID %s to LIMS server.', specimenID)
+
+  def saveAnnotationJson(self, annotationNode):
+    tempdir = os.path.join(slicer.app.temporaryPath, 'json')
+    tempfile = os.path.join(tempdir, 'annotation.json')
+
+    if not (os.path.exists(tempdir) and os.path.isdir(tempdir)):
+      os.mkdir(tempdir)
+
+    slicer.util.saveNode(annotationNode, tempfile)
+    self.logic.annotationStored(annotationNode)
+    self.updateGUIFromMRML()
+
+    with open(tempfile, 'r') as f:
+      data = json.load(f)
+
+    shutil.rmtree(tempdir)
+
+    return data
+
   def onAnnotationLoaded(self, newAnnotationNode):
 
     sliceNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeSlice')
@@ -987,6 +1085,7 @@ def setupConnections(self):
     self.get('SaveAnnotationButton').connect("clicked()", self.onSaveAnnotationButtonClicked)
     self.get('SaveAsAnnotationButton').connect("clicked()", self.onSaveAsAnnotationButtonClicked)
     self.get('LoadAnnotationButton').connect("clicked()", self.onLoadAnnotationButtonClicked)
+    self.get('UploadAnnotationButton').connect("clicked()", self.onUploadAnnotationButtonClicked)
 
     self.get('ResetFieldOfViewButton').connect("clicked()", self.resetFieldOfView)
     self.get('ReferenceViewComboBox').connect("currentTextChanged(QString)", self.setReferenceView)

Modules/Scripted/Home/Resources/UI/Home.ui

@@ -139,6 +139,22 @@
             </item>
            </layout>
           </item>
+          <item>
+           <layout class="QHBoxLayout" name="horizontalLayout_8">
+            <item>
+             <widget class="QPushButton" name="UploadAnnotationButton">
+              <property name="text">
+               <string>Save to LIMS</string>
+              </property>
+              <property name="icon">
+               <iconset>
+                <normalon>:/Icons/save_icon.svg.png</normalon>
+               </iconset>
+              </property>
+             </widget>
+            </item>
+           </layout>
+          </item>
           <item>
            <widget class="ctkPathLineEdit" name="AnnotationPathLineEdit">
             <property name="enabled">