From 964d5573adf3f3721d9bbbd7acaa48f08fbac6de Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Tue, 16 May 2023 15:12:45 -0700 Subject: [PATCH 01/51] update poetry version --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 44b2477fa..af83b5ee0 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -27,7 +27,7 @@ jobs: test: runs-on: ubuntu-latest env: - POETRY_VERSION: 1.2.0rc1 + POETRY_VERSION: 1.2.0 strategy: fail-fast: false matrix: From 2c344f689bccceba7d4771b0b01a0b2ab24a68c7 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Tue, 16 May 2023 15:16:15 -0700 Subject: [PATCH 02/51] add `--durations` flag to test workflow --- .github/workflows/test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index af83b5ee0..2dd019cc7 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -127,7 +127,7 @@ jobs: if: ${{ contains(github.event.head_commit.message, 'runcombos') }} run: > source .venv/bin/activate; - pytest --cov-report=term --cov-report=html:htmlcov --cov=schematic/ + pytest --durations=0 --cov-report=term --cov-report=html:htmlcov --cov=schematic/ -m "not (google_credentials_needed or schematic_api or table_operations)" - name: Run tests @@ -137,7 +137,7 @@ jobs: if: ${{ false == contains(github.event.head_commit.message, 'runcombos') }} run: > source .venv/bin/activate; - pytest --cov-report=term --cov-report=html:htmlcov --cov=schematic/ + pytest --durations=0 --cov-report=term --cov-report=html:htmlcov --cov=schematic/ -m "not (google_credentials_needed or rule_combos or schematic_api or table_operations)" - name: Upload pytest test results From bd24269615cebdf74a69c478e385dd2e66522c48 Mon Sep 17 00:00:00 2001 From: Mialy DeFelice Date: Tue, 11 Jul 2023 09:43:25 -0700 Subject: [PATCH 03/51] add Component as a required attribute to the example data model --- tests/data/example.model.csv | 87 +++++++++++++++++---------------- tests/data/example.model.jsonld | 34 ++++++------- 2 files changed, 61 insertions(+), 60 deletions(-) diff --git a/tests/data/example.model.csv b/tests/data/example.model.csv index 1f6c9589c..fad3dfe61 100644 --- a/tests/data/example.model.csv +++ b/tests/data/example.model.csv @@ -1,43 +1,44 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Patient,,,"Patient ID, Sex, Year of Birth, Diagnosis, Component",,FALSE,DataType,,, -Patient ID,,,,,TRUE,DataProperty,,, -Sex,,"Female, Male, Other",,,TRUE,DataProperty,,, -Year of Birth,,,,,FALSE,DataProperty,,, -Diagnosis,,"Healthy, Cancer",,,TRUE,DataProperty,,, -Cancer,,,"Cancer Type, Family History",,FALSE,ValidValue,,, -Cancer Type,,"Breast, Colorectal, Lung, Prostate, Skin",,,TRUE,DataProperty,,, -Family History,,"Breast, Colorectal, Lung, Prostate, Skin",,,TRUE,DataProperty,,,list strict -Biospecimen,,,"Sample ID, Patient ID, Tissue Status, Component",,FALSE,DataType,Patient,, -Sample ID,,,,,TRUE,DataProperty,,, -Tissue Status,,"Healthy, Malignant",,,TRUE,DataProperty,,, -Bulk RNA-seq Assay,,,"Filename, Sample ID, File Format, Component",,FALSE,DataType,Biospecimen,, -Filename,,,,,TRUE,DataProperty,,, -File Format,,"FASTQ, BAM, CRAM, CSV/TSV",,,TRUE,DataProperty,,, -BAM,,,Genome Build,,FALSE,ValidValue,,, -CRAM,,,"Genome Build, Genome FASTA",,FALSE,ValidValue,,, -CSV/TSV,,,Genome Build,,FALSE,ValidValue,,, -Genome Build,,"GRCh37, GRCh38, GRCm38, GRCm39",,,TRUE,DataProperty,,, -Genome FASTA,,,,,TRUE,DataProperty,,, -MockComponent,,,"Component, Check List, Check Regex List, Check Regex Single, Check Regex Format, Check Num, Check Float, Check Int, Check String, Check URL,Check Match at Least, Check Match at Least values, Check Match Exactly, Check Match Exactly values, Check Recommended, Check Ages, Check Unique, Check Range, Check Date, Check NA",,FALSE,DataType,,, -Check List,,"ab, cd, ef, gh",,,TRUE,DataProperty,,,list strict -Check Regex List,,,,,TRUE,DataProperty,,,list strict::regex match [a-f] -Check Regex Single,,,,,TRUE,DataProperty,,,regex search [a-f] -Check Regex Format,,,,,TRUE,DataProperty,,,regex match [a-f] -Check Num,,,,,TRUE,DataProperty,,,num -Check Float,,,,,TRUE,DataProperty,,,float -Check Int,,,,,TRUE,DataProperty,,,int -Check String,,,,,TRUE,DataProperty,,,str -Check URL,,,,,TRUE,DataProperty,,,url -Check Match at Least,,,,,TRUE,DataProperty,,,matchAtLeastOne Patient.PatientID set -Check Match Exactly,,,,,TRUE,DataProperty,,,matchExactlyOne MockComponent.checkMatchExactly set -Check Match at Least values,,,,,TRUE,DataProperty,,,matchAtLeastOne MockComponent.checkMatchatLeastvalues value -Check Match Exactly values,,,,,TRUE,DataProperty,,,matchExactlyOne MockComponent.checkMatchExactlyvalues value -Check Recommended,,,,,FALSE,DataProperty,,,recommended -Check Ages,,,,,TRUE,DataProperty,,,protectAges -Check Unique,,,,,TRUE,DataProperty,,,unique error -Check Range,,,,,TRUE,DataProperty,,,inRange 50 100 error -Check Date,,,,,TRUE,DataProperty,,,date -Check NA,,,,,TRUE,DataProperty,,,int::IsNA -MockRDB,,,"Component, MockRDB_id, SourceManifest",,FALSE,DataType,,, -MockRDB_id,,,,,TRUE,DataProperty,,,int -SourceManifest,,,,,TRUE,DataProperty,,, +Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules +Component,,,,,TRUE,,,, +Patient,,,"Patient ID, Sex, Year of Birth, Diagnosis, Component",,FALSE,DataType,,, +Patient ID,,,,,TRUE,DataProperty,,, +Sex,,"Female, Male, Other",,,TRUE,DataProperty,,, +Year of Birth,,,,,FALSE,DataProperty,,, +Diagnosis,,"Healthy, Cancer",,,TRUE,DataProperty,,, +Cancer,,,"Cancer Type, Family History",,FALSE,ValidValue,,, +Cancer Type,,"Breast, Colorectal, Lung, Prostate, Skin",,,TRUE,DataProperty,,, +Family History,,"Breast, Colorectal, Lung, Prostate, Skin",,,TRUE,DataProperty,,,list strict +Biospecimen,,,"Sample ID, Patient ID, Tissue Status, Component",,FALSE,DataType,Patient,, +Sample ID,,,,,TRUE,DataProperty,,, +Tissue Status,,"Healthy, Malignant",,,TRUE,DataProperty,,, +Bulk RNA-seq Assay,,,"Filename, Sample ID, File Format, Component",,FALSE,DataType,Biospecimen,, +Filename,,,,,TRUE,DataProperty,,, +File Format,,"FASTQ, BAM, CRAM, CSV/TSV",,,TRUE,DataProperty,,, +BAM,,,Genome Build,,FALSE,ValidValue,,, +CRAM,,,"Genome Build, Genome FASTA",,FALSE,ValidValue,,, +CSV/TSV,,,Genome Build,,FALSE,ValidValue,,, +Genome Build,,"GRCh37, GRCh38, GRCm38, GRCm39",,,TRUE,DataProperty,,, +Genome FASTA,,,,,TRUE,DataProperty,,, +MockComponent,,,"Component, Check List, Check Regex List, Check Regex Single, Check Regex Format, Check Num, Check Float, Check Int, Check String, Check URL,Check Match at Least, Check Match at Least values, Check Match Exactly, Check Match Exactly values, Check Recommended, Check Ages, Check Unique, Check Range, Check Date, Check NA",,FALSE,DataType,,, +Check List,,"ab, cd, ef, gh",,,TRUE,DataProperty,,,list strict +Check Regex List,,,,,TRUE,DataProperty,,,list strict::regex match [a-f] +Check Regex Single,,,,,TRUE,DataProperty,,,regex search [a-f] +Check Regex Format,,,,,TRUE,DataProperty,,,regex match [a-f] +Check Num,,,,,TRUE,DataProperty,,,num +Check Float,,,,,TRUE,DataProperty,,,float +Check Int,,,,,TRUE,DataProperty,,,int +Check String,,,,,TRUE,DataProperty,,,str +Check URL,,,,,TRUE,DataProperty,,,url +Check Match at Least,,,,,TRUE,DataProperty,,,matchAtLeastOne Patient.PatientID set +Check Match Exactly,,,,,TRUE,DataProperty,,,matchExactlyOne MockComponent.checkMatchExactly set +Check Match at Least values,,,,,TRUE,DataProperty,,,matchAtLeastOne MockComponent.checkMatchatLeastvalues value +Check Match Exactly values,,,,,TRUE,DataProperty,,,matchExactlyOne MockComponent.checkMatchExactlyvalues value +Check Recommended,,,,,FALSE,DataProperty,,,recommended +Check Ages,,,,,TRUE,DataProperty,,,protectAges +Check Unique,,,,,TRUE,DataProperty,,,unique error +Check Range,,,,,TRUE,DataProperty,,,inRange 50 100 error +Check Date,,,,,TRUE,DataProperty,,,date +Check NA,,,,,TRUE,DataProperty,,,int::IsNA +MockRDB,,,"Component, MockRDB_id, SourceManifest",,FALSE,DataType,,, +MockRDB_id,,,,,TRUE,DataProperty,,,int +SourceManifest,,,,,TRUE,DataProperty,,, \ No newline at end of file diff --git a/tests/data/example.model.jsonld b/tests/data/example.model.jsonld index 2d65b72bf..2dcf89f24 100644 --- a/tests/data/example.model.jsonld +++ b/tests/data/example.model.jsonld @@ -1972,6 +1972,23 @@ "@id": "bts:OntologyClass" } }, + { + "@id": "bts:Component", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Component", + "rdfs:subClassOf": [ + { + "@id": "schema:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Component", + "sms:required": "sms:true", + "sms:validationRules": [] + }, { "@id": "bts:Patient", "@type": "rdfs:Class", @@ -2987,23 +3004,6 @@ "sms:required": "sms:true", "sms:validationRules": [] }, - { - "@id": "bts:Component", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Component", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Component", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:Female", "@type": "rdfs:Class", From c7aa0405b30fe68683a239f50271fece5dc27f9f Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 8 Sep 2023 13:26:07 -0700 Subject: [PATCH 04/51] add securitySchema component to api --- schematic_api/api/openapi/api.yaml | 8 ++++++++ schematic_api/api/security_controller_.py | 14 ++++++++++++++ 2 files changed, 22 insertions(+) create mode 100644 schematic_api/api/security_controller_.py diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index 850baab57..06c5dc6a9 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -9,6 +9,14 @@ info: servers: - url: /v1 +components: + securitySchemes: + bearerAuth: + type: http + scheme: bearer + bearerFormat: JWT + x-bearerInfoFunc: schematic_api.api.security_controller_.info_from_bearerAuth + # TO DO: refactor query parameters and remove access_token paths: /manifest/generate: diff --git a/schematic_api/api/security_controller_.py b/schematic_api/api/security_controller_.py new file mode 100644 index 000000000..ee336dcb0 --- /dev/null +++ b/schematic_api/api/security_controller_.py @@ -0,0 +1,14 @@ +from typing import List + + +def info_from_bearerAuth(token): + """ + Check and retrieve authentication information from custom bearer token. + Returned value will be passed in 'token_info' parameter of your operation function, if there is one. + 'sub' or 'uid' will be set in 'user' parameter of your operation function, if there is one. + :param token Token provided by Authorization header + :type token: str + :return: Decoded token information or None if token is invalid + :rtype: dict | None + """ + return {"uid": "user_id"} \ No newline at end of file From 8a11e3ab1d95ee8f93c94bdb845e9a8f46b18056 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 8 Sep 2023 13:30:43 -0700 Subject: [PATCH 05/51] add function to get token from header --- schematic_api/api/routes.py | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index ba9b1a7bc..23f4d79ff 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -14,6 +14,7 @@ from flask_cors import cross_origin from flask import send_from_directory from flask import current_app as app +from flask import request import pandas as pd import json @@ -146,7 +147,19 @@ def convert_json_file_to_csv(self, file_key): else: temp_path = save_file(file_key='file_name') return temp_path - + +def get_access_token() -> str: + """Get access token from header""" + bearer_token = None + # Check if the Authorization header is present + if "Authorization" in request.headers: + auth_header = request.headers["Authorization"] + + # Ensure the header starts with 'Bearer ' and retrieve the token + if auth_header.startswith("Bearer "): + bearer_token = auth_header.split(" ")[1] + return bearer_token + def parse_bool(str_bool): if str_bool.lower().startswith('t'): return True @@ -196,7 +209,7 @@ def get_temp_jsonld(schema_url): return tmp_file.name # @before_request -def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, asset_view = None, output_format=None, title=None, access_token=None, strict_validation:bool=True): +def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, asset_view = None, output_format=None, title=None, bearerAuth=None, strict_validation:bool=True): """Get the immediate dependencies that are related to a given source node. Args: schema_url: link to data model in json ld format @@ -210,6 +223,7 @@ def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, Returns: Googlesheet URL (if sheet_url is True), or pandas dataframe (if sheet_url is False). """ + access_token = get_access_token() # call config_handler() config_handler(asset_view = asset_view) @@ -819,6 +833,9 @@ def get_schematic_version() -> str: """ Return the current version of schematic """ + + access_token = get_access_token() + if "VERSION" in os.environ: version = os.environ["VERSION"] else: From 1f7b53fe07b383c06e7b695ff2666376c8b83d48 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 8 Sep 2023 13:32:01 -0700 Subject: [PATCH 06/51] Revert "add function to get token from header" This reverts commit 2408be4700e72ce774670a388ee4d6ff998d38a3. --- schematic_api/api/routes.py | 21 ++------------------- 1 file changed, 2 insertions(+), 19 deletions(-) diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index 23f4d79ff..ba9b1a7bc 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -14,7 +14,6 @@ from flask_cors import cross_origin from flask import send_from_directory from flask import current_app as app -from flask import request import pandas as pd import json @@ -147,19 +146,7 @@ def convert_json_file_to_csv(self, file_key): else: temp_path = save_file(file_key='file_name') return temp_path - -def get_access_token() -> str: - """Get access token from header""" - bearer_token = None - # Check if the Authorization header is present - if "Authorization" in request.headers: - auth_header = request.headers["Authorization"] - - # Ensure the header starts with 'Bearer ' and retrieve the token - if auth_header.startswith("Bearer "): - bearer_token = auth_header.split(" ")[1] - return bearer_token - + def parse_bool(str_bool): if str_bool.lower().startswith('t'): return True @@ -209,7 +196,7 @@ def get_temp_jsonld(schema_url): return tmp_file.name # @before_request -def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, asset_view = None, output_format=None, title=None, bearerAuth=None, strict_validation:bool=True): +def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, asset_view = None, output_format=None, title=None, access_token=None, strict_validation:bool=True): """Get the immediate dependencies that are related to a given source node. Args: schema_url: link to data model in json ld format @@ -223,7 +210,6 @@ def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, Returns: Googlesheet URL (if sheet_url is True), or pandas dataframe (if sheet_url is False). """ - access_token = get_access_token() # call config_handler() config_handler(asset_view = asset_view) @@ -833,9 +819,6 @@ def get_schematic_version() -> str: """ Return the current version of schematic """ - - access_token = get_access_token() - if "VERSION" in os.environ: version = os.environ["VERSION"] else: From 21254d55f204fc1672702232350772fb5c4fee93 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 8 Sep 2023 13:32:39 -0700 Subject: [PATCH 07/51] add method to get token from header --- schematic_api/api/routes.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index ba9b1a7bc..12e5c449e 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -14,6 +14,7 @@ from flask_cors import cross_origin from flask import send_from_directory from flask import current_app as app +from flask import request import pandas as pd import json @@ -146,6 +147,18 @@ def convert_json_file_to_csv(self, file_key): else: temp_path = save_file(file_key='file_name') return temp_path + +def get_access_token() -> str: + """Get access token from header""" + bearer_token = None + # Check if the Authorization header is present + if "Authorization" in request.headers: + auth_header = request.headers["Authorization"] + + # Ensure the header starts with 'Bearer ' and retrieve the token + if auth_header.startswith("Bearer "): + bearer_token = auth_header.split(" ")[1] + return bearer_token def parse_bool(str_bool): if str_bool.lower().startswith('t'): From d90a1bdefdb10d3d2a8e07223cdb783969f32a6b Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 8 Sep 2023 13:35:53 -0700 Subject: [PATCH 08/51] move `manifest/generation` token to header --- schematic_api/api/openapi/api.yaml | 8 ++------ schematic_api/api/routes.py | 5 ++++- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index 06c5dc6a9..1743545de 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -23,6 +23,8 @@ paths: get: summary: Endpoint to facilitate manifest generation description: Endpoint to create dynamically create metadata manifest files + security: + - bearerAuth: [] parameters: - in: query name: schema_url @@ -32,12 +34,6 @@ paths: example: >- https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld required: true - - in: query - name: access_token - schema: - type: string - description: Token is needed if getting an existing manifest on AWS - required: false - in: query name: title schema: diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index 12e5c449e..d06ce47c8 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -209,7 +209,7 @@ def get_temp_jsonld(schema_url): return tmp_file.name # @before_request -def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, asset_view = None, output_format=None, title=None, access_token=None, strict_validation:bool=True): +def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, asset_view = None, output_format=None, title=None, strict_validation:bool=True): """Get the immediate dependencies that are related to a given source node. Args: schema_url: link to data model in json ld format @@ -224,6 +224,9 @@ def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, Googlesheet URL (if sheet_url is True), or pandas dataframe (if sheet_url is False). """ + # Get access token from request header + access_token = get_access_token() + # call config_handler() config_handler(asset_view = asset_view) From a07b8c790fd41713bfbd94ac0ffc67974a99248f Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 8 Sep 2023 13:58:15 -0700 Subject: [PATCH 09/51] add fixture for request headers --- tests/test_api.