Merge pull request #93 from appukuttan-shailesh/master

Multiple changes

hbp_validation_framework/datastores.py

@@ -26,7 +26,7 @@
 
 import requests
 
-import hbp_seafile
+import ebrains_drive
 
 mimetypes.init()
 
@@ -49,8 +49,8 @@ class CollabV2DataStore(object):
     A class for uploading and downloading data from HBP Collaboratory v2 seafile storage.
     """
 
-    def __init__(self, project_id=None, base_folder="/", auth=None, **kwargs):
-        self.project_id = project_id
+    def __init__(self, collab_id=None, base_folder="/", auth=None, **kwargs):
+        self.collab_id = collab_id
         self.base_folder = base_folder.strip("/")
         self._auth = auth  # we defer authorization until needed
         self._authorized = False
@@ -62,9 +62,9 @@ def authorized(self):
     def authorize(self, auth=None):
         if auth is None:
             auth = self._auth
-        self.client = hbp_seafile.connect(token=auth.token)
+        self.client = ebrains_drive.connect(token=auth.token)
         self._authorized = True
-        self.repo = self.client.repos.get_repo_by_url(self.project_id)
+        self.repo = self.client.repos.get_repo_by_url(self.collab_id)
 
     def upload_data(self, file_paths, overwrite=False):
         if not self.authorized:
@@ -93,7 +93,8 @@ def upload_data(self, file_paths, overwrite=False):
             filename = os.path.basename(relative_path)
             seafdir = self.repo.get_dir(parent)
             file_entity = seafdir.upload_local_file(local_path, overwrite=overwrite)
-            uploaded_file_paths.append(upload_path_prefix + file_entity.path)
+            uploaded_file_paths.append({"filepath": upload_path_prefix + file_entity.path, "filesize": file_entity.size})
+            # uploaded_file_paths.append(file_entity._get_download_link()) # this does not work as the link changes with token
         return uploaded_file_paths
 
     def _make_folders(self, folder_path, parent):
@@ -205,7 +206,7 @@ def load_data(self, remote_path):
 
 class SwiftDataStore(object):
     """
-    A class for downloading data from CSCS Swift storage.
+    A class for uploading and downloading data from CSCS Swift storage.
     Note: data from public containers can also be downloaded via `HTTPDataStore`
     """
 
@@ -228,7 +229,10 @@ def upload_data(self, file_paths, username="", container="", project=None, remot
             container = input("Please enter target container name: ")
         container_obj = Container(container, username, project=project)
         remote_paths = container_obj.upload(file_paths, remote_directory=remote_directory, overwrite=overwrite)
-        return remote_paths
+        uploaded_file_paths = []
+        for ind, f in enumerate(file_paths):
+            uploaded_file_paths.append({"filepath": remote_paths[ind], "filesize": os.path.getsize(f)})
+        return uploaded_file_paths
 
     def get_container(self, remote_path, username=""):
         try:

hbp_validation_framework/utils.py

@@ -278,7 +278,7 @@ def run_test_offline(model="", test_config_file=""):
         pickle.dump(score, file)
     return test_result_file
 
-def upload_test_result(username="", password=None, environment="production", test_result_file="", storage_project_id="", register_result=True, client_obj=None):
+def upload_test_result(username="", password=None, environment="production", test_result_file="", storage_collab_id="", register_result=True, client_obj=None):
     """Register the result with the Validation Service
 
     This method will register the validation result specified via the test result file
@@ -298,7 +298,7 @@ def upload_test_result(username="", password=None, environment="production", tes
         be read (the latter is currently not implemented).
     test_result_file : string
         Absolute path of the test result file generated by :meth:`run_test_offline`
-    storage_project_id : string
+    storage_collab_id : string
         Collab ID where output files should be stored; if empty, stored in model's host Collab.
     register_result : boolean
         Specify whether the test results are to be scored on the validation framework.
@@ -315,8 +315,8 @@ def upload_test_result(username="", password=None, environment="production", tes
 
     Returns
     -------
-    UUID
-        UUID of the test result that has been created.
+    dict
+        data of test result that has been created.
     object
         score object evaluated by the test.
 
