Added meta data to unstage operation.

nomad/api/upload.py

@@ -89,8 +89,25 @@ upload_with_calcs_model = api.inherit('UploadWithPaginatedCalculations', upload_
     }))
 })
 
+meta_data_model = api.model('MetaData', {
+    'with_embargo': fields.Boolean(default=False, description='Data with embargo is only visible to the upload until the embargo period ended.'),
+    'comments': fields.List(fields.String, description='Comments are shown in the repository for each calculation.'),
+    'references': fields.List(fields.String, descriptions='References allow to link calculations to external source, e.g. URLs.'),
+    'coauthors': fields.List(fields.String, description='A list of co-authors given by user_id.'),
+    'share_with': fields.List(fields.String, description='A list of users to share calculations with given by user_id.')
+})
+
+calc_meta_data_model = api.inherit('CalcMetaData', meta_data_model, {
+    'mainfile': fields.String(description='The calculation main output file is used to identify the calculation in the upload.')
+})
+
+upload_meta_data_model = api.inherit('UploadMetaData', meta_data_model, {
+    'calculations': fields.List(fields.Nested(model=calc_meta_data_model), description='Specific per calculation data that will override the upload data.')
+})
+
 upload_operation_model = api.model('UploadOperation', {
-    'operation': fields.String(description='Currently unstage is the only operation.')
+    'operation': fields.String(description='Currently unstage is the only operation.'),
+    'metadata': fields.Nested(model=upload_meta_data_model, description='Additional upload and calculation meta data that should be considered for the operation')
 })
 
 
@@ -278,8 +295,11 @@ class Upload(Resource):
         """
         Execute an upload operation. Available operations: ``unstage``
 
-        Untage changes the visibility of the upload. Clients can specify, if the calcs
-        should be restricted.
+        Unstage accepts further meta data that allows to provide coauthors, comments,
+        external references, etc.
+
+        Unstage changes the visibility of the upload. Clients can specify the visibility
+        via meta data.
         """
         try:
             upload = UploadProc.get(upload_id)
@@ -294,12 +314,13 @@ class Upload(Resource):
             json_data = {}
 
         operation = json_data.get('operation')
+        meta_data = json_data.get('meta_data', {})
         if operation == 'unstage':
             if not upload.in_staging:
                 abort(400, message='Operation not allowed, upload is not in staging.')
 
             try:
-                upload.unstage()
+                upload.unstage(meta_data)
             except NotAllowedDuringProcessing:
                 abort(400, message='You must not unstage an upload during processing.')
 

nomad/coe_repo.py

@@ -49,15 +49,34 @@ from nomad.repo import RepoCalc
 Base = declarative_base()
 
 
-def add_upload(upload, restricted: bool) -> int:
+class UploadMetaData:
+    def __init__(self, user_meta_data_dict):
+        self._upload_data = user_meta_data_dict
+        self._calc_data = {
+            calc['mainfile']: calc
+            for calc in self._upload_data.get('calculations', [])}
+
+    def get(self, mainfile):
+        return self._calc_data.get(mainfile, self._upload_data)
+
+
+def add_upload(upload, user_meta_data: dict = {}) -> int:
     """
     Add the processed upload to the NOMAD-coe repository db. It creates an
     uploads-entry, respective calculation and property entries. Everything in one
-    transaction. Triggers an updates the NOMAD-coe repository elastic search index after
-    success.
+    transaction.
+
+    Triggers and updates the NOMAD-coe repository elastic search index after
+    success (TODO).
+
+    Arguments:
+        upload: The upload to add
+        upload_meta_data: A dictionary with additional meta data (e.g. user meta data)
+            that should be added to upload and calculations.
 
-    TODO deal with the restricted parameter
+    TODO deal with user_meta_data
     """
+    upload_meta_data = UploadMetaData(user_meta_data)
     repo_db = infrastructure.repository_db
     repo_db.begin()
 
@@ -81,7 +100,8 @@ def add_upload(upload, restricted: bool) -> int:
         has_calcs = False
         for repo_calc in RepoCalc.upload_calcs(upload.upload_id):
             has_calcs = True
-            add_calculation(upload, coe_upload, repo_calc, restricted)
+            add_calculation(
+                upload, coe_upload, repo_calc, upload_meta_data.get(repo_calc.mainfile))
 
         # commit
         if has_calcs:
@@ -101,7 +121,7 @@ def add_upload(upload, restricted: bool) -> int:
     return result
 
 
-def add_calculation(upload, coe_upload, calc: RepoCalc, restricted: bool) -> None:
+def add_calculation(upload, coe_upload, calc: RepoCalc, calc_meta_data: dict) -> None:
     repo_db = infrastructure.repository_db
 
     # table based properties
@@ -133,7 +153,7 @@ def add_calculation(upload, coe_upload, calc: RepoCalc, restricted: bool) -> Non
 
     user_metadata = UserMetaData(
         calc=coe_calc,
-        permission=0 if not restricted else 1)
+        permission=1 if calc_meta_data.get('restricted', False) else 0)
     repo_db.add(user_metadata)
 
     spacegroup = Spacegroup(

nomad/processing/data.py

@@ -420,7 +420,7 @@ class Upload(Chord):
 
         return self
 
-    def unstage(self):
+    def unstage(self, meta_data):
         self.get_logger().info('unstage')
 
         if not (self.completed or self.current_task == 'uploading'):
@@ -428,7 +428,7 @@ class Upload(Chord):
 
         self.in_staging = False
         RepoCalc.unstage(upload_id=self.upload_id)
-        coe_repo.add_upload(self, restricted=False)  # TODO allow users to choose restricted
+        coe_repo.add_upload(self, meta_data)
         self.save()
 
     @process

tests/test_coe_repo.py

@@ -48,10 +48,10 @@ def assert_coe_upload(upload_hash, repository_db, empty=False):
 
 @pytest.mark.timeout(10)
 def test_add_upload(repository_db, processed_upload):
-    coe_upload_id = add_upload(processed_upload, restricted=False)
+    coe_upload_id = add_upload(processed_upload)
     if coe_upload_id:
         assert_coe_upload(processed_upload.upload_hash, repository_db)
 
-    coe_upload_id = add_upload(processed_upload, restricted=False)
+    coe_upload_id = add_upload(processed_upload)
     if coe_upload_id:
         assert_coe_upload(processed_upload.upload_hash, repository_db)