Yoda 1.9.5 [draft]

.github/workflows/api-and-integration-tests.yml

@@ -34,7 +34,7 @@ jobs:
     # For other branches, we use the Docker setup of the development branch.
     - name: Determine Yoda repository branch
       run: |
-        if [ "${{ steps.extract_branch.outputs.branch }}" = "release-1.9" ]; then
+        if [ "${{ steps.extract_branch.outputs.branch }}" = "release-1.9" ] || [[ "${{ steps.extract_branch.outputs.branch }}" == rc-1.9.* ]]; then
           echo "branch=release-1.9" >> $GITHUB_OUTPUT
         else
           echo "branch=development" >> $GITHUB_OUTPUT
@@ -74,12 +74,19 @@ jobs:
         docker exec provider.yoda sh -c "set -x ; cd /etc/irods/yoda-ruleset && sudo -u irods git checkout ${{ steps.extract_branch.outputs.branch }} && sudo -u irods python -m pip --no-cache-dir install --user -r /etc/irods/yoda-ruleset/requirements.txt && sudo -u irods make && sudo -u irods make install"
         docker exec provider.yoda sh -c "set -x ; sudo -u irods /var/lib/irods/irodsctl restart"
 
+    - name: Upgrade UU microservices for testing the RC version of Yoda 1.9.5
+      if: github.event.pull_request.head.ref == 'rc-1.9.5'
+      shell: bash
+      run: |
+        docker exec provider.yoda sh -c 'set -x ; sudo yum remove -y irods-uu-microservices ; sudo wget https://github.com/UtrechtUniversity/irods-uu-microservices/releases/download/v1.2.0/irods-uu-microservices-4.2.12_1.2.0-0.rpm ; sudo rpm -ivh irods-uu-microservices-4.2.12_1.2.0-0.rpm'
+
     - name: Pull and install latest version of portal
       shell: bash
       run: |
         cd yoda/docker/compose
         docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && git config remote.origin.fetch  "+refs/heads/*:refs/remotes/origin/*" && git pull'
         docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && git checkout ${{ steps.extract_branch.outputs.branch }} || git checkout development'
+        docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && . venv/bin/activate && venv/bin/pip3 install -r requirements.txt'
         docker exec portal.yoda sh -c 'set -x ; cd /var/www/yoda && git status'
         docker exec portal.yoda sh -c 'set -x ; touch /var/www/yoda/*.wsgi'
 
@@ -118,6 +125,12 @@ jobs:
       run: |
         docker exec provider.yoda sh -c 'set -x ; cat /var/lib/irods/log/rodsLog*'
 
+
+    - name: Output web server logs
+      if: failure()
+      run: |
+        docker exec portal.yoda sh -c 'set -x ; for log in error_log portal_access.log ; do echo "${log}:" ; cat "/var/log/httpd/$log" ; echo; done'
+
 # Uncomment section below when needed for debugging.
 #
 #    - name: Setup tmate session for debugging

__init__.py

@@ -24,30 +24,31 @@
 # Import all modules containing rules into the package namespace,
 # so that they become visible to iRODS.
 
-from browse                 import *
-from folder                 import *
-from groups                 import *
-from json_datacite          import *
-from json_landing_page      import *
-from mail                   import *
-from meta                   import *
-from meta_form              import *
-from provenance             import *
-from research               import *
-from resources              import *
-from schema                 import *
-from schema_transformation  import *
-from schema_transformations import *
-from vault                  import *
-from datacite               import *
-from epic                   import *
-from publication            import *
-from policies               import *
-from replication            import *
-from revisions              import *
-from settings               import *
-from notifications          import *
-from integration_tests      import *
+from browse                   import *
+from folder                   import *
+from groups                   import *
+from json_datacite            import *
+from json_landing_page        import *
+from mail                     import *
+from meta                     import *
+from meta_form                import *
+from provenance               import *
+from research                 import *
+from resources                import *
+from schema                   import *
+from schema_transformation    import *
+from schema_transformations   import *
+from publication_troubleshoot import *
+from vault                    import *
+from datacite                 import *
+from epic                     import *
+from publication              import *
+from policies                 import *
+from replication              import *
+from revisions                import *
+from settings                 import *
+from notifications            import *
+from integration_tests        import *
 
 # Import certain modules only when enabled.
 from .util.config import config

browse.py

@@ -264,7 +264,7 @@ def transform(row):
         if sort_on == 'modified':
             cols = ['COLL_NAME', 'COLL_PARENT_NAME', 'MIN(COLL_CREATE_TIME)', 'ORDER(COLL_MODIFY_TIME)']
         else:
-            cols = ['ORDER(COLL_NAME)', 'COLL_PARENT_NAME' 'MIN(COLL_CREATE_TIME)', 'MAX(COLL_MODIFY_TIME)']
+            cols = ['ORDER(COLL_NAME)', 'COLL_PARENT_NAME', 'MIN(COLL_CREATE_TIME)', 'MAX(COLL_MODIFY_TIME)']
         where = "COLL_PARENT_NAME like '{}%%' AND COLL_NAME like '%%{}%%'".format("/" + zone + "/home", search_string)
     elif search_type == 'metadata':
         if sort_on == 'modified':
@@ -310,7 +310,7 @@ def _filter_vault_deposit_index(row):
 
        :param row: row of results data from GenQuery, containing collection name (COLL_NAME)
 
-       :returns: boolean value that indicated whether row should be displayed
+       :returns: boolean value that indicates whether row should be displayed
     """
     # Remove ORDER_BY etc. wrappers from column names.
     x = {re.sub('.*\((.*)\)', '\\1', k): v for k, v in row.items()}

datarequest.py

@@ -496,7 +496,10 @@ def datarequest_owner_get(ctx, request_id):
                                       + JSON_EXT)
 
     # Get and return data request owner
-    return jsonutil.read(ctx, file_path)['owner']
+    try:
+        return jsonutil.read(ctx, file_path)['owner']
+    except Exception:
+        return None
 
 
 def datarequest_is_reviewer(ctx, request_id, pending=False):
@@ -1046,7 +1049,10 @@ def api_datarequest_get(ctx, request_id):
     datarequest_action_permitted(ctx, request_id, ["PM", "DM", "DAC", "OWN"], None)
 
     # Get request type
-    datarequest_type = type_get(ctx, request_id).value
+    try:
+        datarequest_type = type_get(ctx, request_id).value
+    except Exception as e:
+        return api.Error("datarequest_type_fail", "Error: {}".format(e))
 
     # Get request status
     datarequest_status = status_get(ctx, request_id).value

deposit.py

@@ -25,15 +25,16 @@
 
 
 @api.make()
-def api_deposit_copy_data_package(ctx, reference):
+def api_deposit_copy_data_package(ctx, reference, deposit_group):
     """Create deposit collection and copies selected datapackage into the newly created deposit
 
-    :param ctx:       Combined type of a callback and rei struct
-    :param reference: Data Package Reference (UUID4)
+    :param ctx:           Combined type of a callback and rei struct
+    :param reference:     Data Package Reference (UUID4)
+    :param deposit_group: Deposit group to copy to
 
     :returns: Path to created deposit collection or API error
     """
-    result = deposit_create(ctx)
+    result = deposit_create(ctx, deposit_group)
     if result["deposit_path"] == "not_allowed":
         return api.Error('not_allowed', 'Could not create deposit collection.')