@@ -340,15 +340,15 @@ def upload_test_result(username="", password=None, environment="production", tes
         model_catalog = ModelCatalog.from_existing(client_obj)
     else:
         model_catalog = ModelCatalog(username, password, environment=environment)
-    model_instance_uuid = model_catalog.find_model_instance_else_add(score.model)
+    model_instance_uuid = model_catalog.find_model_instance_else_add(score.model)["id"]
     model_instance_json = model_catalog.get_model_instance(instance_id=model_instance_uuid)
     model_json = model_catalog.get_model(model_id=model_instance_json["model_id"])
-    model_host_project_id = model_json["project_id"]
+    model_host_collab_id = model_json["collab_id"]
     model_name = model_json["name"]
 
-    if not storage_project_id:
-        storage_project_id = model_host_project_id
-    score.related_data["project_id"] = storage_project_id
+    if not storage_collab_id:
+        storage_collab_id = model_host_collab_id
+    score.related_data["collab_id"] = storage_collab_id
 
     # Check if result with same hash has already been uploaded for
     # this (model instance, test instance) combination; if yes, don't register result
@@ -369,14 +369,14 @@ def upload_test_result(username="", password=None, environment="production", tes
 
     # `.replace(" ", "_")` used to avoid Collab storage path errors due to spaces
     collab_folder = "validation_results/{}/{}_{}".format(datetime.now().strftime("%Y-%m-%d"),model_name.replace(" ", "_"), datetime.now().strftime("%Y%m%d-%H%M%S"))
-    collab_storage = CollabV2DataStore(project_id=storage_project_id,
+    collab_storage = CollabV2DataStore(collab_id=storage_collab_id,
                                        base_folder=collab_folder,
                                        auth=test_library.auth)
 
     response = test_library.register_result(test_result=score, data_store=collab_storage)
     return response, score
 
-def run_test(username="", password=None, environment="production", model="", test_instance_id="", test_id="", test_alias="", test_version="", storage_project_id="", register_result=True, client_obj=None, **params):
+def run_test(username="", password=None, environment="production", model="", test_instance_id="", test_id="", test_alias="", test_version="", storage_collab_id="", register_result=True, client_obj=None, **params):
     """Run validation test and register result
 
     This will execute the following methods by relaying the output of one to the next:
@@ -406,7 +406,7 @@ def run_test(username="", password=None, environment="production", model="", tes
         User-assigned unique identifier associated with test definition.
     test_version : string
         User-assigned identifier (unique for each test) associated with test instance.
-    storage_project_id : string
+    storage_collab_id : string
         Collab ID where output files should be stored; if empty, stored in model's host Collab.
     register_result : boolean
         Specify whether the test results are to be scored on the validation framework.
@@ -425,24 +425,24 @@ def run_test(username="", password=None, environment="production", model="", tes
 
     Returns
     -------
-    UUID
-        UUID of the test result that has been created.
+    dict
+        data of test result that has been created.
     object
         score object evaluated by the test.
 
     Examples
     --------
-    >>> result_id, score = utils.run_test(username="HBP_USERNAME", password="HBP_PASSWORD" environment="production", model=cell_model, test_alias="basalg_msn_d1", test_version="1.0", storage_project_id="8123", register_result=True)
+    >>> result_id, score = utils.run_test(username="HBP_USERNAME", password="HBP_PASSWORD" environment="production", model=cell_model, test_alias="basalg_msn_d1", test_version="1.0", storage_collab_id="8123", register_result=True)
     """
 
     test_config_file = prepare_run_test_offline(username=username, password=password, environment=environment, test_instance_id=test_instance_id, test_id=test_id, test_alias=test_alias, test_version=test_version, client_obj=client_obj, **params)
     test_result_file = run_test_offline(model=model, test_config_file=test_config_file)
-    result_id, score = upload_test_result(username=username, password=password, environment=environment, test_result_file=test_result_file, storage_project_id=storage_project_id, register_result=register_result, client_obj=client_obj)
+    result_id, score = upload_test_result(username=username, password=password, environment=environment, test_result_file=test_result_file, storage_collab_id=storage_collab_id, register_result=register_result, client_obj=client_obj)
     return result_id, score
 
 def generate_HTML_report(username="", password=None, environment="production", model_list=[],
                          model_instance_list=[], test_list=[], test_instance_list=[],
-                         result_list=[], project_id=None, client_obj=None):
+                         result_list=[], show_links=True, client_obj=None):
     """Generates an HTML report for specified test results
 
