oarepo-runtime 1.3.10__py3-none-any.whl → 1.3.13__py3-none-any.whl

oarepo_runtime/cli/check.py

@@ -6,6 +6,7 @@ from flask import current_app
 from flask.cli import with_appcontext
 from invenio_files_rest.models import Location
 from invenio_pidstore.models import PersistentIdentifier
+from invenio_db import db
 from invenio_records_resources.proxies import current_service_registry
 from opensearchpy import TransportError
 
@@ -32,18 +33,21 @@ def check(output_file):
 
 def check_database():
     try:
-        PersistentIdentifier.query.all()[:1]
-    except:
-        return 'not_initialized'
-    alembic = current_app.extensions['invenio-db'].alembic
-    context = alembic.migration_context
-    db_heads = set(context.get_current_heads())
-    source_heads = [x.revision for x in alembic.current()]
-    for h in source_heads:
-        if h not in db_heads:
-            return 'migration_pending'
-    return 'ok'
-
+        db.session.begin()
+        try:
+            PersistentIdentifier.query.all()[:1]
+        except:
+            return 'not_initialized'
+        alembic = current_app.extensions['invenio-db'].alembic
+        context = alembic.migration_context
+        db_heads = set(context.get_current_heads())
+        source_heads = [x.revision for x in alembic.current()]
+        for h in source_heads:
+            if h not in db_heads:
+                return 'migration_pending'
+        return 'ok'
+    finally:
+        db.session.rollback()
 
 def check_opensearch():
     services = current_service_registry._services.keys()
@@ -63,9 +67,15 @@ def check_opensearch():
 
 
 def check_files():
-    # check that there is the default location and that is readable
-    default_location = Location.get_default()
-    if default_location:
-        return 'ok'
-    else:
-        return 'default-location-missing'
+    try:
+        db.session.begin()
+        # check that there is the default location and that is readable
+        default_location = Location.get_default()
+        if default_location:
+            return 'ok'
+        else:
+            return 'default-location-missing'
+    except:
+        return 'db-error'
+    finally:
+        db.session.rollback()

oarepo_runtime/cli/index.py

@@ -76,6 +76,10 @@ def reindex(model):
 
         service = current_service_registry.get(service_id)
         record_class = service.config.record_cls
+
+        if not hasattr(service, 'indexer'):
+            continue
+
         try:
             id_generator = (
                 x[0]

oarepo_runtime/datastreams/cli.py

@@ -19,12 +19,13 @@ def fixtures():
 @click.argument("fixture_dir", required=False)
 @click.option("--include", multiple=True)
 @click.option("--exclude", multiple=True)
+@click.option("--system-fixtures/--no-system-fixtures", default=True, is_flag=True)
 @with_appcontext
-def load(fixture_dir=None, include=None, exclude=None):
+def load(fixture_dir=None, include=None, exclude=None, system_fixtures=None):
     """Loads fixtures"""
     with current_app.wsgi_app.mounts["/api"].app_context():
         results: FixturesResult = load_fixtures(
-            fixture_dir, _make_list(include), _make_list(exclude)
+            fixture_dir, _make_list(include), _make_list(exclude), system_fixtures=system_fixtures
         )
         _show_stats(results, "Load fixtures")
 

oarepo_runtime/datastreams/datastreams.py

@@ -182,6 +182,9 @@ class DataStream(AbstractDataStream):
             try:
                 writer.write(stream_entry)
             except WriterError as err:
+                log.error(
+                    "Error in writer: %s: %s", err, repr(stream_entry.entry)
+                )
                 stream_entry.errors.append(StreamEntryError.from_exception(err))
             except Exception as err:
                 log.error(

oarepo_runtime/datastreams/fixtures.py

@@ -33,7 +33,7 @@ class FixturesResult:
         self.results[fixture_name] = result
 
