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SwissDataScienceCenter / renku-python

A Python library for the Renku collaborative data science platform.
https://renku-python.readthedocs.io/
Apache License 2.0
37 stars 29 forks source link

1.0.0 Migration Issues #2487

Closed Panaetius closed 2 years ago

Panaetius commented 2 years ago

Collection of issues in migrations:

4 (prov:Agent set to Email instead of software agent, potential SHACL problem

366f655c2421a873c4bc6d37c8a0c1d2f04a2ce |      12329 | cyril.matthey-doret/sequence-loopability
Caused by: ammonite.ops.ShelloutException: CommandResult 1;
Error: Validation Report;
Conforms: False;
Results (2):;
Constraint Violation in ClassConstraintComponent (http://www.w3.org/ns/shacl#ClassConstraintComponent):;
Severity: sh:Violation;
Source Shape: [ sh:class prov:SoftwareAgent ;
sh:maxCount Literal("1", datatype=xsd:integer) ;
sh:minCount Literal("1", datatype=xsd:integer) ;
sh:path prov:agent ];
Focus Node: <https:
//david.dev.renku.ch/activities/bc7ddb08d42a4cbe8caa2815f4e86264/association>;
Value Node: <mailto:cyril.matthey-doret@pasteur.fr>;
Result Path: prov:agent;
Message: Value does not have class prov:SoftwareAgent;
Constraint Violation in ClassConstraintComponent (http://www.w3.org/ns/shacl#ClassConstraintComponent):;
Severity: sh:Violation;
Source Shape: [ sh:class prov:SoftwareAgent ;
sh:maxCount Literal("1", datatype=xsd:integer) ;
sh:minCount Literal("1", datatype=xsd:integer) ;
sh:path prov:agent ];
Focus Node: <https://david.dev.renku.ch/activities/4b3729f7d3704543b12c859e1b95a709/association>;
Value Node: <mailto:cyril.matthey-doret@pasteur.fr>;
Result Path: prov:agent;
Message: Value does not have class
 prov:SoftwareAgent;
 ;
 Couldn't export: Invalid Knowledge Graph data;
 ;

8 Submodule Migration issue

cafeb1cbed77fdc312f4c3af278bbb03ba068086 |        145 | erbou/celegans-genome-analysis-1