     This method will generate an HTML report for the specified test results.
@@ -467,9 +467,9 @@ def generate_HTML_report(username="", password=None, environment="production", m
         List of test instance UUIDs for which score matrix is to be generated.
     result_list : list
         List of result UUIDs for which score matrix is to be generated.
-    project_id : string, optional
-        Collaboratory ID where hyperlinks to results are to be redirected.
-        If unspecified, these data units will not have clickable hyperlinks.
+    show_links : boolean, optional
+        To specify if hyperlinks to results are to be provided.
+        If false, these data units will not have clickable hyperlinks.
     client_obj : ModelCatalog/TestLibrary object
         Used to easily create a new ModelCatalog/TestLibrary object if either exist already.
         Avoids need for repeated authentications; improves performance. Also, helps minimize
@@ -502,13 +502,6 @@ def generate_HTML_report(username="", password=None, environment="production", m
         model_catalog = ModelCatalog(username, password, environment=environment)
     test_library = TestLibrary.from_existing(model_catalog)
 
-    if project_id:
-        # check if app exists; if not then create
-        MCapp_navID = model_catalog.exists_in_collab_else_create(project_id)
-        model_catalog.set_app_config(project_id=project_id, app_id=MCapp_navID, only_if_new="True")
-        VFapp_navID = test_library.exists_in_collab_else_create(project_id)
-        test_library.set_app_config(project_id=project_id, app_id=VFapp_navID, only_if_new="True")
-
     # retrieve all model instances from specified models
     if model_list:
         for entry in model_list:
@@ -543,8 +536,6 @@ def generate_HTML_report(username="", password=None, environment="production", m
     # remove duplicate result UUIDs
     result_list = list(collections.OrderedDict.fromkeys(result_list).keys())
 
-    # TODO: ensure atleast one valid result UUID to be evaluated; else create no report, alert user
-
     # utilize each result entry
     result_summary_table = [] # list of dicts, each with 4 keys -> result_id, model_label, test_label, score
     list_results = []
@@ -569,11 +560,10 @@ def generate_HTML_report(username="", password=None, environment="production", m
 
         model_label = (model["alias"] if model["alias"] else model["name"]) + " (" + str(model_instance["version"]) + ")"
         test_label = (test["alias"] if test["alias"] else test["name"]) + " (" + str(test_instance["version"]) + ")"
-        if project_id:
-            # TODO: update URLs for Collab v2
-            result_url = "https://collab.humanbrainproject.eu/#/collab/{}/nav/{}?state=result.{}".format(str(project_id),str(VFapp_navID), r_id)
-            model_url = "https://collab.humanbrainproject.eu/#/collab/{}/nav/{}?state=model.{}".format(str(project_id),str(MCapp_navID), model["id"])
-            test_url = "https://collab.humanbrainproject.eu/#/collab/{}/nav/{}?state=test.{}".format(str(project_id),str(VFapp_navID), test["id"])
+        if show_links:
+            result_url = "https://model-catalog.brainsimulation.eu/#result_id.{}".format(r_id)
+            model_url = "https://model-catalog.brainsimulation.eu/#model_id.{}".format(model["id"])
+            test_url = "https://model-catalog.brainsimulation.eu/#test_id.{}".format(test["id"])
             result_summary_table.append({"result_id": (r_id, result_url),
                                          "model_label": (model_label, model_url),
                                          "test_label": (test_label, test_url),
@@ -608,7 +598,7 @@ def generate_HTML_report(username="", password=None, environment="production", m
 
 def generate_PDF_report(html_report_path=None, username="", password=None,
                         environment="production", model_list=[], model_instance_list=[],
-                        test_list=[], test_instance_list=[], result_list=[], project_id=None,
+                        test_list=[], test_instance_list=[], result_list=[], show_links=True, 
                         only_results=False, client_obj=None):
     """Generates a PDF report for specified test results
 