 
-def load_fixtures(fixture_dir=None, include=None, exclude=None) -> FixturesResult:
+def load_fixtures(fixture_dir=None, include=None, exclude=None, system_fixtures=True) -> FixturesResult:
     """
     Loads fixtures. If fixture dir is set, fixtures are loaded from that directory first.
     The directory must contain a catalogue.yaml file containing datastreams to load the
@@ -55,15 +55,16 @@ def load_fixtures(fixture_dir=None, include=None, exclude=None) -> FixturesResul
     if fixture_dir:
         catalogue = DataStreamCatalogue(Path(fixture_dir) / "catalogue.yaml")
         _load_fixtures_from_catalogue(catalogue, fixtures, include, exclude, result)
-    for r in reversed(
-        sorted(pkg_resources.iter_entry_points("oarepo.fixtures"), key=lambda r: r.name)
-    ):
-        pkg = r.load()
-        pkg_fixture_dir = Path(pkg.__file__)
-        if pkg_fixture_dir.is_file():
-            pkg_fixture_dir = pkg_fixture_dir.parent
-        catalogue = DataStreamCatalogue(pkg_fixture_dir / "catalogue.yaml")
-        _load_fixtures_from_catalogue(catalogue, fixtures, include, exclude, result)
+    if system_fixtures:
+        for r in reversed(
+            sorted(pkg_resources.iter_entry_points("oarepo.fixtures"), key=lambda r: r.name)
+        ):
+            pkg = r.load()
+            pkg_fixture_dir = Path(pkg.__file__)
+            if pkg_fixture_dir.is_file():
+                pkg_fixture_dir = pkg_fixture_dir.parent
+            catalogue = DataStreamCatalogue(pkg_fixture_dir / "catalogue.yaml")
+            _load_fixtures_from_catalogue(catalogue, fixtures, include, exclude, result)
     return result
 
 

oarepo_runtime/datastreams/writers/service.py

@@ -1,3 +1,5 @@
+import traceback
+
 from invenio_access.permissions import system_identity
 from invenio_pidstore.errors import PIDAlreadyExists
 from invenio_records.systemfields.relations.errors import InvalidRelationValue
@@ -42,10 +44,12 @@ class ServiceWriter(BaseWriter):
             service_kwargs["uow"] = uow
         try:
             try:
+                print("Calling service create")
                 entry = self._service.create(self._identity, entry, **service_kwargs)
             except PIDAlreadyExists:
                 if not self._update:
                     raise WriterError([f"Entry already exists: {entry}"])
+                print("Calling service update")
                 entry_id = self._entry_id(entry)
                 current = self._resolve(entry_id)
                 updated = dict(current.to_dict(), **entry)
@@ -60,6 +64,9 @@ class ServiceWriter(BaseWriter):
         except InvalidRelationValue as err:
             # TODO: Check if we can get the error message easier
             raise WriterError([{"InvalidRelationValue": err.args[0]}])
+        except Exception as err:
+            traceback.print_exc()
+            raise WriterError([{"Unknown error": str(err)}])
 
     def delete(self, stream_entry: StreamEntry, uow=None):
         service_kwargs = {}

{oarepo_runtime-1.3.10.dist-info → oarepo_runtime-1.3.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oarepo-runtime
-Version: 1.3.10
+Version: 1.3.13
 Summary: A set of runtime extensions of Invenio repository
 Description-Content-Type: text/markdown
 License-File: LICENSE