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/tests/test_api.py b/tests/test_api.py index eb690d59a..39f75c619 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -93,6 +93,13 @@ def syn_token(config:Configuration): token = config_parser["authentication"]["authtoken"] yield token +@pytest.fixture +def request_headers(syn_token): + headers = { + "Authorization": "Bearer " + syn_token + } + yield headers + @pytest.mark.schematic_api class TestSynapseStorage: @pytest.mark.synapse_credentials_needed From 905668b074b76170bf9ce0cc33820f7eada7a57a Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 8 Sep 2023 14:54:11 -0700 Subject: [PATCH 10/51] Update tests to send auth token in header tests now send the access token in the headers of the request --- tests/test_api.py | 96 +++++++++++++++++++++-------------------------- 1 file changed, 43 insertions(+), 53 deletions(-) diff --git a/tests/test_api.py b/tests/test_api.py index 39f75c619..3c5e5fc0d 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -104,14 +104,13 @@ def request_headers(syn_token): class TestSynapseStorage: @pytest.mark.synapse_credentials_needed @pytest.mark.parametrize("return_type", ["json", "csv"]) - def test_get_storage_assets_tables(self, client, syn_token, return_type): + def test_get_storage_assets_tables(self, client, return_type, request_headers): params = { - "access_token": syn_token, "asset_view": "syn23643253", "return_type": return_type } - response = client.get('http://localhost:3001/v1/storage/assets/tables', query_string=params) + response = client.get('http://localhost:3001/v1/storage/assets/tables', query_string=params, headers=request_headers) assert response.status_code == 200 @@ -132,9 +131,8 @@ def test_get_storage_assets_tables(self, client, syn_token, return_type): @pytest.mark.synapse_credentials_needed @pytest.mark.parametrize("full_path", [True, False]) @pytest.mark.parametrize("file_names", [None, "Sample_A.txt"]) - def test_get_dataset_files(self,full_path, file_names, syn_token, client): + def test_get_dataset_files(self,full_path, file_names, request_headers, client): params = { - "access_token": syn_token, "asset_view": "syn23643253", "dataset_id": "syn23643250", "full_path": full_path, @@ -143,7 +141,7 @@ def test_get_dataset_files(self,full_path, file_names, syn_token, client): if file_names: params["file_names"] = file_names - response = client.get('http://localhost:3001/v1/storage/dataset/files', query_string=params) + response = client.get('http://localhost:3001/v1/storage/dataset/files', query_string=params, headers=request_headers) assert response.status_code == 200 response_dt = json.loads(response.data) @@ -160,53 +158,50 @@ def test_get_dataset_files(self,full_path, file_names, syn_token, client): else: assert ["syn25705259","Boolean Test"] and ["syn23667202","DataTypeX_table"] in response_dt + @pytest.mark.synapse_credentials_needed - def test_get_storage_project_dataset(self, syn_token, client): + def test_get_storage_project_dataset(self, request_headers, client): params = { - "access_token": syn_token, "asset_view": "syn23643253", "project_id": "syn26251192" } - response = client.get("http://localhost:3001/v1/storage/project/datasets", query_string = params) + response = client.get("http://localhost:3001/v1/storage/project/datasets", query_string = params, headers = request_headers) assert response.status_code == 200 response_dt = json.loads(response.data) assert ["syn26251193","Issue522"] in response_dt @pytest.mark.synapse_credentials_needed - def test_get_storage_project_manifests(self, syn_token, client): + def test_get_storage_project_manifests(self, request_headers, client): params = { - "access_token": syn_token, "asset_view": "syn23643253", "project_id": "syn30988314" } - response = client.get("http://localhost:3001/v1/storage/project/manifests", query_string=params) + response = client.get("http://localhost:3001/v1/storage/project/manifests", query_string=params, headers=request_headers) assert response.status_code == 200 @pytest.mark.synapse_credentials_needed - def test_get_storage_projects(self, syn_token, client): + def test_get_storage_projects(self, request_headers, client): params = { - "access_token": syn_token, "asset_view": "syn23643253" } - response = client.get("http://localhost:3001/v1/storage/projects", query_string = params) + response = client.get("http://localhost:3001/v1/storage/projects", query_string = params, headers = request_headers) assert response.status_code == 200 @pytest.mark.synapse_credentials_needed @pytest.mark.parametrize("entity_id", ["syn34640850", "syn23643253", "syn24992754"]) - def test_get_entity_type(self, syn_token, client, entity_id): + def test_get_entity_type(self, request_headers, client, entity_id): params = { - "access_token": syn_token, "asset_view": "syn23643253", "entity_id": entity_id } - response = client.get("http://localhost:3001/v1/storage/entity/type", query_string = params) + response = client.get("http://localhost:3001/v1/storage/entity/type", query_string = params, headers = request_headers) assert response.status_code == 200 response_dt = json.loads(response.data) @@ -219,13 +214,12 @@ def test_get_entity_type(self, syn_token, client, entity_id): @pytest.mark.synapse_credentials_needed @pytest.mark.parametrize("entity_id", ["syn30988314", "syn27221721"]) - def test_if_in_assetview(self, syn_token, client, entity_id): + def test_if_in_assetview(self, request_headers, client, entity_id): params = { - "access_token": syn_token, "asset_view": "syn23643253", "entity_id": entity_id } - response = client.get("http://localhost:3001/v1/storage/if_in_asset_view", query_string = params) + response = client.get("http://localhost:3001/v1/storage/if_in_asset_view", query_string = params, headers = request_headers) assert response.status_code == 200 response_dt = json.loads(response.data) @@ -418,7 +412,7 @@ def ifPandasDataframe(self, response_dt): #@pytest.mark.parametrize("output_format", [None, "excel", "google_sheet", "dataframe (only if getting existing manifests)"]) @pytest.mark.parametrize("output_format", ["excel"]) @pytest.mark.parametrize("data_type", ["Biospecimen", "Patient", "all manifests", ["Biospecimen", "Patient"]]) - def test_generate_existing_manifest(self, client, data_model_jsonld, data_type, output_format, caplog): + def test_generate_existing_manifest(self, client, data_model_jsonld, data_type, output_format, caplog, request_headers): # set dataset if data_type == "Patient": dataset_id = ["syn51730545"] #Mock Patient Manifest folder on synapse @@ -435,15 +429,18 @@ def test_generate_existing_manifest(self, client, data_model_jsonld, data_type, "title": "Example", "data_type": data_type, "use_annotations": False, - "access_token": None } + + # Previous form of the test had `access_token` set to `None` + request_headers["Authorization"] = None + if dataset_id: params['dataset_id'] = dataset_id if output_format: params['output_format'] = output_format - response = client.get('http://localhost:3001/v1/manifest/generate', query_string=params) + response = client.get('http://localhost:3001/v1/manifest/generate', query_string=params, headers=request_headers) assert response.status_code == 200 @@ -474,7 +471,7 @@ def test_generate_existing_manifest(self, client, data_model_jsonld, data_type, @pytest.mark.empty_token @pytest.mark.parametrize("output_format", ["excel", "google_sheet", "dataframe (only if getting existing manifests)", None]) @pytest.mark.parametrize("data_type", ["all manifests", ["Biospecimen", "Patient"], "Patient"]) - def test_generate_new_manifest(self, caplog, client, data_model_jsonld, data_type, output_format): + def test_generate_new_manifest(self, caplog, client, data_model_jsonld, data_type, output_format, request_headers): params = { "schema_url": data_model_jsonld, "asset_view": "syn23643253", @@ -482,9 +479,11 @@ def test_generate_new_manifest(self, caplog, client, data_model_jsonld, data_typ "data_type": data_type, "use_annotations": False, "dataset_id": None, - "access_token": None } + # Previous form of the test had `access_token` set to `None` + request_headers["Authorization"] = None + if output_format: params["output_format"] = output_format @@ -639,14 +638,13 @@ def test_validate_manifest(self, data_model_jsonld, client, json_str, restrict_r assert "warnings" in response_dt.keys() @pytest.mark.synapse_credentials_needed - def test_get_datatype_manifest(self, client, syn_token): + def test_get_datatype_manifest(self, client, request_headers): params = { - "access_token": syn_token, "asset_view": "syn23643253", "manifest_id": "syn27600110" } - response = client.get('http://localhost:3001/v1/get/datatype/manifest', query_string=params) + response = client.get('http://localhost:3001/v1/get/datatype/manifest', query_string=params, headers=request_headers) assert response.status_code == 200 response_dt = json.loads(response.data) @@ -665,16 +663,15 @@ def test_get_datatype_manifest(self, client, syn_token): @pytest.mark.parametrize("manifest_id, expected_component, expected_file_name", [("syn51078535", "BulkRNA-seqAssay", "synapse_storage_manifest.csv"), ("syn51156998", "Biospecimen", "synapse_storage_manifest_biospecimen.csv")]) @pytest.mark.parametrize("new_manifest_name",[None,"Example.csv"]) @pytest.mark.parametrize("as_json",[None,True,False]) - def test_manifest_download(self, config: Configuration, client, syn_token, manifest_id, new_manifest_name, as_json, expected_component, expected_file_name): + def test_manifest_download(self, config: Configuration, client, request_headers, manifest_id, new_manifest_name, as_json, expected_component, expected_file_name): params = { - "access_token": syn_token, "manifest_id": manifest_id, "new_manifest_name": new_manifest_name, "as_json": as_json } - response = client.get('http://localhost:3001/v1/manifest/download', query_string = params) + response = client.get('http://localhost:3001/v1/manifest/download', query_string = params, headers = request_headers) assert response.status_code == 200 # if as_json is set to True or as_json is not defined, then a json gets returned @@ -716,13 +713,12 @@ def test_manifest_download(self, config: Configuration, client, syn_token, manif @pytest.mark.synapse_credentials_needed # test downloading a manifest with access restriction and see if the correct error message got raised - def test_download_access_restricted_manifest(self, client, syn_token): + def test_download_access_restricted_manifest(self, client, request_headers): params = { - "access_token": syn_token, "manifest_id": "syn29862078" } - response = client.get('http://localhost:3001/v1/manifest/download', query_string = params) + response = client.get('http://localhost:3001/v1/manifest/download', query_string = params, headers = request_headers) assert response.status_code == 500 with pytest.raises(TypeError) as exc_info: raise TypeError('the type error got raised') @@ -731,16 +727,15 @@ def test_download_access_restricted_manifest(self, client, syn_token): @pytest.mark.synapse_credentials_needed @pytest.mark.parametrize("as_json", [None, True, False]) @pytest.mark.parametrize("new_manifest_name", [None, "Test"]) - def test_dataset_manifest_download(self, client, as_json, syn_token, new_manifest_name): + def test_dataset_manifest_download(self, client, as_json, request_headers, new_manifest_name): params = { - "access_token": syn_token, "asset_view": "syn28559058", "dataset_id": "syn28268700", "as_json": as_json, "new_manifest_name": new_manifest_name } - response = client.get('http://localhost:3001/v1/dataset/manifest/download', query_string = params) + response = client.get('http://localhost:3001/v1/dataset/manifest/download', query_string = params, headers = request_headers) assert response.status_code == 200 response_dt = response.data @@ -759,11 +754,10 @@ def test_dataset_manifest_download(self, client, as_json, syn_token, new_manifes @pytest.mark.synapse_credentials_needed @pytest.mark.submission - def test_submit_manifest_table_and_file_replace(self, client, syn_token, data_model_jsonld, test_manifest_submit): + def test_submit_manifest_table_and_file_replace(self, client, request_headers, data_model_jsonld, test_manifest_submit): """Testing submit manifest in a csv format as a table and a file. Only replace the table """ params = { - "access_token": syn_token, "schema_url": data_model_jsonld, "data_type": "Biospecimen", "restrict_rules": False, @@ -775,16 +769,15 @@ def test_submit_manifest_table_and_file_replace(self, client, syn_token, data_mo "use_schema_label": True } - response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")}) + response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")}, headers=request_headers) assert response_csv.status_code == 200 @pytest.mark.synapse_credentials_needed @pytest.mark.submission - def test_submit_manifest_file_only_replace(self, client, syn_token, data_model_jsonld, test_manifest_submit): + def test_submit_manifest_file_only_replace(self, client, request_headers, data_model_jsonld, test_manifest_submit): """Testing submit manifest in a csv format as a file """ params = { - "access_token": syn_token, "schema_url": data_model_jsonld, "data_type": "Biospecimen", "restrict_rules": False, @@ -794,17 +787,16 @@ def test_submit_manifest_file_only_replace(self, client, syn_token, data_model_j "table_manipulation": 'replace', "use_schema_label": True } - response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")}) + response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")}, headers=request_headers) assert response_csv.status_code == 200 @pytest.mark.synapse_credentials_needed @pytest.mark.submission - def test_submit_manifest_json_str_replace(self, client, syn_token, data_model_jsonld): + def test_submit_manifest_json_str_replace(self, client, request_headers, data_model_jsonld): """Submit json str as a file """ json_str = '[{"Sample ID": 123, "Patient ID": 1,"Tissue Status": "Healthy","Component": "Biospecimen"}]' params = { - "access_token": syn_token, "schema_url": data_model_jsonld, "data_type": "Biospecimen", "json_str": json_str, @@ -816,14 +808,13 @@ def test_submit_manifest_json_str_replace(self, client, syn_token, data_model_js "use_schema_label": True } params["json_str"] = json_str - response = client.post('http://localhost:3001/v1/model/submit', query_string = params, data={"file_name":''}) + response = client.post('http://localhost:3001/v1/model/submit', query_string = params, data={"file_name":''}, headers = request_headers) assert response.status_code == 200 @pytest.mark.synapse_credentials_needed @pytest.mark.submission - def test_submit_manifest_w_file_and_entities(self, client, syn_token, data_model_jsonld, test_manifest_submit): + def test_submit_manifest_w_file_and_entities(self, client, request_headers, data_model_jsonld, test_manifest_submit): params = { - "access_token": syn_token, "schema_url": data_model_jsonld, "data_type": "Biospecimen", "restrict_rules": False, @@ -835,14 +826,13 @@ def test_submit_manifest_w_file_and_entities(self, client, syn_token, data_model } # test uploading a csv file - response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")}) + response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")}, headers=request_headers) assert response_csv.status_code == 200 @pytest.mark.synapse_credentials_needed @pytest.mark.submission - def test_submit_manifest_table_and_file_upsert(self, client, syn_token, data_model_jsonld, test_upsert_manifest_csv, ): + def test_submit_manifest_table_and_file_upsert(self, client, request_headers, data_model_jsonld, test_upsert_manifest_csv, ): params = { - "access_token": syn_token, "schema_url": data_model_jsonld, "data_type": "MockRDB", "restrict_rules": False, @@ -854,7 +844,7 @@ def test_submit_manifest_table_and_file_upsert(self, client, syn_token, data_mod } # test uploading a csv file - response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_upsert_manifest_csv, 'rb'), "test.csv")},) + response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_upsert_manifest_csv, 'rb'), "test.csv")}, headers=request_headers) assert response_csv.status_code == 200 @pytest.mark.schematic_api From 082b70fd17f341fdea7c9480052a422bf4846bbf Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 8 Sep 2023 14:59:33 -0700 Subject: [PATCH 11/51] fix missed header param --- tests/test_api.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_api.py b/tests/test_api.py index 3c5e5fc0d..31a52b297 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -488,7 +488,7 @@ def test_generate_new_manifest(self, caplog, client, data_model_jsonld, data_typ params["output_format"] = output_format - response = client.get('http://localhost:3001/v1/manifest/generate', query_string=params) + response = client.get('http://localhost:3001/v1/manifest/generate', query_string=params, headers=request_headers) assert response.status_code == 200 From c529fe115f25871d111e94aa786453245c07b77c Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 8 Sep 2023 15:18:08 -0700 Subject: [PATCH 12/51] add marks for tests that need synapse credentials --- tests/test_api.py | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/tests/test_api.py b/tests/test_api.py index 31a52b297..23b32d174 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -127,7 +127,7 @@ def test_get_storage_assets_tables(self, client, return_type, request_headers): os.remove(response_dt) else: pass - + @pytest.mark.synapse_credentials_needed @pytest.mark.parametrize("full_path", [True, False]) @pytest.mark.parametrize("file_names", [None, "Sample_A.txt"]) @@ -158,7 +158,6 @@ def test_get_dataset_files(self,full_path, file_names, request_headers, client): else: assert ["syn25705259","Boolean Test"] and ["syn23667202","DataTypeX_table"] in response_dt - @pytest.mark.synapse_credentials_needed def test_get_storage_project_dataset(self, request_headers, client): params = { @@ -711,7 +710,7 @@ def test_manifest_download(self, config: Configuration, client, request_headers, except: pass - @pytest.mark.synapse_credentials_needed + @pytest.mark.synapse_credentials_needed # test downloading a manifest with access restriction and see if the correct error message got raised def test_download_access_restricted_manifest(self, client, request_headers): params = { @@ -723,7 +722,7 @@ def test_download_access_restricted_manifest(self, client, request_headers): with pytest.raises(TypeError) as exc_info: raise TypeError('the type error got raised') assert exc_info.value.args[0] == "the type error got raised" - + @pytest.mark.synapse_credentials_needed @pytest.mark.parametrize("as_json", [None, True, False]) @pytest.mark.parametrize("new_manifest_name", [None, "Test"]) @@ -751,8 +750,8 @@ def test_dataset_manifest_download(self, client, as_json, request_headers, new_m assert isinstance(response_path, str) assert response_path.endswith(".csv") - - @pytest.mark.synapse_credentials_needed + + @pytest.mark.synapse_credentials_needed @pytest.mark.submission def test_submit_manifest_table_and_file_replace(self, client, request_headers, data_model_jsonld, test_manifest_submit): """Testing submit manifest in a csv format as a table and a file. Only replace the table @@ -789,7 +788,6 @@ def test_submit_manifest_file_only_replace(self, client, request_headers, data_m } response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")}, headers=request_headers) assert response_csv.status_code == 200 - @pytest.mark.synapse_credentials_needed @pytest.mark.submission def test_submit_manifest_json_str_replace(self, client, request_headers, data_model_jsonld): From 856aab1eb0f71e6ff77d4c44ed702f405b8df36e Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 8 Sep 2023 15:26:50 -0700 Subject: [PATCH 