From 02995da69923def1e212d6fd71f5336a304c884a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 26 Mar 2021 21:47:31 +0000 Subject: [PATCH 1/3] Bump lxml from 4.6.2 to 4.6.3 Bumps [lxml](https://github.com/lxml/lxml) from 4.6.2 to 4.6.3. - [Release notes](https://github.com/lxml/lxml/releases) - [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt) - [Commits](https://github.com/lxml/lxml/compare/lxml-4.6.2...lxml-4.6.3) Signed-off-by: dependabot[bot] --- Pipfile.lock | 425 +++++++++++++++++++++------------------------------ 1 file changed, 175 insertions(+), 250 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 2788ee2e..d0246927 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -25,32 +25,24 @@ }, "alembic": { "hashes": [ + "sha256:422883bf429105b9b5f1fece6d79da64ed1ee648af2ef256d9b52edac236bc46", "sha256:e871118b6174681f7e9a9ea67cfcae954c6d18e05b49c6b17f662d2530c76bf5" ], "index": "pypi", "version": "==1.5.4" }, - 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[Release notes](https://github.com/lxml/lxml/releases) - [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt) - [Commits](https://github.com/lxml/lxml/compare/lxml-4.6.2...lxml-4.6.3) Signed-off-by: dependabot[bot] --- Pipfile.lock | 425 +++++++++++++++++++++------------------------------ 1 file changed, 175 insertions(+), 250 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 2788ee2e..d0246927 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -25,32 +25,24 @@ }, "alembic": { "hashes": [ + "sha256:422883bf429105b9b5f1fece6d79da64ed1ee648af2ef256d9b52edac236bc46", "sha256:e871118b6174681f7e9a9ea67cfcae954c6d18e05b49c6b17f662d2530c76bf5" ], "index": "pypi", "version": "==1.5.4" }, - "amqp": { - "hashes": [ - "sha256:1e759a7f202d910939de6eca45c23a107f6b71111f41d1282c648e9ac3d21901", - "sha256:affdd263d8b8eb3c98170b78bf83867cdb6a14901d586e00ddb65bfe2f0c4e60" - ], - "markers": "python_version >= '3.6'", - "version": "==5.0.5" - }, "aniso8601": { "hashes": [ - "sha256:be08b19c19ca527af722f2d4ba4dc569db292ec96f7de963746df4bb0bff9250", - 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"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.10.0" }, "pyparsing": { @@ -1230,7 +1157,6 @@ "sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1", "sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b" ], - "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'", "version": "==2.4.7" }, "pytest": { @@ -1246,7 +1172,6 @@ "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b", "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f" ], - "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'", "version": "==0.10.2" } } From 2100f27976cab4723f03f8eed6f56706431cfed7 Mon Sep 17 00:00:00 2001 From: Dan Date: Fri, 2 Apr 2021 17:10:05 -0400 Subject: [PATCH 3/3] fixing the api.yml file which was starting to throw errors when updating the libraries. Seems that sqlalchemy now has a hard time incrementing sequences, so putting in a fix for this. Upgrading many of our libraries, to avoid any disconnects as we try to handle security patches from these automated bumps. --- Pipfile.lock | 416 +++++++++++----------- crc/api.yml | 26 +- tests/base_test.py | 6 +- tests/workflow/test_workflow_processor.py | 4 +- 4 files changed, 226 insertions(+), 226 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index d0246927..0776d7c5 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -25,11 +25,11 @@ }, "alembic": { "hashes": [ - "sha256:422883bf429105b9b5f1fece6d79da64ed1ee648af2ef256d9b52edac236bc46", - "sha256:e871118b6174681f7e9a9ea67cfcae954c6d18e05b49c6b17f662d2530c76bf5" + "sha256:8a259f0a4c8b350b03579d77ce9e810b19c65bf0af05f84efb69af13ad50801e", + "sha256:e27fd67732c97a1c370c33169ef4578cf96436fa0e7dcfaeeef4a917d0737d56" ], "index": "pypi", - "version": "==1.5.4" + "version": "==1.5.8" }, "aniso8601": { "hashes": [ @@ -168,58 +168,61 @@ }, "coverage": { "hashes": [ - "sha256:03ed2a641e412e42cc35c244508cf186015c217f0e4d496bf6d7078ebe837ae7", - 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"version": "==5.4" + "version": "==5.5" }, "iniconfig": { "hashes": [ diff --git a/crc/api.yml b/crc/api.yml