Applying migration m_0003__0_pyld2...;
Applying migration m_0003__1_jsonld...;
Applying migration m_0003__2_initial...;
Applying migration m_0004__0_pyld2...;
Applying migration m_0004__submodules...;
Applying migration m_0003__0_pyld2...;
Applying migration m_0003__1_jsonld...;
Applying migration m_0003__2_initial...;
Applying migration m_0004__0_pyld2...;
Applying migration m_0004__submodules...;
Applying migration m_0005__1_pyld2...;
Applying migration m_0005__2_cwl...;
Caching commit 1\rCaching commit 2\rCaching commit 3\rCaching commit 4\rCaching commit 5\rCaching commit 6\rCaching commit 7\rCaching commit 8\rCaching commit 9\rCaching commit 10\rCaching commit 11\rCaching commit 12\rCaching commit 13\rCaching commit 14\rCaching commit 15\rCaching commit 16\rCaching commit 17\r                                        \rProcessing commit 1/1\rApplying migration m_0006__dataset_context...;
Applying migration m_0007__source_url...;
Applying migration m_0008__dataset_metadata...;
Applying migration m_0009__new_metadata_storage...;
Processing commits 1/3 e0cf627c320eaaa9e98746ea810acfd9e71c5947\rProcessing commits 2/3 e6c764abbdbfb72247fd858e33c4263957ef930a;
Warning: Cannot process commit 'e6c764abbdbfb72247fd858e33c4263957ef930a' - Exception: Traceback (most recent call last):;
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0009__new_metadata_storage.py", line 194, in generate_new_metadata;
_process_workflows(client=client, activity_gateway=activity_gateway, commit=commit, remove=remove);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0009__new_metadata_storage.py", line 336, in _process_workflows;
workflow = old_schema.Activity.from_yaml(path=path, client=client);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/models/v9.py", line 807, in from_yaml;
data = jsonld.read_yaml(path);
File "/usr/lib/python3.8/site-packages/renku/core/models/jsonld.py", line 62, in read_yaml;
with Path(path).open(mode="r") as fp:;
File "/usr/lib/python3.8/pathlib.py", line 1222, in open;
return io.open(self, mode, buffering, encoding, errors, newline,;
File "/usr/lib/python3.8/pathlib.py", line 1078,in _opener;
return self._accessor.open(self, flags, mode);
FileNotFoundError: [Errno 2] No such file or directory: '.renku/workflow/4c834c484234422a8dc768070b94f9b6_code_runSTAR.sh.yaml';
;
Processing commits 3/3 1e233fbda43e328750b680bb3c69dbe9d5a3833c\rSuccessfully applied 11 migrations.;
Applying migration m_0003__0_pyld2...;
Applying migration m_0003__1_jsonld...;
Applying migration m_0003__2_initial...;
Applying migration m_0004__0_pyld2...;
Applying migration m_0004__submodules...;
Applying migration m_0003__0_pyld2...;
Applying migration m_0003__1_jsonld...;
Applying migration m_0003__2_initial...;
Applying migration m_0004__0_pyld2...;
Applying migration m_0004__submodules...;
Applying migration m_0005__1_pyld2...;
Applying migration m_0005__2_cwl...;
Caching commit 1\rCaching commit 2\rCaching commit 3\rCaching commit 4\rCaching commit 5\rCaching commit 6\rCaching commit 7\rCaching commit 8\rCaching commit 9\rCaching commit 10\rCaching commit 11\rCaching commit 12\rCaching commit 13\rCaching commit 14\rCaching commit 15\r\rProcessing commit 1/1\rApplying migration m_0006__dataset_context...;
Applying migration m_0007__source_url...;
Applying migration m_0008__dataset_metadata...;
Applying migration m_0009__new_metadata_storage...;
Processing commits 1/3 826343464f7de81f2bee38c1332cd217b014e00f\rProcessing commits 2/3 6fad8b741b5cca653c3fc8535ff1fc1015c78808;
Warning: Cannot process commit '6fad8b741b5cca653c3fc8535ff1fc1015c78808' - Exception: Traceback (most recent call last):;
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0009__new_metadata_storage.py", line 194, in generate_new_metadata;
_process_workflows(client=client, activity_gateway=activity_gateway, commit=commit, remove=remove);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0009__new_metadata_storage.py", line 336, in _process_workflows;
workflow = old_schema.Activity.from_yaml(path=path, client=client);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/models/v9.py", line 807, in from_yaml;
data = jsonld.read_yaml(path);
File "/usr/lib/python3.8/site-packages/renku/core/models/jsonld.py", line 62, in read_yaml;
with Path(path).open(mode="r") as fp:;
File "/usr/lib/python3.8/pathlib.py", line 1222, in open;
return io.open(self, mode, buffering, encoding, errors, newline,;
File "/usr/lib/python3.8/pathlib.py", line 1078, in _opener;
return self._accessor.open(self, flags, mode);
FileNotFoundError: [Errno 2] No such file or directory: '.renku/workflow/7137679420a54b7b868ecf2d60ddef9a_code_runSTAR.sh.yaml';
;
Processing commits 3/3 ee9a022644e571da8d75d49e398cc3df103a04a0\rSuccessfully applied 11 migrations.;
Error: Couldn't execute migration;
;
Traceback (most recent call last):;
File "/usr/lib/python3.8/shutil.py", line 791, in move;
os.rename(src, real_dst);