13/51] move token to header for remaining endpoints --- schematic_api/api/openapi/api.yaml | 109 ++++++----------------------- schematic_api/api/routes.py | 58 +++++++++++---- 2 files changed, 66 insertions(+), 101 deletions(-) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index 1743545de..97b23d8d1 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -115,15 +115,9 @@ paths: get: summary: Endpoint to download an existing manifest by using a manifest id description: Endpoint to download an existing manifest by using a manifest id + security: + - bearerAuth: [] parameters: - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - example: Token - required: true - in: query name: manifest_id schema: @@ -164,15 +158,9 @@ paths: get: summary: Endpoint to download an existing manifest by using a dataset id description: Endpoint to download an existing manifest by using a dataset id + security: + - bearerAuth: [] parameters: - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - example: Token - required: true - in: query name: asset_view schema: @@ -303,6 +291,8 @@ paths: description: Upload a json or a csv file. type: string format: binary + security: + - bearerAuth: [] parameters: - in: query name: schema_url @@ -347,13 +337,6 @@ paths: description: If true, annotations with blank values will be hidden from a dataset's annotation list in Synaspe. If false, annotations with blank values will be displayed. Default to false required: false example: false - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - required: true - in: query name: asset_view schema: @@ -503,15 +486,9 @@ paths: summary: Get datatype of attributes in manifest description: Get datatype of attributes in manifest operationId: schematic_api.api.routes.get_manifest_datatype + security: + - bearerAuth: [] parameters: - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - example: Token - required: true - in: query name: asset_view schema: @@ -540,15 +517,9 @@ paths: summary: Get all storage projects the current user has access to description: Gets all storage projects the current user has access to, within the scope of the 'storageFileview' attribute. operationId: schematic_api.api.routes.get_storage_projects + security: + - bearerAuth: [] parameters: - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - example: Token - required: true - in: query name: asset_view schema: @@ -569,15 +540,9 @@ paths: summary: Gets all datasets in folder under a given storage project that the current user has access to. description: Gets all datasets in folder under a given storage project that the current user has access to. operationId: schematic_api.api.routes.get_storage_projects_datasets + security: + - bearerAuth: [] parameters: - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - example: Token - required: true - in: query name: asset_view schema: @@ -606,15 +571,9 @@ paths: summary: Get all files in a given dataset folder description: Get all files in a given dataset folder operationId: schematic_api.api.routes.get_files_storage_dataset + security: + - bearerAuth: [] parameters: - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - example: Token - required: true - in: query name: asset_view schema: @@ -659,15 +618,9 @@ paths: summary: Retrieve asset view table as a dataframe. description: Retrieve asset view table as a dataframe. operationId: schematic_api.api.routes.get_asset_view_table + security: + - bearerAuth: [] parameters: - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - example: Token - required: true - in: query name: asset_view schema: @@ -696,15 +649,9 @@ paths: summary: Gets all metadata manifest files across all datasets in a specified project. description: Gets all metadata manifest files across all datasets in a specified project. operationId: schematic_api.api.routes.get_project_manifests + security: + - bearerAuth: [] parameters: - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - example: Token - required: true - in: query name: project_id schema: @@ -744,15 +691,9 @@ paths: summary: Check type of an entity description: Check type of an entity and return entity type operationId: schematic_api.api.routes.check_entity_type + security: + - bearerAuth: [] parameters: - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - example: Token - required: true - in: query name: entity_id schema: @@ -774,15 +715,9 @@ paths: summary: Check if a file or a folder is in a given asset view. Return "true" or "false" description: Check if a file or a folder is in a given asset view. Return "true" or "false" operationId: schematic_api.api.routes.check_if_files_in_assetview + security: + - bearerAuth: [] parameters: - - in: query - name: access_token - schema: - type: string - nullable: false - description: Token - example: Token - required: true - in: query name: asset_view schema: diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index d06ce47c8..e19fcb859 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -218,7 +218,6 @@ def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, output_format: contains three option: "excel", "google_sheet", and "dataframe". if set to "excel", return an excel spreadsheet use_annotations: Whether to use existing annotations during manifest generation asset_view: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project. - access_token: Token strict: bool, strictness with which to apply validation rules to google sheets. Returns: Googlesheet URL (if sheet_url is True), or pandas dataframe (if sheet_url is False). @@ -267,7 +266,8 @@ def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, f"Please check your submission and try again." ) - + # Since this function is called in `get_manifest_route`, + # it can use the access_token passed in from there and retain `access_token` as a parameter def create_single_manifest(data_type, title, dataset_id=None, output_format=None, access_token=None, strict=strict_validation): # create object of type ManifestGenerator manifest_generator = ManifestGenerator( @@ -393,7 +393,8 @@ def submit_manifest_route(schema_url, asset_view=None, manifest_record_type=None metadata_model = initalize_metadata_model(schema_url) - access_token = connexion.request.args["access_token"] + # Access token now stored in request header + access_token = get_access_token() use_schema_label = connexion.request.args["use_schema_label"] @@ -445,7 +446,10 @@ def populate_manifest_route(schema_url, title=None, data_type=None, return_excel return populated_manifest_link -def get_storage_projects(access_token, asset_view): +def get_storage_projects(asset_view): + # Access token now stored in request header + access_token = get_access_token() + # call config handler config_handler(asset_view=asset_view) @@ -457,7 +461,10 @@ def get_storage_projects(access_token, asset_view): return lst_storage_projects -def get_storage_projects_datasets(access_token, asset_view, project_id): +def get_storage_projects_datasets(asset_view, project_id): + # Access token now stored in request header + access_token = get_access_token() + # call config handler config_handler(asset_view=asset_view) @@ -469,7 +476,10 @@ def get_storage_projects_datasets(access_token, asset_view, project_id): return sorted_dataset_lst -def get_files_storage_dataset(access_token, asset_view, dataset_id, full_path, file_names=None): +def get_files_storage_dataset(asset_view, dataset_id, full_path, file_names=None): + # Access token now stored in request header + access_token = get_access_token() + # call config handler config_handler(asset_view=asset_view) @@ -484,7 +494,10 @@ def get_files_storage_dataset(access_token, asset_view, dataset_id, full_path, f file_lst = store.getFilesInStorageDataset(datasetId=dataset_id, fileNames=file_names, fullpath=full_path) return file_lst -def check_if_files_in_assetview(access_token, asset_view, entity_id): +def check_if_files_in_assetview(asset_view, entity_id): + # Access token now stored in request header + access_token = get_access_token() + # call config handler config_handler(asset_view=asset_view) @@ -496,7 +509,10 @@ def check_if_files_in_assetview(access_token, asset_view, entity_id): return if_exists -def check_entity_type(access_token, entity_id): +def check_entity_type(entity_id): + # Access token now stored in request header + access_token = get_access_token() + # call config handler config_handler() @@ -562,17 +578,19 @@ def get_viz_tangled_tree_layers(schema_url, figure_type): return layers[0] -def download_manifest(access_token, manifest_id, new_manifest_name='', as_json=True): +def download_manifest(manifest_id, new_manifest_name='', as_json=True): """ Download a manifest based on a given manifest id. Args: - access_token: token of asset store manifest_syn_id: syn id of a manifest newManifestName: new name of a manifest that gets downloaded. as_json: boolean; If true, return a manifest as a json. Default to True Return: file path of the downloaded manifest """ + # Access token now stored in request header + access_token = get_access_token() + # call config_handler() config_handler() @@ -592,7 +610,10 @@ def download_manifest(access_token, manifest_id, new_manifest_name='', as_json=T return manifest_local_file_path #@profile(sort_by='cumulative', strip_dirs=True) -def download_dataset_manifest(access_token, dataset_id, asset_view, as_json, new_manifest_name=''): +def download_dataset_manifest(dataset_id, asset_view, as_json, new_manifest_name=''): + # Access token now stored in request header + access_token = get_access_token() + # call config handler config_handler(asset_view=asset_view) @@ -616,7 +637,10 @@ def download_dataset_manifest(access_token, dataset_id, asset_view, as_json, new return manifest_local_file_path -def get_asset_view_table(access_token, asset_view, return_type): +def get_asset_view_table(asset_view, return_type): + # Access token now stored in request header + access_token = get_access_token() + # call config handler config_handler(asset_view=asset_view) @@ -637,7 +661,10 @@ def get_asset_view_table(access_token, asset_view, return_type): return export_path -def get_project_manifests(access_token, project_id, asset_view): +def get_project_manifests(project_id, asset_view): + # Access token now stored in request header + access_token = get_access_token() + # use the default asset view from config config_handler(asset_view=asset_view) @@ -649,7 +676,10 @@ def get_project_manifests(access_token, project_id, asset_view): return lst_manifest -def get_manifest_datatype(access_token, manifest_id, asset_view): +def get_manifest_datatype(manifest_id, asset_view): + # Access token now stored in request header + access_token = get_access_token() + # use the default asset view from config config_handler(asset_view=asset_view) From a4e3f87829a495bc2de72e8d9e81a056d1a129e2 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 11 Sep 2023 10:27:29 -0700 Subject: [PATCH 14/51] make token optional for `/manifest/generate` --- schematic_api/api/openapi/api.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index 97b23d8d1..16c04900d 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -25,6 +25,7 @@ paths: description: Endpoint to create dynamically create metadata manifest files security: - bearerAuth: [] + - {} parameters: - in: query name: schema_url From 6ccb442bb8a33d0d7ef9559b83fa312b4ca4088c Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 11 Sep 2023 15:33:17 -0700 Subject: [PATCH 15/51] use better name --- schematic_api/api/openapi/api.yaml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index 16c04900d..80aabff4e 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -11,7 +11,7 @@ servers: components: securitySchemes: - bearerAuth: + access_token: type: http scheme: bearer bearerFormat: JWT @@ -24,7 +24,7 @@ paths: summary: Endpoint to facilitate manifest generation description: Endpoint to create dynamically create metadata manifest files security: - - bearerAuth: [] + - access_token: [] - {} parameters: - in: query @@ -117,7 +117,7 @@ paths: summary: Endpoint to download an existing manifest by using a manifest id description: Endpoint to download an existing manifest by using a manifest id security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: manifest_id @@ -160,7 +160,7 @@ paths: summary: Endpoint to download an existing manifest by using a dataset id description: Endpoint to download an existing manifest by using a dataset id security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: asset_view @@ -293,7 +293,7 @@ paths: type: string format: binary security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: schema_url @@ -488,7 +488,7 @@ paths: description: Get datatype of attributes in manifest operationId: schematic_api.api.routes.get_manifest_datatype security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: asset_view @@ -519,7 +519,7 @@ paths: description: Gets all storage projects the current user has access to, within the scope of the 'storageFileview' attribute. operationId: schematic_api.api.routes.get_storage_projects security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: asset_view @@ -542,7 +542,7 @@ paths: description: Gets all datasets in folder under a given storage project that the current user has access to. operationId: schematic_api.api.routes.get_storage_projects_datasets security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: asset_view @@ -573,7 +573,7 @@ paths: description: Get all files in a given dataset folder operationId: schematic_api.api.routes.get_files_storage_dataset security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: asset_view @@ -620,7 +620,7 @@ paths: description: Retrieve asset view table as a dataframe. operationId: schematic_api.api.routes.get_asset_view_table security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: asset_view @@ -651,7 +651,7 @@ paths: description: Gets all metadata manifest files across all datasets in a specified project. operationId: schematic_api.api.routes.get_project_manifests security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: project_id @@ -693,7 +693,7 @@ paths: description: Check type of an entity and return entity type operationId: schematic_api.api.routes.check_entity_type security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: entity_id @@ -717,7 +717,7 @@ paths: description: Check if a file or a folder is in a given asset view. Return "true" or "false" operationId: schematic_api.api.routes.check_if_files_in_assetview security: - - bearerAuth: [] + - access_token: [] parameters: - in: query name: asset_view From 7a2baddff4017695a4e55785df94123b4e02c036 Mon Sep 17 00:00:00 2001 From: Mialy DeFelice Date: Tue, 19 Sep 2023 15:32:59 -0700 Subject: [PATCH 16/51] update updateDB to take sg and se --- schematic/store/synapse.py | 68 +++++++++++++++++++++----------------- 1 file changed, 37 insertions(+), 31 deletions(-) diff --git a/schematic/store/synapse.py b/schematic/store/synapse.py index 40915824b..46b5f7a73 100644 --- a/schematic/store/synapse.py +++ b/schematic/store/synapse.py @@ -800,7 +800,7 @@ def getProjectManifests(self, projectId: str) -> List[str]: return manifests - def upload_project_manifests_to_synapse(self, projectId: str) -> List[str]: + def upload_project_manifests_to_synapse(self, sg: SchemaGenerator, se: SchemaExplorer, projectId: str) -> List[str]: """Upload all metadata manifest files across all datasets in a specified project as tables in Synapse. Returns: String of all the manifest_table_ids of all the manifests that have been loaded. @@ -822,7 +822,7 @@ def upload_project_manifests_to_synapse(self, projectId: str) -> List[str]: manifest_name = manifest_info["properties"]["name"] manifest_path = manifest_info["path"] manifest_df = load_df(manifest_path) - manifest_table_id = uploadDB(manifest, datasetId, datasetName) + manifest_table_id = uploadDB(sg=sg, se=se, manifest=manifest, datasetId=datasetId, table_name=datasetName) manifest_loaded.append(datasetName) return manifest_loaded @@ -952,7 +952,8 @@ def get_table_info(self, datasetId: str = None, projectId: str = None) -> List[s @missing_entity_handler def uploadDB(self, - sg: SchemaGenerator, + sg: SchemaGenerator, + se: SchemaExplorer, manifest: pd.DataFrame, datasetId: str, table_name: str, @@ -964,6 +965,7 @@ def uploadDB(self, Method to upload a database to an asset store. In synapse, this will upload a metadata table Args: + sg: schemaGenerator object se: schemaExplorer object manifest: pd.Df manifest to upload datasetId: synID of the dataset for the manifest @@ -981,13 +983,13 @@ def uploadDB(self, """ - col_schema, table_manifest = self.formatDB(sg, manifest, useSchemaLabel) + col_schema, table_manifest = self.formatDB(se=se, manifest=manifest, useSchemaLabel=useSchemaLabel) manifest_table_id = self.buildDB(datasetId, table_name, col_schema, table_manifest, table_manipulation, sg, restrict,) return manifest_table_id, manifest, table_manifest - def formatDB(self, sg, manifest, useSchemaLabel): + def formatDB(self, se, manifest, useSchemaLabel): """ Method to format a manifest appropriatly for upload as table @@ -1010,7 +1012,7 @@ def formatDB(self, sg, manifest, useSchemaLabel): if useSchemaLabel: cols = [ - sg.se.get_class_label_from_display_name( + se.get_class_label_from_display_name( str(col) ).translate({ord(x): '' for x in blacklist_chars}) for col in manifest_columns @@ -1499,13 +1501,14 @@ def upload_manifest_as_table( """ # Upload manifest as a table, get the ID and updated manifest. manifest_synapse_table_id, manifest, table_manifest = self.uploadDB( - schemaGenerator, - manifest, - datasetId, - table_name, - restrict, - useSchemaLabel, - table_manipulation) + sg=schemaGenerator, + se=se, + manifest=manifest, + datasetId=datasetId, + table_name=table_name, + restrict=restrict, + useSchemaLabel=useSchemaLabel, + table_manipulation=table_manipulation) manifest = self.add_annotations_to_entities_files(se, schemaGenerator, manifest, manifest_record_type, datasetId, hideBlanks, manifest_synapse_table_id) # Load manifest to synapse as a CSV File @@ -1518,13 +1521,14 @@ def upload_manifest_as_table( # Update manifest Synapse table with new entity id column. manifest_synapse_table_id, manifest, table_manifest = self.uploadDB( - schemaGenerator, - manifest, - datasetId, - table_name, - restrict, + sg=schemaGenerator, + se=se, + manifest=manifest, + datasetId=datasetId, + table_name=table_name, + restrict=restrict, useSchemaLabel=useSchemaLabel, - table_manipulation='update',) + table_manipulation='update') # Set annotations for the table manifest manifest_annotations = self.format_manifest_annotations(manifest, manifest_synapse_table_id) @@ -1605,13 +1609,14 @@ def upload_manifest_combo( manifest_synapse_file_id (str): SynID of manifest csv uploaded to synapse. """ manifest_synapse_table_id, manifest, table_manifest = self.uploadDB( - se, - manifest, - datasetId, - table_name, - restrict, + sg=schemaGenerator, + se=se, + manifest=manifest, + datasetId=datasetId, + table_name=table_name, + restrict=restrict, useSchemaLabel=useSchemaLabel, - table_manipulation=table_manipulation,) + table_manipulation=table_manipulation) manifest = self.add_annotations_to_entities_files(se, schemaGenerator, manifest, manifest_record_type, datasetId, hideBlanks, manifest_synapse_table_id) @@ -1625,13 +1630,14 @@ def upload_manifest_combo( # Update manifest Synapse table with new entity id column. manifest_synapse_table_id, manifest, table_manifest = self.uploadDB( - se, - manifest, - datasetId, - table_name, - restrict, + sg=schemaGenerator, + se=se, + manifest=manifest, + datasetId=datasetId, + table_name=table_name, + restrict=restrict, useSchemaLabel=useSchemaLabel, - table_manipulation='update',) + table_manipulation='update') # Set annotations for the table manifest manifest_annotations = self.format_manifest_annotations(manifest, manifest_synapse_table_id) From 5b7a913ad3bce234d4c3fef8280406309a445469 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 22 Sep 2023 10:04:43 -0700 Subject: [PATCH 17/51] Revert "Revert "Raise a helpful error when a datatype cannot be found in a schema"" This reverts commit 492fbf112b4aa0973de5c811ef4bfde8216ab0cb. --- schematic/manifest/generator.py | 21 ++++++++++++++++----- tests/test_manifest.py | 27 +++++++++++++++++++++++---- 2 files changed, 39 insertions(+), 9 deletions(-) diff --git a/schematic/manifest/generator.py b/schematic/manifest/generator.py index c9cb81cdf..778ba411d 100644 --- a/schematic/manifest/generator.py +++ b/schematic/manifest/generator.py @@ -54,7 +54,11 @@ def __init__( self.creds = services_creds["creds"] # schema root - self.root = root + if root: + self.root = root + # Raise an error if no DataType has been provided + else: + raise ValueError("No DataType has been provided.") # alphabetize valid values self.alphabetize = alphabetize_valid_values @@ -79,12 +83,19 @@ def __init__( # additional metadata to add to manifest self.additional_metadata = additional_metadata + + # Check if the class is in the schema + root_in_schema = self.sg.se.is_class_in_schema(self.root) + + # If the class could not be found, give a notification + if not root_in_schema: + exception_message = f"The DataType entered ({self.root}) could not be found in the data model schema. " + \ + "Please confirm that the datatype is in the data model and that the spelling matches the class label in the .jsonld file." + raise LookupError(exception_message) # Determine whether current data type is file-based - is_file_based = False - if self.root: - is_file_based = "Filename" in self.sg.get_node_dependencies(self.root) - self.is_file_based = is_file_based + self.is_file_based = "Filename" in self.sg.get_node_dependencies(self.root) + def _attribute_to_letter(self, attribute, manifest_fields): """Map attribute to column letter in a google sheet""" diff --git a/tests/test_manifest.py b/tests/test_manifest.py index 21f2f4285..0eb905cf1 100644 --- a/tests/test_manifest.py +++ b/tests/test_manifest.py @@ -87,13 +87,34 @@ def test_init(self, helpers): generator = ManifestGenerator( title="mock_title", path_to_json_ld=helpers.get_data_path("example.model.jsonld"), + root = "Patient" ) assert type(generator.title) is str # assert generator.sheet_service == mock_creds["sheet_service"] - assert generator.root is None + assert generator.root is "Patient" assert type(generator.sg) is SchemaGenerator + @pytest.mark.parametrize("data_type, exc, exc_message", + [("MissingComponent", LookupError, "could not be found in the data model schema"), + (None, ValueError, "No DataType has been provided.")], + ids = ["DataType not found in Schema", "No DataType provided"]) + def test_missing_root_error(self, helpers, data_type, exc, exc_message): + """ + Test for errors when either no DataType is provided or when a DataType is provided but not found in the schema + """ + + # A LookupError should be raised and include message when the component cannot be found + with pytest.raises(exc) as e: + generator = ManifestGenerator( + path_to_json_ld=helpers.get_data_path("example.model.jsonld"), + root=data_type, + use_annotations=False, + ) + + # Check message contents + assert exc_message in str(e) + @pytest.mark.google_credentials_needed def test_get_manifest_first_time(self, manifest): @@ -145,7 +166,7 @@ def test_get_manifest_first_time(self, manifest): # An annotation merged with an attribute from the data model if use_annotations: assert output["File Format"].tolist() == ["txt", "csv", "fastq"] - + @pytest.mark.parametrize("output_format", [None, "dataframe", "excel", "google_sheet"]) @pytest.mark.parametrize("sheet_url", [None, True, False]) @pytest.mark.parametrize("dataset_id", [None, "syn27600056"]) @@ -412,5 +433,3 @@ def test_populate_existing_excel_spreadsheet(self, simple_manifest_generator, si # remove file os.remove(dummy_output_path) - - From 70302e4cf46fb663f530c52ec0015a59ed048def Mon Sep 17 00:00:00 2001 From: Mialy DeFelice Date: Fri, 22 Sep 2023 12:39:18 -0700 Subject: [PATCH 18/51] add functions to return a node display name and requirement, if coming from biothings --- schematic/schemas/generator.py | 32 +++++++++++++++++++++++++------- 1 file changed, 25 insertions(+), 7 deletions(-) diff --git a/schematic/schemas/generator.py b/schematic/schemas/generator.py index 8cb392470..0207ffc17 100644 --- a/schematic/schemas/generator.py +++ b/schematic/schemas/generator.py @@ -340,6 +340,19 @@ def is_node_required(self, node_display_name: str) -> bool: return node_required + def get_node_display_name(self, node_label: str, mm_graph: nx.MultiDiGraph) -> list: + """Get display name associated with a given node label, return id if no display name. + Args: + node_label, str: Node to retrieve display name for + Returns: + node_display_name: display name of the node, or its id if it does not have a display name. + """ + if "displayName" in mm_graph.nodes[node_label]: + node_display_name = mm_graph.nodes[node_label]["displayName"] + else: + node_display_name = mm_graph.nodes[node_label]["id"].split(':')[1] + return node_display_name + def get_nodes_display_names( self, node_list: List[str], mm_graph: nx.MultiDiGraph ) -> List[str]: @@ -349,12 +362,13 @@ def get_nodes_display_names( node_list: List of nodes whose display names we need to retrieve. Returns: - List of display names. + List of display names, return id if no display name """ - node_list_display_names = [ - mm_graph.nodes[node]["displayName"] for node in node_list - ] - + node_list_display_names = [mm_graph.nodes[node]['displayName'] + if 'displayName' in mm_graph.nodes[node] + else mm_graph.nodes[node]['id'].split(':')[1] + for node in node_list + ] return node_list_display_names def get_range_schema( @@ -430,8 +444,12 @@ def is_required(self, node_name: str, mm_graph: nx.MultiDiGraph) -> bool: Boolean value indicating if the node is required or not. True: yes, it is required. False: no, it is not required. + Return False, if no required key """ - return mm_graph.nodes[node_name]["required"] + if "required" in mm_graph.nodes[node_name]: + return mm_graph.nodes[node_name]["required"] + else: + return False def get_json_schema_requirements(self, source_node: str, schema_name: str) -> Dict: """Consolidated method that aims to gather dependencies and value constraints across terms / nodes in a schema.org schema and store them in a jsonschema /JSON Schema schema. @@ -505,7 +523,7 @@ def get_json_schema_requirements(self, source_node: str, schema_name: str) -> Di ) # get process node display name - node_display_name = mm_graph.nodes[process_node]["displayName"] + node_display_name = self.get_node_display_name(node_label=process_node, mm_graph=mm_graph) # updating map between node and node's valid values for n in node_range_d: From abb0c3cd1946f5232ceac51d1959c0b72a7ce084 Mon Sep 17 00:00:00 2001 From: Mialy DeFelice Date: Fri, 29 Sep 2023 13:35:13 -0700 Subject: [PATCH 19/51] simplify function to get list of display names --- schematic/schemas/generator.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/schematic/schemas/generator.py b/schematic/schemas/generator.py index 0207ffc17..530147736 100644 --- a/schematic/schemas/generator.py +++ b/schematic/schemas/generator.py @@ -364,11 +364,9 @@ def get_nodes_display_names( Returns: List of display names, return id if no display name """ - node_list_display_names = [mm_graph.nodes[node]['displayName'] - if 'displayName' in mm_graph.nodes[node] - else mm_graph.nodes[node]['id'].split(':')[1] - for node in node_list - ] + + node_list_display_names = [self.get_node_display_name(node, mm_graph) for node in node_list] + return node_list_display_names def get_range_schema( From 463cb547fd8cb6385a2369d07654899836144cb5 Mon Sep 17 00:00:00 2001 From: Mialy DeFelice Date: Mon, 2 Oct 2023 10:49:16 -0700 Subject: [PATCH 20/51] simplify sg ref --- schematic/store/synapse.py | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/schematic/store/synapse.py b/schematic/store/synapse.py index 46b5f7a73..f6e7e7096 100644 --- a/schematic/store/synapse.py +++ b/schematic/store/synapse.py @@ -800,7 +800,7 @@ def getProjectManifests(self, projectId: str) -> List[str]: return manifests - def upload_project_manifests_to_synapse(self, sg: SchemaGenerator, se: SchemaExplorer, projectId: str) -> List[str]: + def upload_project_manifests_to_synapse(self, sg: SchemaGenerator, projectId: str) -> List[str]: """Upload all metadata manifest files across all datasets in a specified project as tables in Synapse. Returns: String of all the manifest_table_ids of all the manifests that have been loaded. @@ -822,7 +822,7 @@ def upload_project_manifests_to_synapse(self, sg: SchemaGenerator, se: SchemaExp manifest_name = manifest_info["properties"]["name"] manifest_path = manifest_info["path"] manifest_df = load_df(manifest_path) - manifest_table_id = uploadDB(sg=sg, se=se, manifest=manifest, datasetId=datasetId, table_name=datasetName) + manifest_table_id = uploadDB(sg=sg, manifest=manifest, datasetId=datasetId, table_name=datasetName) manifest_loaded.append(datasetName) return manifest_loaded @@ -953,7 +953,6 @@ def get_table_info(self, datasetId: str = None, projectId: str = None) -> List[s @missing_entity_handler def uploadDB(self, sg: SchemaGenerator, - se: SchemaExplorer, manifest: pd.DataFrame, datasetId: str, table_name: str, @@ -966,7 +965,6 @@ def uploadDB(self, Args: sg: schemaGenerator object - se: schemaExplorer object manifest: pd.Df manifest to upload datasetId: synID of the dataset for the manifest table_name: name of the table to be uploaded @@ -983,18 +981,18 @@ def uploadDB(self, """ - col_schema, table_manifest = self.formatDB(se=se, manifest=manifest, useSchemaLabel=useSchemaLabel) + col_schema, table_manifest = self.formatDB(sg=sg, manifest=manifest, useSchemaLabel=useSchemaLabel) manifest_table_id = self.buildDB(datasetId, table_name, col_schema, table_manifest, table_manipulation, sg, restrict,) return manifest_table_id, manifest, table_manifest - def formatDB(self, se, manifest, useSchemaLabel): + def formatDB(self, sg, manifest, useSchemaLabel): """ Method to format a manifest appropriatly for upload as table Args: - se: schemaExplorer object + sg: schemaGenerator object manifest: pd.Df manifest to upload useSchemaLabel: bool whether to use schemaLabel (True) or display label (False) @@ -1012,7 +1010,7 @@ def formatDB(self, se, manifest, useSchemaLabel): if useSchemaLabel: cols = [ - se.get_class_label_from_display_name( + sg.se.get_class_label_from_display_name( str(col) ).translate({ord(x): '' for x in blacklist_chars}) for col in manifest_columns @@ -1502,7 +1500,6 @@ def upload_manifest_as_table( # Upload manifest as a table, get the ID and updated manifest. manifest_synapse_table_id, manifest, table_manifest = self.uploadDB( sg=schemaGenerator, - se=se, manifest=manifest, datasetId=datasetId, table_name=table_name, @@ -1522,7 +1519,6 @@ def upload_manifest_as_table( # Update manifest Synapse table with new entity id column. manifest_synapse_table_id, manifest, table_manifest = self.uploadDB( sg=schemaGenerator, - se=se, manifest=manifest, datasetId=datasetId, table_name=table_name, @@ -1610,7 +1606,6 @@ def upload_manifest_combo( """ manifest_synapse_table_id, manifest, table_manifest = self.uploadDB( sg=schemaGenerator, - se=se, manifest=manifest, datasetId=datasetId, table_name=table_name, @@ -1631,7 +1626,6 @@ def upload_manifest_combo( # Update manifest Synapse table with new entity id column. manifest_synapse_table_id, manifest, table_manifest = self.uploadDB( sg=schemaGenerator, - se=se, manifest=manifest, datasetId=datasetId, table_name=table_name, From dfa2514a025ec2cff996d1f40e52352566b969d8 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 10:59:34 -0700 Subject: [PATCH 21/51] add access token to `/model/validate` --- schematic_api/api/openapi/api.yaml | 2 ++ schematic_api/api/routes.py | 3 +++ 2 files changed, 5 insertions(+) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index 80aabff4e..627f11948 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -218,6 +218,8 @@ paths: description: Upload a json or a csv file. type: string format: binary + security: + - access_token: [] parameters: - in: query name: schema_url diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index e19fcb859..4e0587c8e 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -340,6 +340,9 @@ def create_single_manifest(data_type, title, dataset_id=None, output_format=None #####profile validate manifest route function #@profile(sort_by='cumulative', strip_dirs=True) def validate_manifest_route(schema_url, data_type, restrict_rules=None, json_str=None): + # Access token now stored in request header + access_token = get_access_token() + # if restrict rules is set to None, default it to False if not restrict_rules: restrict_rules=False From 93a0ac0c43906ade49b72b493d7b91829001a337 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 11:16:54 -0700 Subject: [PATCH 22/51] pass along token to necessary methods --- schematic/models/metadata.py | 13 +++++++++++-- schematic/models/validate_attribute.py | 8 ++++---- schematic/models/validate_manifest.py | 8 ++++---- schematic_api/api/routes.py | 2 +- 4 files changed, 20 insertions(+), 11 deletions(-) diff --git a/schematic/models/metadata.py b/schematic/models/metadata.py index d10d27151..c80b72a31 100644 --- a/schematic/models/metadata.py +++ b/schematic/models/metadata.py @@ -186,7 +186,7 @@ def get_component_requirements( # TODO: abstract validation in its own module def validateModelManifest( - self, manifestPath: str, rootNode: str, restrict_rules: bool = False, jsonSchema: str = None, project_scope: List = None, + self, manifestPath: str, rootNode: str, restrict_rules: bool = False, jsonSchema: str = None, project_scope: List = None, access_token: str = None, ) -> List[str]: """Check if provided annotations manifest dataframe satisfies all model requirements. @@ -251,7 +251,16 @@ def validateModelManifest( return errors, warnings - errors, warnings, manifest = validate_all(self, errors, warnings, manifest, manifestPath, self.sg, jsonSchema, restrict_rules, project_scope) + errors, warnings, manifest = validate_all(self, + errors=errors, + warnings=warnings, + manifest=manifest, + manifestPath=manifestPath, + sg=self.sg, + jsonSchema=jsonSchema, + restrict_rules=restrict_rules, + project_scope=project_scope, + access_token=access_token) return errors, warnings def populateModelManifest(self, title, manifestPath: str, rootNode: str, return_excel = False) -> str: diff --git a/schematic/models/validate_attribute.py b/schematic/models/validate_attribute.py index da98b20ef..44c1f9940 100644 --- a/schematic/models/validate_attribute.py +++ b/schematic/models/validate_attribute.py @@ -564,13 +564,13 @@ class ValidateAttribute(object): - Add string length validator """ - def get_target_manifests(target_component, project_scope: List): + def get_target_manifests(target_component, project_scope: List, access_token: str = None): t_manifest_search = perf_counter() target_manifest_IDs=[] target_dataset_IDs=[] #login - synStore = SynapseStorage(project_scope=project_scope) + synStore = SynapseStorage(access_token=access_token, project_scope=project_scope) #Get list of all projects user has access to projects = synStore.getStorageProjects(project_scope=project_scope) @@ -893,7 +893,7 @@ def url_validation(self, val_rule: str, manifest_col: str, sg: SchemaGenerator,) return errors, warnings def cross_validation( - self, val_rule: str, manifest_col: pd.core.series.Series, project_scope: List, sg: SchemaGenerator, + self, val_rule: str, manifest_col: pd.core.series.Series, project_scope: List, sg: SchemaGenerator, access_token: str, ) -> List[List[str]]: """ Purpose: @@ -921,7 +921,7 @@ def cross_validation( #Get IDs of manifests with target component - synStore, target_manifest_IDs, target_dataset_IDs = ValidateAttribute.get_target_manifests(target_component,project_scope) + synStore, target_manifest_IDs, target_dataset_IDs = ValidateAttribute.get_target_manifests(target_component, project_scope, access_token) t_cross_manifest = perf_counter() #Read each manifest diff --git a/schematic/models/validate_manifest.py b/schematic/models/validate_manifest.py index 244e75d9a..f89b6fe07 100644 --- a/schematic/models/validate_manifest.py +++ b/schematic/models/validate_manifest.py @@ -62,7 +62,7 @@ def get_multiple_types_error( return ["NA", error_col, error_message, error_val] def validate_manifest_rules( - self, manifest: pd.core.frame.DataFrame, sg: SchemaGenerator, restrict_rules: bool, project_scope: List, + self, manifest: pd.core.frame.DataFrame, sg: SchemaGenerator, restrict_rules: bool, project_scope: List, access_token: str, ) -> (pd.core.frame.DataFrame, List[List[str]]): """ Purpose: @@ -208,7 +208,7 @@ def validate_manifest_rules( manifest[col] = manifest_col elif validation_type.lower().startswith("match"): vr_errors, vr_warnings = validation_method( - self, rule, manifest[col], project_scope, sg, + self, rule, manifest[col], project_scope, sg, access_token ) else: vr_errors, vr_warnings = validation_method( @@ -256,9 +256,9 @@ def validate_manifest_values(self, manifest, jsonSchema, sg return errors, warnings -def validate_all(self, errors, warnings, manifest, manifestPath, sg, jsonSchema, restrict_rules, project_scope: List): +def validate_all(self, errors, warnings, manifest, manifestPath, sg, jsonSchema, restrict_rules, project_scope: List, access_token: str): vm = ValidateManifest(errors, manifest, manifestPath, sg, jsonSchema) - manifest, vmr_errors, vmr_warnings = vm.validate_manifest_rules(manifest, sg, restrict_rules, project_scope) + manifest, vmr_errors, vmr_warnings = vm.validate_manifest_rules(manifest, sg, restrict_rules, project_scope, access_token) if vmr_errors: errors.extend(vmr_errors) if vmr_warnings: diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index 4e0587c8e..9e7e08873 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -370,7 +370,7 @@ def validate_manifest_route(schema_url, data_type, restrict_rules=None, json_str ) errors, warnings = metadata_model.validateModelManifest( - manifestPath=temp_path, rootNode=data_type, restrict_rules=restrict_rules + manifestPath=temp_path, rootNode=data_type, restrict_rules=restrict_rules, access_token=access_token ) res_dict = {"errors": errors, "warnings": warnings} From 4e72cbd7afacc9b79cfa96f5ae58a7b9eb5780d4 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 11:18:03 -0700 Subject: [PATCH 23/51] make token optional --- schematic_api/api/openapi/api.