{oarepo_runtime-1.3.10.dist-info → oarepo_runtime-1.3.13.dist-info}/RECORD

@@ -9,8 +9,8 @@ oarepo_runtime/cf/mappings.py,sha256=_Gcje90WpE2e9IKPvr5xZR263Cks2IW4YP0ENp-pjUY
 oarepo_runtime/cli/__init__.py,sha256=VIbVNJh_r856s4sA4-7hZpmyuQtxPIOGRp1YXjXHsjo,178
 oarepo_runtime/cli/assets.py,sha256=yFpHMAI0fvJBy4wUz1GcNjmfzN_9KegqCj9NgGDfZ9g,1444
 oarepo_runtime/cli/base.py,sha256=xZMsR2rati5Mz0DZzmnlhVI7E6ePCfnOiTayrxT9cWU,259
-oarepo_runtime/cli/check.py,sha256=Q9Ye0T1_RZP49QTanTrVOtk-MScSg0lJUNvpHffnLRE,2047
-oarepo_runtime/cli/index.py,sha256=bxw4yE1ah_pSxnmql6fwG8jqbH640DQ5yE0-Y3RBkG8,3145
+oarepo_runtime/cli/check.py,sha256=5_dpCDcnVqsjzxDpgDlU5WPRDOpAfiKLrfdBoj0KEgs,2340
+oarepo_runtime/cli/index.py,sha256=bT28rqf_EyuH1MiiFr3WovW6MapG61IGwSfVD_kbtUs,3212
 oarepo_runtime/cli/validate.py,sha256=hw4aW-DPaZFgvrmeRaIbyKck7w_KypU_6nrnzE8_ibY,1460
 oarepo_runtime/config/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 oarepo_runtime/config/permissions_presets.py,sha256=rQcvTsxyPOGtgjWUunE4oSzIwfm4W6VAOOvnYJSJosY,5766
@@ -18,11 +18,11 @@ oarepo_runtime/config/service.py,sha256=Js5Dyklqt8diul2HdqoAMxy5Jl6jk2moznHLUDPf
 oarepo_runtime/datastreams/__init__.py,sha256=bscO2zTYf1eEppYx74b54-fcb2wz7YUDjGupqafuFc0,724
 oarepo_runtime/datastreams/batch.py,sha256=Xe0kXZigDeHU6Sjvo7w4_zjas8lShc2aTJpaAAQ3Iq0,551
 oarepo_runtime/datastreams/catalogue.py,sha256=QaHLGTzQk76B9q_6vFx1I3fBSGL8SrHni4zA0v2572s,4975
-oarepo_runtime/datastreams/cli.py,sha256=0EMZM3M-A8Yy0Rd9_AgSTWaPplXGHq2Ta41d_XZAVNQ,1936
+oarepo_runtime/datastreams/cli.py,sha256=irtL-1ZKlLapiD_Cevh9rcuPg96Rj4PKZgAe_l5XZBs,2075
 oarepo_runtime/datastreams/config.py,sha256=ALq7otBFMHjT3GV59KpkEV-8ZborWrYLXyB3v5-nFGE,1083
-oarepo_runtime/datastreams/datastreams.py,sha256=c6dDkKdhK82n0q3RyXMpB9tFDADl9SGUriGNquoO8BE,6390
+oarepo_runtime/datastreams/datastreams.py,sha256=slEM2GSM4g1WQ-6VwbwkO6GRjMfOp4rON9N2U2YjR4E,6512
 oarepo_runtime/datastreams/errors.py,sha256=KxtFD2jX8pIoCNYFvh937otySVYjTVCrPSS13AZnVus,690
-oarepo_runtime/datastreams/fixtures.py,sha256=hgu0OOFbx5jmZzv_fhLpM6bSoc9HnGdX09_jVTX7laU,5344
+oarepo_runtime/datastreams/fixtures.py,sha256=hkgu2oy6gZN40CrgiGZKoNghMX1znSxvVMrKSPvB-Ds,5426
 oarepo_runtime/datastreams/transformers.py,sha256=4COh2cza_n2GKnTM2yJkj9-8KkPK2E1fcyRoUH4S2OY,1204
 oarepo_runtime/datastreams/readers/__init__.py,sha256=UyKJbymJyfk7rdAAyNI-t2fDKQNz69_5B7KI8RJ2cWE,858