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/celegans-genome-analysis-1--1300193730710223129/.renku/vendors/renkulab.io/gitlab/erbou/celegans-genome-mapping-3/.renku/vendors/renkulab.io/gitlab/erbou/celegans-genome/data/celegans/metadata.yml' -> '/tmp/celegans-genome-analysis-1--1300193730710223129/.renku/vendors/renkulab.io/gitlab/erbou/celegans-genome-mapping-3/data/wbcel235/celegans-genome/metadata.yml';
;
During handling of the above exception, another exception occurred:;
;
Traceback (most recent call last):;
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0004__submodules.py", line 129, in _migrate_submodule_based_datasets;
shutil.move(target, path);
File "/usr/lib/python3.8/shutil.py", line 811, in move;
copy_function(src, real_dst);
File "/usr/lib/python3.8/shutil.py", line 435, in copy2;
copyfile(src, dst, follow_symlinks=follow_symlinks);
File "/usr/lib/python3.8/shutil.py", line 264, in copyfile;
with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:;
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/celegans-genome-analysis-1--1300193730710223129/.renku/vendors/renkulab.io/gitlab/erbou/celegans-genome-mapping-3/.renku/vendors/renkulab.io/gitlab/erbou/celegans-genome/data/celegans/metadata.yml';
;
During handling of the above exception, another exception occurred:;
;
Traceback (most recent call last):;
File "/usr/lib/python3.8/site-packages/renku/core/management/migrate.py", line 157, in migrate;
module.migrate(migration_context);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0004__submodules.py", line 43, in migrate;
_migrate_submodule_based_datasets(migration_context.client);
File "/usr/lib/python3.8/site-packages/inject/__init__.py", line 342, in injection_wrapper;
return sync_func(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0004__submodules.py", line 131, in _migrate_submodule_based_datasets;
raise errors.InvalidFileOperation(f"File was not found: {target}");
renku.core.errors.InvalidFileOperation: File was not found: /tmp/celegans-genome-analysis-1--1300193730710223129/.renku/vendors/renkulab.io/gitlab/erbou/celegans-genome-mapping-3/.renku/vendors/renkulab.io/gitlab/erbou/celegans-genome/data/celegans/metadata.yml;
;
The above exception was the direct cause of the following exception:;
;
Traceback (most recent call last):;
File "/usr/lib/python3.8/site-packages/renku/core/management/migrate.py", line 157, in migrate;
module.migrate(migration_context);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0004__submodules.py", line 43, in migrate;
_migrate_submodule_based_datasets(migration_context.client);
File "/usr/lib/python3.8/site-packages/inject/__init__.py", line 342, in injection_wrapper;
return sync_func(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0004__submodules.py", line 91, in _migrate_submodule_based_datasets;
migrate(skip_template_update=True, skip_docker_update=True);
File "/usr/lib/python3.8/site-packages/inject/__init__.py", line 342, in injection_wrapper;
return sync_func(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrate.py", line 159, in migrate;
raise MigrationError("Couldn't execute migration") from e;
renku.core.errors.MigrationError: Couldn't execute migration;
;
The above exception was the direct cause of the following exception:;
;
Traceback (most recent call last):;
File "/usr/lib/python3.8/site-packages/renku/cli/exception_handler.py", line 89, in main;
return super().main(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/click/core.py", line 1062, in main;
rv = self.invoke(ctx);
File "/usr/lib/python3.8/site-packages/click/core.py", line 1668,in invoke;
return _process_result(sub_ctx.command.invoke(sub_ctx));
File "/usr/lib/python3.8/site-packages/click/core.py", line 1404, in invoke;
return ctx.invoke(self.callback, **ctx.params);
File "/usr/lib/python3.8/site-packages/click/core.py", line 763, in invoke;
return __callback(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/cli/migrate.py", line 109, in migrate;
result = command.build().execute(;
File "/usr/lib/python3.8/site-packages/renku/core/management/command_builder/command.py", line 256, in execute;
hook(self, context, result, *args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/core/management/command_builder/command.py", line 195, in _post_hook;
raise result.error;File "/usr/lib/python3.8/site-packages/renku/core/management/command_builder/command.py", line 242, in execute;
output = context["click_context"].invoke(self._operation, *args, **kwargs);
File "/usr/lib/python3.8/site-packages/click/core.py", line 763, in invoke;
return __callback(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/core/commands/migrate.py", line 164, in _migrate_project;
return migrate(;
File "/usr/lib/python3.8/site-packages/inject/__init__.py", line 342, in injection_wrapper;
return sync_func(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrate.py", line 159, in migrate;
raise MigrationError("Couldn't execute migration") from e;
renku.core.errors.MigrationError: Couldn't execute migration;