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index 627f11948..363d035bf 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -220,6 +220,7 @@ paths: format: binary security: - access_token: [] + - {} parameters: - in: query name: schema_url From 02af018464d47e7a27cba172d2505f3f341da1d2 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 11:24:59 -0700 Subject: [PATCH 24/51] add error message --- schematic/models/validate_attribute.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/schematic/models/validate_attribute.py b/schematic/models/validate_attribute.py index 44c1f9940..362a86fcc 100644 --- a/schematic/models/validate_attribute.py +++ b/schematic/models/validate_attribute.py @@ -27,6 +27,7 @@ rule_in_rule_list, ) +from synapseclient.core.exceptions import SynapseNoCredentialsError logger = logging.getLogger(__name__) @@ -570,7 +571,12 @@ def get_target_manifests(target_component, project_scope: List, access_token: st target_dataset_IDs=[] #login - synStore = SynapseStorage(access_token=access_token, project_scope=project_scope) + try: + synStore = SynapseStorage(access_token=access_token, project_scope=project_scope) + except SynapseNoCredentialsError as e: + raise ValueError( + "No Synapse credentials were provided. Credentials must be provided to utilize cross-manfiest validation functionality." + ) from e #Get list of all projects user has access to projects = synStore.getStorageProjects(project_scope=project_scope) From d32c6455bfd99c8caa8b8524ef01e0959209644a Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 11:29:22 -0700 Subject: [PATCH 25/51] connect submit route token to validation --- schematic/models/metadata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schematic/models/metadata.py b/schematic/models/metadata.py index c80b72a31..278f4c396 100644 --- a/schematic/models/metadata.py +++ b/schematic/models/metadata.py @@ -337,7 +337,7 @@ def submit_metadata_manifest( # automatic JSON schema generation and validation with that JSON schema val_errors, val_warnings = self.validateModelManifest( - manifestPath=manifest_path, rootNode=validate_component, restrict_rules=restrict_rules, project_scope=project_scope, + manifestPath=manifest_path, rootNode=validate_component, restrict_rules=restrict_rules, project_scope=project_scope, access_token=access_token ) # if there are no errors in validation process From daed0484e2e6ebca8d0b29891ed7299844cbf965 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 13:42:31 -0700 Subject: [PATCH 26/51] add asset view param to `/model/validate` --- schematic_api/api/openapi/api.yaml | 8 ++++++++ schematic_api/api/routes.py | 4 ++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index 363d035bf..6bc1693f2 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -261,6 +261,14 @@ paths: "Cancer Type": "Breast", "Family History": "Breast, Lung", }]' + - in: query + name: asset_view + schema: + type: string + nullable: false + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + example: syn28559058 + required: false operationId: schematic_api.api.routes.validate_manifest_route responses: diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index 9e7e08873..bb8bdf526 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -339,7 +339,7 @@ def create_single_manifest(data_type, title, dataset_id=None, output_format=None #####profile validate manifest route function #@profile(sort_by='cumulative', strip_dirs=True) -def validate_manifest_route(schema_url, data_type, restrict_rules=None, json_str=None): +def validate_manifest_route(schema_url, data_type, restrict_rules=None, json_str=None, asset_view=None,): # Access token now stored in request header access_token = get_access_token() @@ -348,7 +348,7 @@ def validate_manifest_route(schema_url, data_type, restrict_rules=None, json_str restrict_rules=False # call config_handler() - config_handler() + config_handler(asset_view = asset_view) #If restrict_rules parameter is set to None, then default it to False if not restrict_rules: From 632107a618db33f48aeb806a8cf884154dd8cc3a Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 13:44:39 -0700 Subject: [PATCH 27/51] update `asset_view` description --- schematic_api/api/openapi/api.yaml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index 6bc1693f2..9447f6981 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -82,7 +82,7 @@ paths: schema: type: string nullable: true - description: ID of view listing all project data assets. E.g. for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. E.g. for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) required: false - in: query name: output_format @@ -167,7 +167,7 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) example: syn28559058 required: true - in: query @@ -266,7 +266,7 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) example: syn28559058 required: false @@ -354,7 +354,7 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) example: syn28559058 required: true - in: query @@ -506,7 +506,7 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) example: syn23643253 required: true - in: query @@ -537,7 +537,7 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) example: syn23643253 required: true responses: @@ -560,7 +560,7 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) example: syn23643253 required: true - in: query @@ -591,7 +591,7 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) example: syn23643253 required: true - in: query @@ -638,7 +638,7 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) example: syn23643253 required: true - in: query @@ -677,7 +677,7 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) example: syn23643253 required: true responses: @@ -735,7 +735,7 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml) + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) example: syn23643253 required: true - in: query From 06e1c8f858aa6d7dbb466d38c7b40cc8e10de172 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 14:17:08 -0700 Subject: [PATCH 28/51] add project scope to `/model/validate` --- schematic_api/api/openapi/api.yaml | 14 ++++++++++++-- schematic_api/api/routes.py | 4 ++-- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index 9447f6981..bfe815737 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -266,8 +266,18 @@ paths: schema: type: string nullable: false - description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) - example: syn28559058 + description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project (i.e. master_fileview_id in config_example.yml). Required for validating manifests involving cross-manifest validation. + example: syn23643253 + required: false + - in: query + name: project_scope + schema: + type: array + items: + type: string + nullable: false + description: List, a subset of the projects contained within the asset view that are relevant for the current operation. Speeds up some operations that interact with Synapse. Relevant for validating manifests involving cross-manifest validation, but optional. + example: ['syn23643250', 'syn47218127', 'syn47218347'] required: false operationId: schematic_api.api.routes.validate_manifest_route diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index bb8bdf526..8c485518d 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -339,7 +339,7 @@ def create_single_manifest(data_type, title, dataset_id=None, output_format=None #####profile validate manifest route function #@profile(sort_by='cumulative', strip_dirs=True) -def validate_manifest_route(schema_url, data_type, restrict_rules=None, json_str=None, asset_view=None,): +def validate_manifest_route(schema_url, data_type, restrict_rules=None, json_str=None, asset_view=None, project_scope = None): # Access token now stored in request header access_token = get_access_token() @@ -370,7 +370,7 @@ def validate_manifest_route(schema_url, data_type, restrict_rules=None, json_str ) errors, warnings = metadata_model.validateModelManifest( - manifestPath=temp_path, rootNode=data_type, restrict_rules=restrict_rules, access_token=access_token + manifestPath=temp_path, rootNode=data_type, restrict_rules=restrict_rules, project_scope=project_scope, access_token=access_token ) res_dict = {"errors": errors, "warnings": warnings} From 9be306e2c6aebfb2bb0f3426fcf2115b17029f45 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 14:30:45 -0700 Subject: [PATCH 29/51] add project scope param to `/model/submit` --- schematic_api/api/openapi/api.yaml | 10 ++++++++++ schematic_api/api/routes.py | 14 ++++++++++++-- 2 files changed, 22 insertions(+), 2 deletions(-) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index bfe815737..c71342e0e 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -397,6 +397,16 @@ paths: type: boolean default: true required: false + - in: query + name: project_scope + schema: + type: array + items: + type: string + nullable: false + description: List, a subset of the projects contained within the asset view that are relevant for the current operation. Speeds up some operations that interact with Synapse. + example: ['syn23643250', 'syn47218127', 'syn47218347'] + required: false operationId: schematic_api.api.routes.submit_manifest_route responses: "200": diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index 8c485518d..1e3c6dc94 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -379,7 +379,15 @@ def validate_manifest_route(schema_url, data_type, restrict_rules=None, json_str #####profile validate manifest route function #@profile(sort_by='cumulative', strip_dirs=True) -def submit_manifest_route(schema_url, asset_view=None, manifest_record_type=None, json_str=None, table_manipulation=None, data_type=None, hide_blanks=False): +def submit_manifest_route(schema_url, + asset_view=None, + manifest_record_type=None, + json_str=None, + table_manipulation=None, + data_type=None, + hide_blanks=False, + project_scope=None, + ): # call config_handler() config_handler(asset_view = asset_view) @@ -427,7 +435,9 @@ def submit_manifest_route(schema_url, asset_view=None, manifest_record_type=None restrict_rules = restrict_rules, hide_blanks=hide_blanks, table_manipulation = table_manipulation, - use_schema_label=use_schema_label) + use_schema_label=use_schema_label, + project_scope=project_scope, + ) return manifest_id From f78dea19328bd6eece570d8ed83b5c2e3a041185 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 14:32:23 -0700 Subject: [PATCH 30/51] change asset view example to match with project scope ex --- schematic_api/api/openapi/api.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schematic_api/api/openapi/api.yaml b/schematic_api/api/openapi/api.yaml index c71342e0e..ba04b659d 100644 --- a/schematic_api/api/openapi/api.yaml +++ b/schematic_api/api/openapi/api.yaml @@ -365,7 +365,7 @@ paths: type: string nullable: false description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview_id in config_example.yml) - example: syn28559058 + example: syn23643253 required: true - in: query name: json_str From 29a29b8a846c619f820cf42889218e1d655dc806 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 14:50:43 -0700 Subject: [PATCH 31/51] update validation endpoint test with new headers --- tests/test_api.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_api.py b/tests/test_api.py index 23b32d174..0b4165c90 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -597,7 +597,7 @@ def test_populate_manifest(self, client, data_model_jsonld, test_manifest_csv): @pytest.mark.parametrize("restrict_rules", [False, True, None]) @pytest.mark.parametrize("json_str", [None, '[{"Patient ID": 123, "Sex": "Female", "Year of Birth": "", "Diagnosis": "Healthy", "Component": "Patient", "Cancer Type": "Breast", "Family History": "Breast, Lung"}]']) - def test_validate_manifest(self, data_model_jsonld, client, json_str, restrict_rules, test_manifest_csv): + def test_validate_manifest(self, data_model_jsonld, client, json_str, restrict_rules, test_manifest_csv, request_headers): params = { "schema_url": data_model_jsonld, @@ -614,13 +614,13 @@ def test_validate_manifest(self, data_model_jsonld, client, json_str, restrict_r else: params["data_type"] = "MockComponent" - headers = { + request_headers.update({ 'Content-Type': "multipart/form-data", 'Accept': "application/json" - } + }) # test uploading a csv file - response_csv = client.post('http://localhost:3001/v1/model/validate', query_string=params, data={"file_name": (open(test_manifest_csv, 'rb'), "test.csv")}, headers=headers) + response_csv = client.post('http://localhost:3001/v1/model/validate', query_string=params, data={"file_name": (open(test_manifest_csv, 'rb'), "test.csv")}, headers=request_headers) response_dt = json.loads(response_csv.data) assert response_csv.status_code == 200 From 3998d7d688941fa56a379a6a5c1b533623d7457e Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 15:19:41 -0700 Subject: [PATCH 32/51] update fixture params req'd --- tests/conftest.py | 4 ++-- tests/test_store.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index f19b4a9dc..644675355 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -63,7 +63,7 @@ def get_schema_explorer(path=None, *paths): return se @staticmethod - def get_python_version(self): + def get_python_version(): version=sys.version base_version=".".join(version.split('.')[0:2]) @@ -72,7 +72,7 @@ def get_python_version(self): @staticmethod def get_python_project(self): - version = self.get_python_version(Helpers) + version = self.get_python_version() python_projects = { "3.7": "syn47217926", diff --git a/tests/test_store.py b/tests/test_store.py index 0d2f0658b..8828d3fb6 100644 --- a/tests/test_store.py +++ b/tests/test_store.py @@ -65,7 +65,7 @@ def dataset_fileview_table_tidy(dataset_fileview, dataset_fileview_table): @pytest.fixture def version(synapse_store, helpers): - yield helpers.get_python_version(helpers) + yield helpers.get_python_version() @pytest.fixture def projectId(synapse_store, helpers): @@ -75,7 +75,7 @@ def projectId(synapse_store, helpers): @pytest.fixture def datasetId(synapse_store, projectId, helpers): dataset = Folder( - name = 'Table Test Dataset ' + helpers.get_python_version(helpers), + name = 'Table Test Dataset ' + helpers.get_python_version(), parent = projectId, ) From 3a37e60847c485234ad86274e4bbabe865881ab3 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 11 Oct 2023 15:20:11 -0700 Subject: [PATCH 33/51] parametrize submission test --- tests/test_api.py | 33 ++++++++++++++++++++++++++++----- 1 file changed, 28 insertions(+), 5 deletions(-) diff --git a/tests/test_api.py b/tests/test_api.py index 0b4165c90..9d69c63b2 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -773,21 +773,44 @@ def test_submit_manifest_table_and_file_replace(self, client, request_headers, d @pytest.mark.synapse_credentials_needed @pytest.mark.submission - def test_submit_manifest_file_only_replace(self, client, request_headers, data_model_jsonld, test_manifest_submit): + @pytest.mark.parametrize("data_type, manifest_path_fixture",[("Biospecimen","test_manifest_submit"), ("MockComponent", "test_manifest_csv")]) + def test_submit_manifest_file_only_replace(self, helpers, client, request_headers, data_model_jsonld, data_type, manifest_path_fixture, request): """Testing submit manifest in a csv format as a file """ params = { "schema_url": data_model_jsonld, - "data_type": "Biospecimen", + "data_type": data_type, "restrict_rules": False, "manifest_record_type": "file_only", - "asset_view": "syn51514344", - "dataset_id": "syn51514345", "table_manipulation": 'replace', "use_schema_label": True } - response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(test_manifest_submit, 'rb'), "test.csv")}, headers=request_headers) + + if data_type == "Biospecimen": + specific_params = { + "asset_view": "syn51514344", + "dataset_id": "syn51514345", + } + + elif data_type == "MockComponent": + python_version = helpers.get_python_version() + + if python_version == "3.10": + dataset_id = "syn52656106" + elif python_version =="3.9": + dataset_id = "syn52656104" + + specific_params = { + "asset_view": "syn23643253", + "dataset_id": dataset_id + } + + params.update(specific_params) + + manifest_path = request.getfixturevalue(manifest_path_fixture) + response_csv = client.post('http://localhost:3001/v1/model/submit', query_string=params, data={"file_name": (open(manifest_path, 'rb'), "test.csv")}, headers=request_headers) assert response_csv.status_code == 200 + @pytest.mark.synapse_credentials_needed @pytest.mark.submission def test_submit_manifest_json_str_replace(self, client, request_headers, data_model_jsonld): From 66a85ee3d7b466e208b67a81b2c64dede4e2437f Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 13 Oct 2023 09:36:24 -0700 Subject: [PATCH 34/51] project scope the manifest validation tests --- tests/test_validation.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/tests/test_validation.py b/tests/test_validation.py index 22b64199b..c1f115e26 100644 --- a/tests/test_validation.py +++ b/tests/test_validation.py @@ -49,7 +49,8 @@ def test_valid_manifest(self,helpers,metadataModel): errors, warnings = metadataModel.validateModelManifest( manifestPath=manifestPath, - rootNode=rootNode + rootNode=rootNode, + project_scope = ["syn23643250"], ) assert errors == [] @@ -62,7 +63,8 @@ def test_invalid_manifest(self,helpers,sg,metadataModel): errors, warnings = metadataModel.validateModelManifest( manifestPath=manifestPath, - rootNode=rootNode + rootNode=rootNode, + project_scope = ["syn23643250"], ) #Check errors @@ -247,6 +249,7 @@ def test_in_house_validation(self,helpers,sg,metadataModel): manifestPath=manifestPath, rootNode=rootNode, restrict_rules=True, + project_scope = ["syn23643250"], ) #Check errors From 3a92b9772c577697a7268173fd8d2311d0b081bd Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Fri, 13 Oct 2023 09:45:35 -0700 Subject: [PATCH 35/51] use request headers for validation request --- tests/test_api.