@@ -639,9 +629,9 @@ def generate_PDF_report(html_report_path=None, username="", password=None,
         List of test instance UUIDs for which score matrix is to be generated.
     result_list : list
         List of result UUIDs for which score matrix is to be generated.
-    project_id : string, optional
-        Collaboratory ID where hyperlinks to results are to be redirected.
-        If unspecified, these data units will not have clickable hyperlinks.
+    show_links : boolean, optional
+        To specify if hyperlinks to results are to be provided.
+        If false, these data units will not have clickable hyperlinks.
     only_results : boolean, optional
         Indicates whether output PDF should contain only result related info.
         Set to `False` as default. When set to `True`, the PDF will have info
@@ -714,7 +704,7 @@ def generate_PDF_report(html_report_path=None, username="", password=None,
                        goto="temp")
     return filepath, valid_result_uuids
 
-def generate_score_matrix(username="", password=None, environment="production", model_list=[], model_instance_list=[], test_list=[], test_instance_list=[], result_list=[], project_id=None, client_obj=None):
+def generate_score_matrix(username="", password=None, environment="production", model_list=[], model_instance_list=[], test_list=[], test_instance_list=[], result_list=[], show_links=True, client_obj=None):
     """Generates a styled pandas dataframe with score matrix
 
     This method will generate a styled pandas dataframe for the specified test results.
@@ -741,9 +731,9 @@ def generate_score_matrix(username="", password=None, environment="production",
         List of test instance UUIDs for which score matrix is to be generated.
     result_list : list
         List of result UUIDs for which score matrix is to be generated.
-    project_id : string, optional
-        Collaboratory ID where hyperlinks to results are to be redirected.
-        If unspecified, the scores will not have clickable hyperlinks.
+    show_links : boolean, optional
+        To specify if hyperlinks to results are to be provided.
+        If false, these data units will not have clickable hyperlinks.
     client_obj : ModelCatalog/TestLibrary object
         Used to easily create a new ModelCatalog/TestLibrary object if either exist already.
         Avoids need for repeated authentications; improves performance. Also, helps minimize
@@ -785,11 +775,6 @@ def generate_score_matrix(username="", password=None, environment="production",
     else:
         test_library = TestLibrary(username, password, environment=environment)
 
-    if project_id:
-        # check if app exists; if not then create
-        VFapp_navID = test_library.exists_in_collab_else_create(project_id)
-        test_library.set_app_config(project_id=project_id, app_id=VFapp_navID, only_if_new="True")
-
     # retrieve all model instances from specified models
     if model_list:
         for entry in model_list:
@@ -830,7 +815,7 @@ def generate_score_matrix(username="", password=None, environment="production",
 
     excluded_results = []   # not latest entry for a particular model instance and test instance combination
     for r_id in result_list:
-        result = test_library.get_result(result_id = r_id)["results"][0]
+        result = test_library.get_result(result_id = r_id)
         # '#*#' is used as separator between score and result UUID (latter used for constructing hyperlink)
         if result["test_instance_id"] in results_dict.keys():
             if result["model_instance_id"] not in results_dict[result["test_instance_id"]].keys():
@@ -886,8 +871,8 @@ def make_clickable(value):
         if not value:
             return value
         score, result_uuid = value.split('#*#')
-        if project_id:
-            result_url = "https://collab.humanbrainproject.eu/#/collab/{}/nav/{}?state=result.{}".format(str(project_id),str(VFapp_navID), result_uuid)
+        if show_links:
+            result_url = "https://model-catalog.brainsimulation.eu/#result_id.{}".format(result_uuid)
             return '<a target="_blank" href="{}">{}</a>'.format(result_url,score)
         else:
             return score

setup.py

@@ -16,7 +16,7 @@ def package_files(base_dir, directory):
 
 setup(
     name='hbp_validation_framework',
-    version='0.6.0',
+    version='0.6.1',
     packages=['hbp_validation_framework'],
     package_data={'': json_files+template_files},
     url='https://github.com/HumanBrainProject/hbp-validation-client',