9 SHACL Error, License is an IRI

967f1bc6ae49693bc730496918f4863eb7c67274 |       1872 | ren.ku/dataverse-import

Error: Validation Report;
Conforms: False;
Results (1):;
Constraint Violation in NodeKindConstraintComponent (http://www.w3.org/ns/shacl#NodeKindConstraintComponent):;
Severity: sh:Violation;
Source Shape: [ sh:nodeKind sh:Literal ;
sh:or ( [ sh:datatype xsd:string ;
sh:nodeKind sh:Literal ] [ sh:nodeKind sh:BlankNodeOrIRI ] ) ;
sh:path schema:license ];
Focus Node: <https://david.dev.renku.ch/datasets/ee318fea6df64641a08c7e3cb0350fff>;
Value Node: <https://creativecommons.org/publicdomain/zero/1.0/>;
Result Path: schema:license;
Message: Value is not of Node Kind sh:Literal;
;
Couldn't export: Invalid Knowledge Graph data;

12 SHACL needs schema:image on Dataset node

Node <https://david.dev.renku.ch/datasets/617f2eaf232917bb0b046893e3a043e7> is closed. It cannot have value: <https://david.dev.renku.ch/datasets/652eb758-d7d4-4a7f-b76e-6157c21adb20/images/0>

617f2eaf232917bb0b04682549b9230fc337db5b |      13997 | pamela.delgado/forked-test-streamlit-new-base-image

 Error: Validation Report;
 Conforms: False;
 Results (2):;
 Constraint Violation in ClosedConstraintComponent (http://www.w3.org/ns/shacl#ClosedConstraintComponent):;
 Severity: sh:Violation;
 Source Shape: [ rdf:type sh:NodeShape ;
 sh:closed Literal("true" = True, datatype=xsd:boolean) ;
 sh:ignoredProperties ( rdf:type ) ;
 sh:property [ sh:class schema:DigitalDocument ;
 sh:path schema:hasPart ], [ sh:class schema:Language ;
 sh:path schema:inLanguage ], [ sh:class schema:Person ;
 sh:minCount Literal("1", datatype=xsd:integer) ;
 sh:path schema:creator ], [ sh:class schema:PublicationEvent ;
 sh:path schema:subjectOf ], [ sh:class schema:URL ;
 sh:path prov:wasDerivedFrom ], [ sh:class schema:URL ;
 sh:path schema:sameAs ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:minCount Literal("0", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path renku:originalIdentifier ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:minCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path renku:slug ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:minCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path schema:identifier ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:minCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path schema:name ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:moreThanOrEquals schema:dateCreated ;
 sh:nodeKind sh:Literal ;
 sh:path prov:invalidatedAtTime ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path schema:dateCreated ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path schema:datePublished ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path schema:description ], [ sh:datatype xsd:string ;
 sh:nodeKind sh:Literal ;
 sh:path schema:keywords ], [ sh:datatype xsd:string ;
 sh:nodeKind sh:Literal ;
 sh:path schema:url ], [ sh:datatype xsd:string ;
 sh:nodeKind sh:Literal ;
 sh:path schema:version ], [ sh:nodeKind sh:Literal ;
 sh:or ( [ sh:datatype xsd:string ;
 sh:nodeKind sh:Literal ] [ sh:nodeKind sh:BlankNodeOrIRI ] ) ;
 sh:path schema:license ] ;
 sh:targetClass schema:Dataset ];
 Focus Node: <https://david.dev.renku.ch/datasets/617f2eaf232917bb0b046893e3a043e7>;
 Value Node: <https://david.dev.renku.ch/datasets/652eb758-d7d4-4a7f-b76e-6157c21adb20/images/0>;
 Result Path: schema:image;
 Message: Node <https://david.dev.renku.ch/datasets/617f2eaf232917bb0b046893e3a043e7> is closed. It cannot have value: <https://david.dev.renku.ch/datasets/652eb758-d7d4-4a7f-b76e-6157c21adb20/images/0>;
 Constraint Violation in ClosedConstraintComponent (http://www.w3.org/ns/shacl#ClosedConstraintComponent):;
 Severity: sh:Violation;
 Source Shape: [ rdf:type sh:NodeShape ;
 sh:closed Literal("true" = True, datatype=xsd:boolean) ;
 sh:ignoredProperties ( rdf:type ) ;
 sh:property [ sh:class schema:DigitalDocument ;
 sh:path schema:hasPart ], [ sh:class schema:Language ;
 sh:path schema:inLanguage ], [ sh:class schema:Person ;
 sh:minCount Literal("1", datatype=xsd:integer) ;
 sh:path schema:creator ], [ sh:class schema:PublicationEvent ;
 sh:path schema:subjectOf ], [ sh:class schema:URL ;
 sh:path prov:wasDerivedFrom ], [ sh:class schema:URL ;
 sh:path schema:sameAs ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:minCount Literal("0", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path renku:originalIdentifier ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:minCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path renku:slug ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:minCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path schema:identifier ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:minCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path schema:name ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:moreThanOrEquals schema:dateCreated ;
 sh:nodeKind sh:Literal ;
 sh:path prov:invalidatedAtTime ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path schema:dateCreated ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path schema:datePublished ], [ sh:datatype xsd:string ;
 sh:maxCount Literal("1", datatype=xsd:integer) ;
 sh:nodeKind sh:Literal ;
 sh:path schema:description ], [ sh:datatype xsd:string ;
 sh:nodeKind sh:Literal ;
 sh:path schema:keywords ], [ sh:datatype xsd:string ;
 sh:nodeKind sh:Literal ;
 sh:path schema:url ], [ sh:datatype xsd:string ;
 sh:nodeKind sh:Literal ;
 sh:path schema:version ], [ sh:nodeKind sh:Literal ;
 sh:or ( [ sh:datatype xsd:string ;
 sh:nodeKind sh:Literal ] [ sh:nodeKind sh:BlankNodeOrIRI ] ) ;
 sh:path schema:license ] ;
 sh:targetClass schema:Dataset ];
 Focus Node: <https://david.dev.renku.ch/datasets/652eb758d7d44a7fb76e6157c21adb20>;
 Value Node: <https://david.dev.renku.ch/datasets/652eb758-d7d4-4a7f-b76e-6157c21adb20/images/0>;
 Result Path: schema:image;
 Message: Node <https://david.dev.renku.ch/datasets/652eb758d7d44a7fb76e6157c21adb20> is closed. It cannot have value: <https://david.dev.renku.ch/datasets/652eb758-d7d4-4a7f-b76e-6157c21adb20/images/0>;
 ;
 Couldn't export: Invalid Knowledge Graph data;