index 833efd54..6dc1afa6 100644 --- a/crc/api.yml +++ b/crc/api.yml @@ -65,7 +65,8 @@ paths: application/json: schema: type: array - $ref: "#/components/schemas/User" + items: + $ref: "#/components/schemas/User" # /v1.0/study /study: get: @@ -80,7 +81,8 @@ paths: application/json: schema: type: array - $ref: "#/components/schemas/Study" + items: + $ref: "#/components/schemas/Study" post: operationId: crc.api.study.add_study summary: Creates a new study with the given parameters. @@ -159,6 +161,7 @@ paths: /workflow_sync/{workflow_spec_id}/spec: parameters: - name: workflow_spec_id + required: true in: path description: The unique id of an existing workflow specification to modify. schema: @@ -392,7 +395,7 @@ paths: parameters: - name: spec_id in: path - required: false + required: true description: The unique id of an existing workflow specification to modify. schema: type: string @@ -441,7 +444,7 @@ paths: parameters: - name: spec_id in: path - required: false + required: true description: The unique id of an existing workflow specification to validate. schema: type: string @@ -497,7 +500,7 @@ paths: parameters: - name: cat_id in: path - required: false + required: true description: The unique id of an existing workflow spec category to modify. schema: type: string @@ -1513,8 +1516,7 @@ components: example: "random_fact" x-nullable: true file: - type: file - format: binary + type: string Workflow: properties: id: @@ -1522,7 +1524,7 @@ components: type: integer format: int64 status: - type: enum + type: string enum: ['new','user_input_required','waiting','complete'] navigation: type: array @@ -1576,7 +1578,7 @@ components: data: type: object multi_instance_type: - type: enum + type: string enum: ['none', 'looping', 'parallel', 'sequential'] multi_instance_count: type: number @@ -1709,7 +1711,7 @@ components: type: string readOnly: true type: - type: enum + type: string enum: ['string', 'long', 'boolean', 'date', 'enum'] readOnly: true label: @@ -1785,7 +1787,7 @@ components: type: string example: "Chuck Norris" data: - type: any + type: string NavigationItem: properties: id: @@ -1815,7 +1817,7 @@ components: type: integer example: 4 state: - type: enum + type: string enum: ['FUTURE', 'WAITING', 'READY', 'CANCELLED', 'COMPLETED','LIKELY','MAYBE'] readOnly: true is_decision: diff --git a/tests/base_test.py b/tests/base_test.py index 46a68422..a9fcfce1 100644 --- a/tests/base_test.py +++ b/tests/base_test.py @@ -166,8 +166,10 @@ class BaseTest(unittest.TestCase): study_model = StudyModel(**study_json) session.add(study_model) StudyService._add_all_workflow_specs_to_study(study_model) - session.execute(Sequence(StudyModel.__tablename__ + '_id_seq')) - session.commit() + session.commit() + update_seq = f"ALTER SEQUENCE %s RESTART WITH %s" % (StudyModel.__tablename__ + '_id_seq', study_model.id + 1) + print("Update Sequence." + update_seq) + session.execute(update_seq) session.flush() specs = session.query(WorkflowSpecModel).all() diff --git a/tests/workflow/test_workflow_processor.py b/tests/workflow/test_workflow_processor.py index 1d1813ed..879882c4 100644 --- a/tests/workflow/test_workflow_processor.py +++ b/tests/workflow/test_workflow_processor.py @@ -253,10 +253,8 @@ class TestWorkflowProcessor(BaseTest): processor = self.get_processor(study, workflow_spec_model) self.assertTrue(processor.get_version_string().startswith('v2.1.1')) - def test_hard_reset(self): self.load_example_data() - # Start the two_forms workflow, and enter some data in the first form. study = session.query(StudyModel).first() workflow_spec_model = self.load_test_spec("two_forms") @@ -275,6 +273,8 @@ class TestWorkflowProcessor(BaseTest): # Assure that creating a new processor doesn't cause any issues, and maintains the spec version. processor.workflow_model.bpmn_workflow_json = processor.serialize() + db.session.add(processor.workflow_model) ## Assure this isn't transient, which was causing some errors. + self.assertIsNotNone(processor.workflow_model.bpmn_workflow_json) processor2 = WorkflowProcessor(processor.workflow_model) self.assertFalse(processor2.is_latest_spec) # Still at version 1.