added controlled vocabulary when datasettypes are fetched. added experiment...

added controlled vocabulary when datasettypes are fetched. added experiment and properties to dataset upload. added some debug information on server side.

jupyter-openbis-extension/server.py

@@ -2,7 +2,6 @@ from notebook.utils import url_path_join
 from notebook.base.handlers import IPythonHandler
 from pybis import Openbis
 import numpy as np
-
 import os
 from urllib.parse import unquote
 import yaml
@@ -31,8 +30,8 @@ def _load_configuration(paths, filename='openbis-connections.yaml'):
                     config = yaml.safe_load(stream)
                     for connection in config['connections']:
                         connections.append(connection)
-                except yaml.YAMLexception as exc:
-                    print(exc)
+                except yaml.YAMLexception as e:
+                    print(e)
                     return None
 
     return connections
@@ -473,9 +472,14 @@ class DataSetTypesHandler(IPythonHandler):
             # and add it to the dataset collection
             for dt in dts:
                 dataset_type = conn.openbis.get_dataset_type(dt['code'])
-                pa = dataset_type.get_propertyAssignments()
-                pa_dict = pa.to_dict(orient='records')
-                dt['propertyAssignments'] = pa_dict
+                pa = dataset_type.get_propertyAssignments(including_vocabulary=True)
+                pa_dicts = pa.to_dict(orient='records')
+                for pa_dict in pa_dicts:
+                    if pa_dict['dataType'] == 'CONTROLLEDVOCABULARY':
+                        terms = conn.openbis.get_terms(pa_dict['vocabulary']['code'])
+                        pa_dict['terms'] = terms.df[['code','label','description','official','ordinal']].to_dict(orient='records')
+
+                dt['propertyAssignments'] = pa_dicts
 
             self.write({
                 "dataSetTypes": dts
@@ -483,6 +487,7 @@ class DataSetTypesHandler(IPythonHandler):
             return
 
         except Exception as e:
+            print(e)
             self.set_status(500)
             self.write({
                 "reason":'Could not fetch dataset-types: {}'.format(e)
@@ -491,60 +496,112 @@ class DataSetTypesHandler(IPythonHandler):
 
 
 class DataSetUploadHandler(IPythonHandler):
-    """Handle the requests for /openbis/dataset/connection"""
+    """Handle the POST requests for /openbis/dataset/connection_name"""
 
     def upload_data(self, conn, data):
         if not conn.is_session_active():
             try:
                 conn.login()
-            except Exception as exc:
+            except Exception as e:
+                print(e)
+                self.set_status(500)
                 self.write({
-                    "reason": 'connection to {} could not be established: {}'.format(conn.name, exc)
+                    "reason": 'connection to {} could not be established: {}'.format(conn.name, e)
                 })
                 return
 
-        try:
-            sample = conn.openbis.get_sample(data.get('sampleIdentifier'))
-        except Exception as exc:
-            self.set_status(404)
-            self.write({
-                "reason" : 'No such sample: {}'.format(data.get('sampleIdentifier'))
-            })
-            return
+        errors = []
+
+        sample = None
+        experiment = None
+
+        if (data.get('sampleIdentifier')):
+            try:
+                sample = conn.openbis.get_sample(data.get('sampleIdentifier'))
+            except Exception as e:
+                print(e)
+                errors.append(
+                    {"sampleIdentifier" : 'No such sample: {}'.format(data.get('sampleIdentifier')) }
+                )
+        else:
+            errors.append(
+                {"sampleIdentifier": "please provide a sample identifier"}
+            )
+        print("--------------_HERE_-----------1")
+
+        if (data.get('experimentIdentifier')):
+            try:
+                experiment = conn.openbis.get_experiment(data.get('experimentIdentifier'))
+            except Exception as e:
+                print(e)
+                errors.append(
+                    {"experimentIdentifier" : 'No such experiment: {}'.format(data.get('experimentIdentifier')) }
+                )
+        print("--------------_HERE_-----------2")
 
         filenames = []
         for filename in data.get('files'):
             filename = unquote(filename)
-            filenames.append(filename)
+            if os.path.isfile(filename):
+                filenames.append(filename)
+            else:
+                errors.append({
+                    "file": "File not found: {}".format(filename)
+                })
+        print("--------------_HERE_-----------3")
 
-        try: 
-            ds = conn.openbis.new_dataset(
-                name        = data.get('name'),
-                description = data.get('description'),
-                type        = data.get('type'),
-                sample      = sample,
-                files       = filenames
-            ) 
-        except Exception as exc:
-            self.write({
-                "reason": 'Error while creating the dataset: {}'.format(exc)
+        try:
+            dataset = conn.openbis.new_dataset(
+                type   = data.get('type'),
+                sample = sample,
+                experiment = experiment,
+                files  = filenames,
+            )
+        except Exception as e:
+            print(e)
+            errors.append({
+                "create": 'Error while creating the dataset: {}'.format(e)
             })
+        print("--------------_HERE_-----------4")
+
+        # write errors back if already occured
+        if errors:
+            self.set_status(500)
+            self.write({ "errors": errors })
             return
+        print("--------------_HERE_-----------5")
+
+        # try to set the properties
+        if (data.get('props')):
+            props = data.et('props')
+            for prop, value in props.items():
+                try:
+                    setattr(dataset.props, prop, value)
+                except Exception as e:
+                    errors.append({
+                        "prop."+prop : e
+                    })
+        print("--------------_HERE_-----------6")
 
         try:
-            ds.save()
-        except Exception as exc:
+            dataset.save()
+        except Exception as e:
+            errors.append({
+                "save": 'Error while saving the dataset: {}'.format(e)
+            })
+        print("--------------_HERE_-----------7")
+
+        # write errors back if they occured
+        if errors:
+            self.set_status(500)
+            self.write({ "errors": errors })
+        else:
+            # ...or return a success message
             self.write({
-                "reason": 'Error while saving the dataset: {}'.format(exc)
+                'status': 200,
+                'statusText': 'Jupyter Notebook was successfully uploaded to: {} with permId: {}'.format(conn.name, dataset.permId)
             })
-            return
-        
-            
-        # return success message
-        self.write({
-            'status': 200,
-            'statusText': 'Jupyter Notebook was successfully uploaded to: {} with permId: {}'.format(conn.name, ds.permId)
-        })
+        print("--------------_HERE_-----------8")
 
     def post(self, **params):
         """Handle a request to /openbis/dataset/connection_name/permId
@@ -560,4 +617,6 @@ class DataSetUploadHandler(IPythonHandler):
             return
 
         data = self.get_json_body()
-        results = self.upload_data(conn=conn,data=data)
+        print("Received DATA")
+        print(data)
+        self.upload_data(conn=conn,data=data)