13 Probably due to data/*/metadata.yml being stored in git lfs, verify and ignore if that's the case

aec9988f217a1022a16f4410d9f55bcf585c68d7 |       2493 | luis.salamanca/democ_sentiment

Applying migration m_0003__0_pyld2...;
Applying migration m_0003__1_jsonld...;
Applying migration m_0003__2_initial...;
Error: Couldn't execute migration;
;
Traceback (most recent call last):;
File "/usr/lib/python3.8/site-packages/renku/core/management/migrate.py", line 157, in migrate;
module.migrate(migration_context);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0003__2_initial.py", line 45, in migrate;
_migrate_datasets_pre_v0_3(client);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/m_0003__2_initial.py", line 87, in _migrate_datasets_pre_v0_3;
dataset = Dataset.from_yaml(old_path, client);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/models/v3.py", line 175, in from_yaml;
self = DatasetSchemaV3(client=client, commit=commit).load(data);
File "/usr/lib/python3.8/site-packages/marshmallow/schema.py", line 719, in load;
return self._do_load(;
File "/usr/lib/python3.8/site-packages/marshmallow/schema.py", line 844, in _do_load;
processed_data = self._invoke_load_processors(;
File "/usr/lib/python3.8/site-packages/marshmallow/schema.py", line 1090, in _invoke_load_processors;
data = self._invoke_processors(;
File "/usr/lib/python3.8/site-packages/marshmallow/schema.py", line 1220, in _invoke_processors;
data = processor(data, many=many, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/models/v3.py", line 360, in fix_files_context;
data = migrate_types(data);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/utils/__init__.py", line 169, in migrate_types;
replace_types(data);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrations/utils/__init__.py", line 152, in replace_types;
for key, value in data_.items():;
AttributeError: 'str' object has no attribute 'items';
;
The above exception was the direct cause of the following exception:;
;
Traceback (most recent call last):;
File "/usr/lib/python3.8/site-packages/renku/cli/exception_handler.py", line 89, in main;
return super().main(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/click/core.py", line 1062, in main;
rv = self.invoke(ctx);
File "/usr/lib/python3.8/site-packages/click/core.py", line 1668, in invoke;
return _process_result(sub_ctx.command.invoke(sub_ctx));
File "/usr/lib/python3.8/site-packages/click/core.py", line 1404, in invoke;
return ctx.invoke(self.callback, **ctx.params);
File "/usr/lib/python3.8/site-packages/click/core.py", line 763, in invoke;
return __callback(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/cli/migrate.py", line 109, in migrate;
result = command.build().execute(;
File "/usr/lib/python3.8/site-packages/renku/core/management/command_builder/command.py", line 256, in execute;
hook(self, context, result, *args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/core/management/command_builder/command.py", line 195, in _post_hook;
raise result.error;
File "/usr/lib/python3.8/site-packages/renku/core/management/command_builder/command.py", line 242, in execute;
output = context["click_context"].invoke(self._operation, *args, **kwargs);
File "/usr/lib/python3.8/site-packages/click/core.py", line 763, in invoke;
return __callback(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/core/commands/migrate.py", line 164, in _migrate_project;
return migrate(;
File "/usr/lib/python3.8/site-packages/inject/__init__.py", line 342, in injection_wrapper;
return sync_func(*args, **kwargs);
File "/usr/lib/python3.8/site-packages/renku/core/management/migrate.py", line 159, in migrate;
raise MigrationError("Couldn't execute migration") from e;
renku.core.errors.MigrationError: Couldn't execute migration;

We can fix all these in one PR.

m-alisafaee commented 2 years ago

Migration for luis.salamanca/democ_sentiment fails because data/models/metadata.yml and data/amazon_german/metadata.yml are in LFS. Migration works when they are pulled from LFS.