 oarepo_runtime/datastreams/readers/excel.py,sha256=QP_1a75jlW1udNgBx8FIdWkaoWiTrQ2ysjbi8H1wPmw,3287
@@ -30,7 +30,7 @@ oarepo_runtime/datastreams/readers/json.py,sha256=ZZfD71ymnoaAYgsQ67wLdtWUx7rpDE
 oarepo_runtime/datastreams/readers/service.py,sha256=NrlUqjGCtqYekEYVGauYgcNyidorSgX6O6jt3gnWcfs,947
 oarepo_runtime/datastreams/readers/yaml.py,sha256=15P4faTmtBBpzg8RBJ42pQOP4iWdrrvyZNsEtdQc1UY,332
 oarepo_runtime/datastreams/writers/__init__.py,sha256=8HIRwHxacUxvluqKxog8pUE1iKMwSqeI9wtlSyfx00E,1366
-oarepo_runtime/datastreams/writers/service.py,sha256=JLtaLy8qP9Wi8mdoyh9hnWH4RwCGMjY54FXLjBseza0,2688
+oarepo_runtime/datastreams/writers/service.py,sha256=r9ybLer6sHVH5M0wlSPzP9Bpw6QhTiZBjRiKEECwel8,2930
 oarepo_runtime/datastreams/writers/yaml.py,sha256=B4lv-85UYB9K-3B35O1_vsRhH8AdhYfL8IgB3SS1LFw,1312
 oarepo_runtime/expansions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 oarepo_runtime/expansions/expandable_fields.py,sha256=7DWKFL6ml8J7zGI6wm9LO7Xd6R0LSylsuq4lyRumNHQ,745
@@ -70,9 +70,9 @@ oarepo_runtime/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hS
 oarepo_runtime/utils/path.py,sha256=V1NVyk3m12_YLbj7QHYvUpE1wScO78bYsX1LOLeXDkI,3108
 oarepo_runtime/validation/__init__.py,sha256=lU7DgZq8pGD5Pa-QqL9gvLsib3IYtM-Y56k-NwHrPG0,166
 oarepo_runtime/validation/dates.py,sha256=fahqKGDdIYWux5ZeoljrEe8VD2fDZR9VpfvYmTYAmpw,1050
-oarepo_runtime-1.3.10.dist-info/LICENSE,sha256=h2uWz0OaB3EN-J1ImdGJZzc7yvfQjvHVYdUhQ-H7ypY,1064
-oarepo_runtime-1.3.10.dist-info/METADATA,sha256=8fC5WbN7Eml64_fTFi0N4Yz4C7x_lAItHlwJjHzbgT4,2552
-oarepo_runtime-1.3.10.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-oarepo_runtime-1.3.10.dist-info/entry_points.txt,sha256=C32W4eT-8OypMCfwOO5WREioVKSneDfY51D78Uvdbp0,231
-oarepo_runtime-1.3.10.dist-info/top_level.txt,sha256=Vdo5ohKvEHniyXfcy3hv92nVSYIngDYGQtinWviujlw,15
-oarepo_runtime-1.3.10.dist-info/RECORD,,
+oarepo_runtime-1.3.13.dist-info/LICENSE,sha256=h2uWz0OaB3EN-J1ImdGJZzc7yvfQjvHVYdUhQ-H7ypY,1064
+oarepo_runtime-1.3.13.dist-info/METADATA,sha256=lPPpdGdmHUNNJjHa0mjEDKPZG3cr-B6Zl9kLbnkgCAw,2552
+oarepo_runtime-1.3.13.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+oarepo_runtime-1.3.13.dist-info/entry_points.txt,sha256=C32W4eT-8OypMCfwOO5WREioVKSneDfY51D78Uvdbp0,231
+oarepo_runtime-1.3.13.dist-info/top_level.txt,sha256=Vdo5ohKvEHniyXfcy3hv92nVSYIngDYGQtinWviujlw,15
+oarepo_runtime-1.3.13.dist-info/RECORD,,