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_api.py b/tests/test_api.py index 23b32d174..0b4165c90 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -597,7 +597,7 @@ def test_populate_manifest(self, client, data_model_jsonld, test_manifest_csv): @pytest.mark.parametrize("restrict_rules", [False, True, None]) @pytest.mark.parametrize("json_str", [None, '[{"Patient ID": 123, "Sex": "Female", "Year of Birth": "", "Diagnosis": "Healthy", "Component": "Patient", "Cancer Type": "Breast", "Family History": "Breast, Lung"}]']) - def test_validate_manifest(self, data_model_jsonld, client, json_str, restrict_rules, test_manifest_csv): + def test_validate_manifest(self, data_model_jsonld, client, json_str, restrict_rules, test_manifest_csv, request_headers): params = { "schema_url": data_model_jsonld, @@ -614,13 +614,13 @@ def test_validate_manifest(self, data_model_jsonld, client, json_str, restrict_r else: params["data_type"] = "MockComponent" - headers = { + request_headers.update({ 'Content-Type': "multipart/form-data", 'Accept': "application/json" - } + }) # test uploading a csv file - response_csv = client.post('http://localhost:3001/v1/model/validate', query_string=params, data={"file_name": (open(test_manifest_csv, 'rb'), "test.csv")}, headers=headers) + response_csv = client.post('http://localhost:3001/v1/model/validate', query_string=params, data={"file_name": (open(test_manifest_csv, 'rb'), "test.csv")}, headers=request_headers) response_dt = json.loads(response_csv.data) assert response_csv.status_code == 200 From db7054f36a29f3eddf4e1db802e17c31a6156ee6 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 16 Oct 2023 10:18:30 -0700 Subject: [PATCH 36/51] regen poetry lock no changes to `.toml` --- poetry.lock | 4504 +++++++++++++++++++++++++-------------------------- 1 file changed, 2213 insertions(+), 2291 deletions(-) diff --git a/poetry.lock b/poetry.lock index d1f5b59a4..7b1258fc1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,18 +1,26 @@ +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. + [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" 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= {version = "*", markers = "platform_system == \"Darwin\""} @@ -836,7 +1365,7 @@ comm = ">=0.1.1" debugpy = ">=1.6.5" ipython = ">=7.23.1" jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" matplotlib-inline = ">=0.1" nest-asyncio = "*" packaging = "*" @@ -854,17 +1383,21 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio" [[package]] name = "ipython" -version = "8.14.0" +version = "8.16.1" description = "IPython: Productive Interactive Computing" -category = "main" optional = false python-versions = ">=3.9" +files = [ + {file = "ipython-8.16.1-py3-none-any.whl", hash = "sha256:0852469d4d579d9cd613c220af7bf0c9cc251813e12be647cb9d463939db9b1e"}, + {file = "ipython-8.16.1.tar.gz", hash = "sha256:ad52f58fca8f9f848e256c629eff888efc0528c12fe0f8ec14f33205f23ef938"}, +] [package.dependencies] appnope = {version = "*", markers = "sys_platform == \"darwin\""} backcall = "*" colorama = {version = "*", markers = "sys_platform == \"win32\""} decorator = "*" +exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} jedi = ">=0.16" matplotlib-inline = "*" pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} @@ -876,9 +1409,9 @@ traitlets = ">=5" typing-extensions = {version = "*", markers = "python_version < \"3.10\""} [package.extras] -all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"] +all = ["black", "curio", "docrepr", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", 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"main" -optional = false -python-versions = "*" - [[package]] name = "ipywidgets" -version = "8.0.7" +version = "8.1.1" description = "Jupyter interactive widgets" -category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "ipywidgets-8.1.1-py3-none-any.whl", hash = "sha256:2b88d728656aea3bbfd05d32c747cfd0078f9d7e159cf982433b58ad717eed7f"}, + {file = "ipywidgets-8.1.1.tar.gz", hash = "sha256:40211efb556adec6fa450ccc2a77d59ca44a060f4f9f136833df59c9f538e6e8"}, +] [package.dependencies] -ipykernel = ">=4.5.1" +comm = ">=0.1.3" ipython = ">=6.1.0" -jupyterlab-widgets = ">=3.0.7,<3.1.0" +jupyterlab-widgets = ">=3.0.9,<3.1.0" traitlets = ">=4.3.1" -widgetsnbextension = ">=4.0.7,<4.1.0" +widgetsnbextension = ">=4.0.9,<4.1.0" [package.extras] test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"] @@ -918,9 +1446,12 @@ test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"] name = "isodate" version = "0.6.1" description = "An ISO 8601 date/time/duration parser and formatter" -category = "main" optional = false python-versions = "*" +files = [ + {file = "isodate-0.6.1-py2.py3-none-any.whl", hash = "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96"}, + {file = "isodate-0.6.1.tar.gz", hash = "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"}, +] [package.dependencies] six = "*" @@ -929,9 +1460,12 @@ six = "*" name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" -category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"}, + {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"}, +] [package.dependencies] arrow = ">=0.15.0" @@ -940,9 +1474,12 @@ arrow = ">=0.15.0" name = "isort" version = "5.12.0" description = "A Python utility / library to sort Python imports." -category = "dev" optional = false python-versions = ">=3.8.0" +files = [ + {file = "isort-5.12.0-py3-none-any.whl", hash = "sha256:f84c2818376e66cf843d497486ea8fed8700b340f308f076c6fb1229dff318b6"}, + {file = "isort-5.12.0.tar.gz", hash = "sha256:8bef7dde241278824a6d83f44a544709b065191b95b6e50894bdc722fcba0504"}, +] [package.extras] colors = ["colorama (>=0.4.3)"] @@ -954,33 +1491,42 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] name = "itsdangerous" version = "2.1.2" description = "Safely pass data to untrusted environments and back." -category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "itsdangerous-2.1.2-py3-none-any.whl", hash = "sha256:2c2349112351b88699d8d4b6b075022c0808887cb7ad10069318a8b0bc88db44"}, + {file = "itsdangerous-2.1.2.tar.gz", hash = "sha256:5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a"}, +] [[package]] name = "jedi" -version = "0.18.2" +version = "0.19.1" description = "An autocompletion tool for Python that can be used for text editors." -category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "jedi-0.19.1-py2.py3-none-any.whl", hash = "sha256:e983c654fe5c02867aef4cdfce5a2fbb4a50adc0af145f70504238f18ef5e7e0"}, + {file = "jedi-0.19.1.tar.gz", hash = "sha256:cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd"}, +] [package.dependencies] -parso = ">=0.8.0,<0.9.0" +parso = ">=0.8.3,<0.9.0" [package.extras] docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme 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"jinja2" version = "3.1.2" description = "A very fast and expressive template engine." -category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"}, + {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"}, +] [package.dependencies] MarkupSafe = ">=2.0" @@ -1000,13 +1549,30 @@ MarkupSafe = ">=2.0" [package.extras] i18n = ["Babel (>=2.7)"] +[[package]] +name = "json5" +version = "0.9.14" +description = "A Python implementation of the JSON5 data format." +optional = false +python-versions = "*" +files = [ + {file = "json5-0.9.14-py2.py3-none-any.whl", hash = "sha256:740c7f1b9e584a468dbb2939d8d458db3427f2c93ae2139d05f47e453eae964f"}, + {file = "json5-0.9.14.tar.gz", hash = "sha256:9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02"}, +] + +[package.extras] +dev = ["hypothesis"] + 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python-dateutil = ">=2.8.2" pyzmq = ">=23.0" tornado = ">=6.2" @@ -1078,11 +1656,14 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt [[package]] name = "jupyter-core" -version = "5.3.1" +version = "5.4.0" description = "Jupyter core package. A base package on which Jupyter projects rely." -category = "main" optional = false python-versions = ">=3.8" +files = [ + {file = "jupyter_core-5.4.0-py3-none-any.whl", hash = "sha256:66e252f675ac04dcf2feb6ed4afb3cd7f68cf92f483607522dc251f32d471571"}, + {file = "jupyter_core-5.4.0.tar.gz", hash = "sha256:e4b98344bb94ee2e3e6c4519a97d001656009f9cb2b7f2baf15b3c205770011d"}, +] [package.dependencies] platformdirs = ">=2.5" @@ -1095,16 +1676,20 @@ test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] [[package]] name = "jupyter-events" -version = "0.6.3" +version = "0.8.0" description = "Jupyter Event System library" -category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" +files = [ + {file = "jupyter_events-0.8.0-py3-none-any.whl", hash = "sha256:81f07375c7673ff298bfb9302b4a981864ec64edaed75ca0fe6f850b9b045525"}, + {file = "jupyter_events-0.8.0.tar.gz", hash = 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Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 16 Oct 2023 10:32:25 -0700 Subject: [PATCH 38/51] regen with `poetry==1.3.0` --- poetry.lock | 251 ++++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 232 insertions(+), 19 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7b1258fc1..47974b13a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry and should not be changed by hand. [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -15,6 +16,7 @@ files = [ name = "altair" version = "4.2.0" description = "Altair: A declarative statistical visualization library for Python." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -37,6 +39,7 @@ dev = ["black", "docutils", "flake8", "ipython", "m2r", "mistune (<2.0.0)", "pyt name = "anyio" version = "4.0.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -58,6 +61,7 @@ trio = ["trio (>=0.22)"] name = "appnope" version = "0.1.3" description = "Disable App Nap on macOS >= 10.9" +category = "main" optional = false python-versions = "*" files = [ @@ -69,6 +73,7 @@ files = [ name = "argon2-cffi" version = "23.1.0" description = "Argon2 for Python" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -89,6 +94,7 @@ typing = ["mypy"] name = "argon2-cffi-bindings" version = "21.2.0" description = "Low-level CFFI bindings for Argon2" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -126,6 +132,7 @@ tests = ["pytest"] name = "arrow" version = "1.3.0" description = "Better dates & times for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -139,12 +146,13 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] +test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] [[package]] name = "astroid" version = "2.15.8" description = "An abstract syntax tree for Python with inference support." +category = "dev" optional = false python-versions = ">=3.7.2" files = [ @@ -161,6 +169,7 @@ wrapt = {version = ">=1.11,<2", markers = "python_version < \"3.11\""} name = "asttokens" version = "2.4.0" description = "Annotate AST trees with source code positions" +category = "main" optional = false python-versions = "*" files = [ @@ -178,6 +187,7 @@ test = ["astroid", "pytest"] name = "async-lru" version = "2.0.4" description = "Simple LRU cache for asyncio" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -192,6 +202,7 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -210,6 +221,7 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "babel" version = "2.13.0" description = "Internationalization utilities" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -224,6 +236,7 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] name = "backcall" version = "0.2.0" description = "Specifications for callback functions passed in to an API" +category = "main" optional = false python-versions = "*" files = [ @@ -235,6 +248,7 @@ files = [ name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" +category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -253,6 +267,7 @@ lxml = ["lxml"] name = "black" version = "23.9.1" description = "The uncompromising code formatter." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -299,6 +314,7 @@ uvloop = ["uvloop (>=0.15.2)"] name = "bleach" version = "6.1.0" description = "An easy safelist-based HTML-sanitizing tool." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -317,6 +333,7 @@ css = ["tinycss2 (>=1.1.0,<1.3)"] name = "cachetools" version = "5.3.1" description = "Extensible memoizing collections and decorators" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -328,6 +345,7 @@ files = [ name = "certifi" version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -339,6 +357,7 @@ files = [ name = "cffi" version = "1.16.0" description = "Foreign Function Interface for Python calling C code." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -403,6 +422,7 @@ pycparser = "*" name = "charset-normalizer" version = "3.3.0" description = "The Real First Universal Charset Detector. 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= [ @@ -717,6 +745,7 @@ test-randomorder = ["pytest-randomly"] name = "dateparser" version = "1.1.8" description = "Date parsing library designed to parse dates from HTML pages" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -739,6 +768,7 @@ langdetect = ["langdetect"] name = "debugpy" version = "1.8.0" description = "An implementation of the Debug Adapter Protocol for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -766,6 +796,7 @@ files = [ name = "decorator" version = "5.1.1" description = "Decorators for Humans" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -777,6 +808,7 @@ files = [ name = "defusedxml" version = "0.7.1" description = "XML bomb protection for Python stdlib modules" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -788,6 +820,7 @@ files = [ name = "deprecated" version = "1.2.14" description = "Python @deprecated decorator to deprecate old python classes, functions or methods." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -805,6 +838,7 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"] name = "deprecation" version = "2.1.0" description = "A library to handle automated deprecations" +category = "main" optional = false python-versions = "*" files = [ @@ -819,6 +853,7 @@ packaging = "*" name = "dill" version = "0.3.7" description = "serialize all of Python" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -833,6 +868,7 @@ graph = ["objgraph (>=1.7.2)"] name = "docutils" version = "0.20.1" description = "Docutils -- Python Documentation Utilities" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -844,6 +880,7 @@ files = [ name = "entrypoints" version = "0.4" description = "Discover and load entry points from installed packages." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -855,6 +892,7 @@ files = [ name = "et-xmlfile" version = "1.1.0" description = "An implementation of lxml.xmlfile for the standard library" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -866,6 +904,7 @@ files = [ name = "exceptiongroup" version = "1.1.3" description = "Backport of PEP 654 (exception groups)" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -880,6 +919,7 @@ test = ["pytest (>=6)"] name = "executing" version = "2.0.0" description = "Get the currently executing AST node of a frame, and other information" +category = "main" optional = false python-versions = "*" files = [ @@ -894,6 +934,7 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth name = "fastjsonschema" version = "2.18.1" description = "Fastest Python implementation of JSON schema" +category = "main" optional = false python-versions = "*" files = [ @@ -908,6 +949,7 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= [ @@ -972,6 +1017,7 @@ files = [ name = "google-api-core" version = "2.12.0" description = "Google API client core library" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -994,6 +1040,7 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] name = "google-api-python-client" version = "2.103.0" description = "Google API Client Library for Python" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1002,7 +1049,7 @@ files = [ ] [package.dependencies] -google-api-core = ">=1.31.5,<2.0.dev0 || >2.3.0,<3.0.0.dev0" +google-api-core = ">=1.31.5,<2.0.0 || >2.3.0,<3.0.0.dev0" google-auth = ">=1.19.0,<3.0.0.dev0" google-auth-httplib2 = ">=0.1.0" httplib2 = ">=0.15.0,<1.dev0" @@ -1012,6 +1059,7 @@ uritemplate = ">=3.0.1,<5" name = "google-auth" version = "2.23.3" description = "Google Authentication Library" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1035,6 +1083,7 @@ requests = ["requests (>=2.20.0,<3.0.0.dev0)"] name = "google-auth-httplib2" version = "0.1.1" description = "Google Authentication Library: httplib2 transport" +category = "main" optional = false python-versions = "*" files = [ @@ -1050,6 +1099,7 @@ httplib2 = ">=0.19.0" name = "google-auth-oauthlib" version = "0.8.0" description = "Google Authentication Library" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1068,6 +1118,7 @@ tool = ["click (>=6.0.0)"] name = "googleapis-common-protos" version = "1.61.0" description = "Common protobufs used in Google APIs" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1085,6 +1136,7 @@ grpc = ["grpcio (>=1.44.0,<2.0.0.dev0)"] name = "graphviz" version = "0.20.1" description = "Simple Python interface for Graphviz" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1101,6 +1153,7 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>= name = "great-expectations" version = "0.15.50" description = "Always know what to expect from your data." +category = "main" optional = false python-versions = "*" files = [ @@ -1175,6 +1228,7 @@ vertica = ["sqlalchemy (>=1.3.18,<2.0.0)", "sqlalchemy-vertica-python (>=0.5.10) name = "greenlet" version = "3.0.0" description = "Lightweight in-process concurrent programming" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1250,6 +1304,7 @@ test = ["objgraph", "psutil"] name = "httplib2" version = "0.22.0" description = "A comprehensive HTTP client library." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1264,6 +1319,7 @@ pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0 name = "idna" version = "3.4" description = "Internationalized Domain Names in Applications (IDNA)" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -1275,6 +1331,7 @@ files = [ name = "imagesize" version = "1.4.1" 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[ @@ -1316,6 +1375,7 @@ files = [ name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1327,6 +1387,7 @@ files = [ name = "interrogate" version = "1.5.0" description = "Interrogate a codebase for docstring coverage." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1352,6 +1413,7 @@ tests = ["pytest", "pytest-cov", "pytest-mock"] name = "ipykernel" version = "6.25.2" description = "IPython Kernel for Jupyter" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1365,7 +1427,7 @@ comm = ">=0.1.1" debugpy = ">=1.6.5" ipython = ">=7.23.1" jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" matplotlib-inline = ">=0.1" nest-asyncio = "*" packaging = "*" @@ -1385,6 +1447,7 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio" name = "ipython" version = "8.16.1" description = "IPython: Productive Interactive Computing" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -1425,6 +1488,7 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pa name = "ipywidgets" version = "8.1.1" description = "Jupyter interactive widgets" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1446,6 +1510,7 @@ test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"] name = "isodate" version = "0.6.1" description = "An ISO 8601 date/time/duration parser and formatter" +category = "main" optional = false python-versions = "*" files = [ @@ -1460,6 +1525,7 @@ six = "*" name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1474,6 +1540,7 @@ arrow = ">=0.15.0" name = "isort" version = "5.12.0" description = "A Python utility / library to sort Python imports." +category = "dev" optional = false python-versions = ">=3.8.0" files = [ @@ -1491,6 +1558,7 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] name = "itsdangerous" version = "2.1.2" description = "Safely pass data to untrusted environments and back." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1502,6 +1570,7 @@ files = [ name = "jedi" version = "0.19.1" description = "An autocompletion tool for Python that can be used for text editors." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1521,6 +1590,7 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] name = "jeepney" version = "0.8.0" description = "Low-level, pure Python DBus protocol wrapper." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1536,6 +1606,7 @@ trio = ["async_generator", "trio"] name = "jinja2" version = "3.1.2" description = "A very fast and expressive template engine." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1553,6 +1624,7 @@ i18n = ["Babel (>=2.7)"] name = "json5" version = "0.9.14" description = "A Python implementation of the JSON5 data format." +category = "main" optional = false python-versions = "*" files = [ @@ -1567,6 +1639,7 @@ dev = ["hypothesis"] name = "jsonpatch" version = "1.33" description = "Apply JSON-Patches (RFC 6902)" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -1581,6 +1654,7 @@ jsonpointer = ">=1.9" name = "jsonpointer" version = "2.4" description = "Identify specific nodes in a JSON document (RFC 6901)" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -1592,6 +1666,7 @@ files = [ name = "jsonschema" version = "4.19.1" description = "An implementation of JSON Schema validation for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1621,6 +1696,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jsonschema-specifications" version = "2023.7.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1635,6 +1711,7 @@ referencing = ">=0.28.0" name = "jupyter-client" version = "8.4.0" description = "Jupyter protocol implementation and client libraries" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1644,7 +1721,7 @@ files = [ [package.dependencies] importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} -jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" tornado = ">=6.2" @@ -1658,6 +1735,7 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt name = "jupyter-core" version = "5.4.0" description = "Jupyter core package. A base package on which Jupyter projects rely." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1678,6 +1756,7 @@ test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] name = "jupyter-events" version = "0.8.0" description = "Jupyter Event System library" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1703,6 +1782,7 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p name = "jupyter-lsp" version = "2.2.0" description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1718,6 +1798,7 @@ jupyter-server = ">=1.1.2" name = "jupyter-server" version = "2.8.0" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1730,7 +1811,7 @@ anyio = ">=3.1.0" argon2-cffi = "*" jinja2 = "*" jupyter-client = ">=7.4.4" -jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" jupyter-events = ">=0.6.0" jupyter-server-terminals = "*" nbconvert = ">=6.4.4" @@ -1754,6 +1835,7 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-sc name = "jupyter-server-terminals" version = "0.4.4" description = "A Jupyter Server Extension Providing Terminals." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1773,6 +1855,7 @@ test = ["coverage", "jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-cov", name = "jupyterlab" version = "4.0.7" description = "JupyterLab computational environment" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1805,6 +1888,7 @@ test = ["coverage", "pytest (>=7.0)", "pytest-check-links (>=0.7)", "pytest-cons name = "jupyterlab-pygments" version = "0.2.2" description = "Pygments theme using JupyterLab CSS variables" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1816,6 +1900,7 @@ files = [ name = "jupyterlab-server" version = "2.25.0" description = "A set of server components for JupyterLab and JupyterLab like applications." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1842,6 +1927,7 @@ test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-v name = "jupyterlab-widgets" version = "3.0.9" description = "Jupyter interactive widgets for JupyterLab" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1853,6 +1939,7 @@ files = [ name = "keyring" version = "23.4.1" description = "Store and access your passwords safely." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1874,6 +1961,7 @@ testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", name = "keyrings-alt" version = "3.1" description = "Alternate keyring implementations" +category = "main" optional = false python-versions = ">=2.7" files = [ @@ -1892,6 +1980,7 @@ testing = ["backports.unittest-mock", "collective.checkdocs", "fs (>=0.5,<2)", " name = "lazy-object-proxy" version = "1.9.0" description = "A fast and thorough lazy object proxy." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1937,6 +2026,7 @@ files = [ name = "makefun" version = "1.15.1" description = "Small library to dynamically create python functions." +category = "main" optional = false python-versions = "*" files = [ @@ -1948,6 +2038,7 @@ files = [ name = "markupsafe" version = "2.1.0" description = "Safely add untrusted strings to HTML/XML markup." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1997,6 +2088,7 @@ files = [ name = "marshmallow" version = "3.20.1" description = "A lightweight library for converting complex datatypes to and from native Python datatypes." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2017,6 +2109,7 @@ tests = ["pytest", "pytz", "simplejson"] name = "matplotlib-inline" version = "0.1.6" description = "Inline Matplotlib backend for Jupyter" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -2031,6 +2124,7 @@ traitlets = "*" name = "mccabe" version = "0.7.0" description = "McCabe checker, plugin for flake8" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2042,6 +2136,7 @@ files = [ name = "mistune" version = "3.0.2" description = "A sane and fast Markdown parser with useful plugins and renderers" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2053,6 +2148,7 @@ files = [ name = "mypy" version = "1.6.0" description = "Optional static typing for Python" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2099,6 +2195,7 @@ reports = ["lxml"] name = "mypy-extensions" version = "1.0.0" description = "Type system extensions for programs checked with the mypy type checker." +category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -2110,6 +2207,7 @@ files = [ name = "nbclient" version = "0.8.0" description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." +category = "main" optional = false python-versions = ">=3.8.0" files = [ @@ -2119,7 +2217,7 @@ files = [ [package.dependencies] jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" nbformat = ">=5.1" traitlets = ">=5.4" @@ -2132,6 +2230,7 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>= name = "nbconvert" version = "7.9.2" description = "Converting Jupyter Notebooks" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2170,6 +2269,7 @@ webpdf = ["playwright"] name = "nbformat" version = "5.9.2" description = "The Jupyter Notebook format" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2191,6 +2291,7 @@ test = ["pep440", "pre-commit", "pytest", "testpath"] name = "nest-asyncio" version = "1.5.8" description = "Patch asyncio to allow nested event loops" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -2202,6 +2303,7 @@ files = [ name = "networkx" version = "2.8.8" description = "Python package for creating and manipulating graphs and networks" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2220,6 +2322,7 @@ test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"] name = "notebook" version = "7.0.5" description = "Jupyter Notebook - A web-based notebook environment for interactive computing" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2243,6 +2346,7 @@ test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4 name = "notebook-shim" version = "0.2.3" description = "A shim layer for notebook traits and config" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2260,6 +2364,7 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync" name = "numpy" version = "1.26.1" description = "Fundamental package for array computing in Python" +category = "main" optional = false python-versions = "<3.13,>=3.9" files = [ @@ -2301,6 +2406,7 @@ files = [ name = "oauth2client" version = "4.1.3" description = "OAuth 2.0 client library" +category = "main" optional = false python-versions = "*" files = [ @@ -2319,6 +2425,7 @@ six = ">=1.6.1" name = "oauthlib" version = "3.2.2" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2335,6 +2442,7 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"] name = "openpyxl" version = "3.1.2" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2349,6 +2457,7 @@ et-xmlfile = "*" name = "overrides" version = "7.4.0" description = "A decorator to automatically detect mismatch when overriding a method." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2360,6 +2469,7 @@ files = [ name = "packaging" version = "23.2" description = "Core utilities for Python packages" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2371,6 +2481,7 @@ files = [ name = "pandarallel" version = "1.6.5" description = "An easy to use library to speed up computation (by parallelizing on multi CPUs) with pandas." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2390,6 +2501,7 @@ doc = ["mkdocs-material"] name = "pandas" version = "1.5.3" description = "Powerful data structures for data analysis, time series, and statistics" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2437,6 +2549,7 @@ test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] name = "pandocfilters" version = "1.5.0" description = "Utilities for writing pandoc filters in python" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -2448,6 +2561,7 @@ files = [ name = "parso" version = "0.8.3" description = "A Python Parser" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2463,6 +2577,7 @@ testing = ["docopt", "pytest (<6.0.0)"] name = "pathspec" version = "0.11.2" description = "Utility library for gitignore style pattern matching of file paths." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2474,6 +2589,7 @@ files = [ name = "pdoc" version = "12.3.1" description = "API Documentation for Python Projects" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2493,6 +2609,7 @@ dev = ["black", "hypothesis", "mypy", "pytest", "pytest-cov", "pytest-timeout", name = "pexpect" version = "4.8.0" description = "Pexpect allows easy control of interactive console applications." +category = "main" optional = false python-versions = "*" files = [ @@ -2507,6 +2624,7 @@ ptyprocess = ">=0.5" name = "pickleshare" version = "0.7.5" description = "Tiny 'shelve'-like database with concurrency support" +category = "main" optional = false python-versions = "*" files = [ @@ -2518,6 +2636,7 @@ files = [ name = "platformdirs" version = "3.11.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2533,6 +2652,7 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co name = "pluggy" version = "1.3.0" description = "plugin and hook calling mechanisms for python" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2548,6 +2668,7 @@ testing = ["pytest", "pytest-benchmark"] name = "prometheus-client" version = "0.17.1" description = "Python client for the Prometheus monitoring system." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2562,6 +2683,7 @@ twisted = ["twisted"] name = "prompt-toolkit" version = "3.0.39" description = "Library for building powerful interactive command lines in Python" +category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -2576,6 +2698,7 @@ wcwidth = "*" name = "protobuf" version = "4.24.4" description = "" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2598,6 +2721,7 @@ files = [ name = "psutil" version = "5.9.6" description = "Cross-platform lib for process and system monitoring in Python." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -2626,6 +2750,7 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "ptyprocess" version = "0.7.0" description = "Run a subprocess in a pseudo terminal" +category = "main" optional = false python-versions = "*" files = [ @@ -2637,6 +2762,7 @@ files = [ name = "pure-eval" version = "0.2.2" description = "Safely evaluate AST nodes without side effects" +category = "main" optional = false python-versions = "*" files = [ @@ -2651,6 +2777,7 @@ tests = ["pytest"] name = "py" version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -2662,6 +2789,7 @@ files = [ name = "pyasn1" version = "0.5.0" description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -2673,6 +2801,7 @@ files = [ name = "pyasn1-modules" version = "0.3.0" description = "A collection of ASN.1-based protocols modules" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -2687,6 +2816,7 @@ pyasn1 = ">=0.4.6,<0.6.0" name = "pycodestyle" version = "2.11.1" description = "Python style guide checker" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2698,6 +2828,7 @@ files = [ name = "pycparser" version = "2.21" description = "C parser in Python" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -2709,6 +2840,7 @@ files = [ name = "pydantic" version = "1.10.13" description = "Data validation and settings management using python type hints" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2761,6 +2893,7 @@ email = ["email-validator (>=1.0.3)"] name = "pyflakes" version = "3.1.0" description = "passive checker of Python programs" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2772,6 +2905,7 @@ files = [ name = "pygments" version = "2.16.1" description = "Pygments is a syntax highlighting package written in Python." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2786,6 +2920,7 @@ plugins = ["importlib-metadata"] name = "pygsheets" version = "2.0.6" description = "Google Spreadsheets Python API v4" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -2804,6 +2939,7 @@ pandas = ["pandas (>=0.14.0)"] name = "pylint" version = "2.17.7" description = "python code static checker" +category = "dev" optional = false python-versions = ">=3.7.2" files = [ @@ -2830,6 +2966,7 @@ testutils = ["gitpython (>3)"] name = "pyopenssl" version = "23.2.0" description = "Python wrapper module around the OpenSSL library" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2848,6 +2985,7 @@ test = ["flaky", "pretend", "pytest (>=3.0.1)"] name = "pyparsing" version = "3.1.1" description = "pyparsing module - Classes and methods to define and execute parsing grammars" +category = "main" optional = false python-versions = ">=3.6.8" files = [ @@ -2862,6 +3000,7 @@ diagrams = ["jinja2", "railroad-diagrams"] name = "pytest" version = "7.4.2" description = "pytest: simple powerful testing with Python" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2884,6 +3023,7 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-cov" version = "4.1.0" description = "Pytest plugin for measuring coverage." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2902,6 +3042,7 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale name = "pytest-mock" version = "3.11.1" description = "Thin-wrapper around the mock package for easier use with pytest" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2919,6 +3060,7 @@ dev = ["pre-commit", "pytest-asyncio", "tox"] name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -2933,6 +3075,7 @@ six = ">=1.5" name = "python-dotenv" version = "0.21.1" description = "Read key-value pairs from a .env file and set them as environment variables" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2947,6 +3090,7 @@ cli = ["click (>=5.0)"] name = "python-json-logger" version = "2.0.7" description = "A python library adding a json log formatter" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2958,6 +3102,7 @@ files = [ name = "pytz" version = "2023.3.post1" description = "World timezone definitions, modern and historical" +category = "main" optional = false python-versions = "*" files = [ @@ -2969,6 +3114,7 @@ files = [ name = "pywin32" version = "306" description = "Python for Window Extensions" +category = "main" optional = false python-versions = "*" files = [ @@ -2992,6 +3138,7 @@ files = [ name = "pywin32-ctypes" version = "0.2.2" description = "A (partial) reimplementation of pywin32 using ctypes/cffi" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3003,6 +3150,7 @@ files = [ name = "pywinpty" version = "2.0.12" description = "Pseudo terminal support for Windows from Python." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3018,6 +3166,7 @@ files = [ name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3077,6 +3226,7 @@ files = [ name = "pyzmq" version = "25.1.1" description = "Python bindings for 0MQ" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3182,6 +3332,7 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""} name = "rdflib" version = "6.3.2" description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information." +category = "main" optional = false python-versions = ">=3.7,<4.0" files = [ @@ -3203,6 +3354,7 @@ networkx = ["networkx (>=2.0.0,<3.0.0)"] name = "referencing" version = "0.30.2" description = "JSON Referencing + Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3218,6 +3370,7 @@ rpds-py = ">=0.7.0" name = "regex" version = "2023.10.3" description = "Alternative regular expression module, to replace re." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3315,6 +3468,7 @@ files = [ name = "requests" version = "2.31.0" description = "Python HTTP for Humans." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3336,6 +3490,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "requests-oauthlib" version = "1.3.1" description = "OAuthlib authentication support for Requests." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3354,6 +3509,7 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"] name = "rfc3339-validator" version = "0.1.4" description = "A pure python RFC3339 validator" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3368,6 +3524,7 @@ six = "*" name = "rfc3986-validator" version = "0.1.1" description = "Pure python rfc3986 validator" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3379,6 +3536,7 @@ files = [ name = "rpds-py" version = "0.10.6" description = "Python bindings to Rust's persistent data structures (rpds)" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3487,6 +3645,7 @@ files = [ name = "rsa" version = "4.9" description = "Pure-Python RSA implementation" +category = "main" optional = false python-versions = ">=3.6,<4" files = [ @@ -3501,6 +3660,7 @@ pyasn1 = ">=0.1.3" name = "ruamel-yaml" version = "0.17.17" description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order" +category = "main" optional = false python-versions = ">=3" files = [ @@ -3519,6 +3679,7 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"] name = "ruamel-yaml-clib" version = "0.2.8" description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3564,6 +3725,7 @@ files = [ name = "schematic-db" version = "0.0.29" description = "" +category = "main" optional = false python-versions = ">=3.9,<4.0" files = [ @@ -3594,6 +3756,7 @@ synapse = ["synapseclient (>=2.7.0,<3.0.0)"] name = "scipy" version = "1.11.3" description = "Fundamental algorithms for scientific computing in Python" +category = "main" optional = false python-versions = "<3.13,>=3.9" files = [ @@ -3636,6 +3799,7 @@ test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeo name = "secretstorage" version = "3.3.3" description = "Python bindings to FreeDesktop.org Secret Service API" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3651,6 +3815,7 @@ jeepney = ">=0.6" name = "send2trash" version = "1.8.2" description = "Send file to trash natively under Mac OS X, Windows and Linux" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" files = [ @@ -3667,6 +3832,7 @@ win32 = ["pywin32"] name = "setuptools" version = "66.1.1" description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3683,6 +3849,7 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs ( name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -3694,6 +3861,7 @@ files = [ name = "sniffio" version = "1.3.0" description = "Sniff out which async library your code is running under" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3705,6 +3873,7 @@ files = [ name = "snowballstemmer" version = "2.2.0" description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." +category = "main" optional = false python-versions = "*" files = [ @@ -3716,6 +3885,7 @@ files = [ name = "soupsieve" version = "2.5" description = "A modern CSS selector implementation for Beautiful Soup." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3727,6 +3897,7 @@ files = [ name = "sphinx" version = "7.2.6" description = "Python documentation generator" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3762,6 +3933,7 @@ test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools name = "sphinx-click" version = "4.4.0" description = "Sphinx extension that automatically documents click applications" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3778,6 +3950,7 @@ sphinx = ">=2.0" name = "sphinxcontrib-applehelp" version = "1.0.7" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3796,6 +3969,7 @@ test = ["pytest"] name = "sphinxcontrib-devhelp" version = "1.0.5" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3814,6 +3988,7 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.4" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3832,6 +4007,7 @@ test = ["html5lib", "pytest"] name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -3846,6 +4022,7 @@ test = ["flake8", "mypy", "pytest"] name = "sphinxcontrib-qthelp" version = "1.0.6" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3864,6 +4041,7 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.9" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3882,6 +4060,7 @@ test = ["pytest"] name = "sqlalchemy" version = "1.4.49" description = "Database Abstraction Library" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -3963,6 +4142,7 @@ sqlcipher = ["sqlcipher3-binary"] name = "sqlalchemy-utils" version = "0.38.3" description = "Various utility functions for SQLAlchemy." +category = "main" optional = false python-versions = "~=3.6" files = [ @@ -3991,6 +4171,7 @@ url = ["furl (>=0.4.1)"] name = "stack-data" version = "0.6.3" description = "Extract data from python stack frames and tracebacks for informative displays" +category = "main" optional = false python-versions = "*" files = [ @@ -4010,6 +4191,7 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] name = "swagger-ui-bundle" version = "0.0.9" description = "swagger_ui_bundle - swagger-ui files in a pip package" +category = "main" optional = false python-versions = "*" files = [ @@ -4022,25 +4204,28 @@ Jinja2 = ">=2.0" [[package]] name = "synapseclient" -version = "2.7.0" +version = "2.7.2" description = "A client for Synapse, a collaborative compute space that allows scientists to share and analyze data together." +category = "main" optional = false -python-versions = ">=3.7.*" +python-versions = ">=3.7" files = [ - {file = "synapseclient-2.7.0-py3-none-any.whl", hash = "sha256:29f5e3c87474cb2629e9ce77c97e81e80a08f24ec2c5889f9fba14530b8c4bf7"}, - {file = "synapseclient-2.7.0.tar.gz", hash = "sha256:241f170f0e8c8c3735cd73f81711e592a581c55f7a5c4566be7bee82d72a56bc"}, + {file = "synapseclient-2.7.2-py3-none-any.whl", hash = "sha256:dd8b1a1b4667d08311bb651469431f43fe2eeab83c0ef1fe5a03c2929aeb26cd"}, + {file = "synapseclient-2.7.2.tar.gz", hash = "sha256:dc5a61f9f495109a0c89aa7d42b641b6ff278280d7961fb450dd5015704fe15b"}, ] [package.dependencies] deprecated = ">=1.2.4,<2.0" +importlib-metadata = "<5.0" keyring = ">=15,<23.5" "keyrings.alt" = {version = "3.1", markers = "sys_platform == \"linux\""} requests = ">=2.22.0,<3.0" +urllib3 = "<2" [package.extras] boto3 = ["boto3 (>=1.7.0,<2.0)"] -docs = ["sphinx (>=3.0,<4.0)", "sphinx-argparse (>=0.2,<0.3)"] -pandas = ["pandas (>=0.25.0,<2.0)"] +docs = ["sphinx (>=4.0,<5.0)", "sphinx-argparse (>=0.2,<0.3)"] +pandas = ["pandas (>=0.25.0,<1.5)"] pysftp = ["pysftp (>=0.2.8,<0.3)"] tests = ["flake8 (>=3.7.0,<4.0)", "pytest (>=5.0.0,<7.0)", "pytest-mock (>=3.0,<4.0)", "pytest-xdist[psutil] (>=2.2,<3.0.0)"] @@ -4048,6 +4233,7 @@ tests = ["flake8 (>=3.7.0,<4.0)", "pytest (>=5.0.0,<7.0)", "pytest-mock (>=3.0,< name = "tabulate" version = "0.9.0" description = "Pretty-print tabular data" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4062,6 +4248,7 @@ widechars = ["wcwidth"] name = "tenacity" version = "8.2.3" description = "Retry code until it succeeds" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4076,6 +4263,7 @@ doc = ["reno", "sphinx", "tornado (>=4.5)"] name = "terminado" version = "0.17.1" description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4096,6 +4284,7 @@ test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"] name = "tinycss2" version = "1.2.1" description = "A tiny CSS parser" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4114,6 +4303,7 @@ test = ["flake8", "isort", "pytest"] name = "toml" version = "0.10.2" description = "Python Library for Tom's Obvious, Minimal Language" +category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -4125,6 +4315,7 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4136,6 +4327,7 @@ files = [ name = "tomlkit" version = "0.12.1" description = "Style preserving TOML library" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4147,6 +4339,7 @@ files = [ name = "toolz" version = "0.12.0" description = "List processing tools and functional utilities" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -4158,6 +4351,7 @@ files = [ name = "tornado" version = "6.3.3" description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." +category = "main" optional = false python-versions = ">= 3.8" files = [ @@ -4178,6 +4372,7 @@ files = [ name = "tqdm" version = "4.66.1" description = "Fast, Extensible Progress Meter" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4198,6 +4393,7 @@ telegram = ["requests"] name = "traitlets" version = "5.11.2" description = "Traitlets Python configuration system" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4213,6 +4409,7 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest (>=7.0, name = "types-python-dateutil" version = "2.8.19.14" description = "Typing stubs for python-dateutil" +category = "main" optional = false python-versions = "*" files = [ @@ -4224,6 +4421,7 @@ files = [ name = "typing-extensions" version = "4.5.0" description = "Backported and Experimental Type Hints for Python 3.7+" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4235,6 +4433,7 @@ files = [ name = "tzdata" version = "2023.3" description = "Provider of IANA time zone data" +category = "main" optional = false python-versions = ">=2" files = [ @@ -4246,6 +4445,7 @@ files = [ name = "tzlocal" version = "5.1" description = "tzinfo object for the local timezone" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4263,6 +4463,7 @@ devenv = ["black", "check-manifest", "flake8", "pyroma", "pytest (>=4.3)", "pyte name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4277,6 +4478,7 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "uritemplate" version = "4.1.1" description = "Implementation of RFC 6570 URI Templates" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -4288,6 +4490,7 @@ files = [ name = "urllib3" version = "1.26.17" description = "HTTP library with thread-safe connection pooling, file post, and more." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -4304,6 +4507,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "uwsgi" version = "2.0.22" description = "The uWSGI server" +category = "dev" optional = false python-versions = "*" files = [ @@ -4314,6 +4518,7 @@ files = [ name = "validators" version = "0.20.0" description = "Python Data Validation for Humans™." +category = "main" optional = false python-versions = ">=3.4" files = [ @@ -4330,6 +4535,7 @@ test = ["flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)"] name = "wcwidth" version = "0.2.8" description = "Measures the displayed width of unicode strings in a terminal" +category = "main" optional = false python-versions = "*" files = [ @@ -4341,6 +4547,7 @@ files = [ name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4356,6 +4563,7 @@ tests = ["pytest", "pytest-cov"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" +category = "main" optional = false python-versions = "*" files = [ @@ -4367,6 +4575,7 @@ files = [ name = "websocket-client" version = "1.6.4" description = "WebSocket client for Python with low level API options" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4383,6 +4592,7 @@ test = ["websockets"] name = "werkzeug" version = "2.1.2" description = "The comprehensive WSGI web application library." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4397,6 +4607,7 @@ watchdog = ["watchdog"] name = "widgetsnbextension" version = "4.0.9" description = "Jupyter interactive widgets for Jupyter Notebook" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4408,6 +4619,7 @@ files = [ name = "wrapt" version = "1.15.0" description = "Module for decorators, wrappers and monkey patching." +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" files = [ @@ -4492,6 +4704,7 @@ files = [ name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.8" files = [ From a2686d1dd80a89ce6dc7449db575213991a79a54 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 16 Oct 2023 10:33:47 -0700 Subject: [PATCH 39/51] use poetry `1.3.0` --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 6cb52dfbe..7b4367c27 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -27,7 +27,7 @@ jobs: test: runs-on: ubuntu-latest env: - POETRY_VERSION: 1.6.1 + POETRY_VERSION: 1.3.0 strategy: fail-fast: false matrix: From 2363139f4e6a61a8707166fad97bd92dcd8f183d Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 16 Oct 2023 10:35:39 -0700 Subject: [PATCH 40/51] Update README.md for req'd poetry version --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 051e0c6e1..7d3890de8 100644 --- a/README.md +++ b/README.md @@ -59,7 +59,7 @@ Please note we have a [code of conduct](CODE_OF_CONDUCT.md), please follow it in ``` git clone https://github.com/Sage-Bionetworks/schematic.git ``` -2. Install `poetry` (version 1.2 or later) using either the [official installer](https://python-poetry.org/docs/#installing-with-the-official-installer) or [pipx](https://python-poetry.org/docs/#installing-with-pipx). If you have an older installation of Poetry, we recommend uninstalling it first. +2. Install `poetry` (version 1.3.0 or later) using either the [official installer](https://python-poetry.org/docs/#installing-with-the-official-installer) or [pipx](https://python-poetry.org/docs/#installing-with-pipx). If you have an older installation of Poetry, we recommend uninstalling it first. 3. Start the virtual environment by doing: ``` From 41c078e1762f01343e2bbe280f3616c28f546afc Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 16 Oct 2023 10:41:11 -0700 Subject: [PATCH 41/51] Update api_test.yml --- .github/workflows/api_test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/api_test.yml b/.github/workflows/api_test.yml index fd54e8d9e..103b1a98d 100644 --- a/.github/workflows/api_test.yml +++ b/.github/workflows/api_test.yml @@ -15,7 +15,7 @@ jobs: test: runs-on: ubuntu-latest env: - POETRY_VERSION: 1.2.0 + POETRY_VERSION: 1.3.0 strategy: fail-fast: false matrix: @@ -85,4 +85,4 @@ jobs: if: ${{ false == inputs.perform_benchmarking }} run: > source .venv/bin/activate; - pytest -m "schematic_api and not submission and not rule_benchmark" \ No newline at end of file + pytest -m "schematic_api and not submission and not rule_benchmark" From 39f04e3eb469cb2596298be0cfeb89adfd682068 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 16 Oct 2023 10:41:57 -0700 Subject: [PATCH 42/51] Update pdoc.yml --- .github/workflows/pdoc.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pdoc.yml b/.github/workflows/pdoc.yml index 8823d0c02..1a1627c99 100644 --- a/.github/workflows/pdoc.yml +++ b/.github/workflows/pdoc.yml @@ -27,7 +27,7 @@ jobs: build: runs-on: ubuntu-latest env: - POETRY_VERSION: 1.2.0 + POETRY_VERSION: 1.3.0 strategy: matrix: python-version: ["3.9", "3.10"] @@ -93,4 +93,4 @@ jobs: url: ${{ steps.deployment.outputs.page_url }} steps: - id: deployment - uses: actions/deploy-pages@v1 \ No newline at end of file + uses: actions/deploy-pages@v1 From 8be89bf911fd7f8372ccb89eefb150e349c4da77 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 16 Oct 2023 10:42:09 -0700 Subject: [PATCH 43/51] Update publish.yml --- .github/workflows/publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 2255a52e2..804ef19e2 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -9,7 +9,7 @@ jobs: pypi_release: runs-on: ubuntu-latest env: - POETRY_VERSION: 1.2.0 + POETRY_VERSION: 1.3.0 if: github.event_name == 'push' && contains(github.ref, 'refs/tags') steps: #---------------------------------------------- From 722a084a033d501e0b31683aebe508f376088812 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 23 Oct 2023 13:47:17 -0700 Subject: [PATCH 44/51] set default for access token --- schematic/models/validate_manifest.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schematic/models/validate_manifest.py b/schematic/models/validate_manifest.py index f89b6fe07..f616d08ca 100644 --- a/schematic/models/validate_manifest.py +++ b/schematic/models/validate_manifest.py @@ -62,7 +62,7 @@ def get_multiple_types_error( return ["NA", error_col, error_message, error_val] def validate_manifest_rules( - self, manifest: pd.core.frame.DataFrame, sg: SchemaGenerator, restrict_rules: bool, project_scope: List, access_token: str, + self, manifest: pd.core.frame.DataFrame, sg: SchemaGenerator, restrict_rules: bool, project_scope: List, access_token: str = None, ) -> (pd.core.frame.DataFrame, List[List[str]]): """ Purpose: From 3b13d5914b9c9f9bee85efb348cd2b9390b613a5 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Mon, 23 Oct 2023 14:23:58 -0700 Subject: [PATCH 45/51] fix type hinting --- schematic/models/validate_manifest.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schematic/models/validate_manifest.py b/schematic/models/validate_manifest.py index f616d08ca..a525d0e7b 100644 --- a/schematic/models/validate_manifest.py +++ b/schematic/models/validate_manifest.py @@ -62,7 +62,7 @@ def get_multiple_types_error( return ["NA", error_col, error_message, error_val] def validate_manifest_rules( - self, manifest: pd.core.frame.DataFrame, sg: SchemaGenerator, restrict_rules: bool, project_scope: List, access_token: str = None, + self, manifest: pd.core.frame.DataFrame, sg: SchemaGenerator, restrict_rules: bool, project_scope: List, access_token: Optional[str] = None, ) -> (pd.core.frame.DataFrame, List[List[str]]): """ Purpose: From 7f29929b8e447caabafdae8340331d556df5f86e Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Tue, 31 Oct 2023 10:26:00 -0700 Subject: [PATCH 46/51] update version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9b32bdb5a..e44a47e47 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "schematicpy" -version = "22.3.2" +version = "23.11.1" description = "Package for biomedical data model and metadata ingress management" authors = [ "Milen Nikolov ", From 735823c19849b5ae4dbf7c4d730251004d562713 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Tue, 31 Oct 2023 10:26:12 -0700 Subject: [PATCH 47/51] remove `pyopenssl` dep --- poetry.lock | 980 ++++++++++++++++++------------------------------- pyproject.toml | 1 - 2 files changed, 354 insertions(+), 627 deletions(-) diff --git a/poetry.lock b/poetry.lock index 47974b13a..f2d421a9a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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implementation and client libraries" -category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "jupyter_client-8.4.0-py3-none-any.whl", hash = "sha256:6a2a950ec23a8f62f9e4c66acec7f0ea6c7d1f80ba0992e747b10c56ce2e6dbe"}, - {file = "jupyter_client-8.4.0.tar.gz", hash = "sha256:dc1b857d5d7d76ac101766c6e9b646bf18742721126e72e5d484c75a993cada2"}, + {file = "jupyter_client-8.5.0-py3-none-any.whl", hash = "sha256:c3877aac7257ec68d79b5c622ce986bd2a992ca42f6ddc9b4dd1da50e89f7028"}, + {file = "jupyter_client-8.5.0.tar.gz", hash = "sha256:e8754066510ce456358df363f97eae64b50860f30dc1fe8c6771440db3be9a63"}, ] [package.dependencies] importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" tornado = ">=6.2" @@ -1733,14 +1635,13 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt 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- A web-based notebook environment for interactive computing" -category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "notebook-7.0.5-py3-none-any.whl", hash = "sha256:f26bd66accd54fcd96cc6696fb6c2911f15843b1c524318fd7cbdb32a763e6a6"}, - {file = "notebook-7.0.5.tar.gz", hash = "sha256:9e7c7a91de138bc8b5ee50486a20e70fa4d82d407b5622ec8beac9e13e773181"}, + {file = "notebook-7.0.6-py3-none-any.whl", hash = "sha256:0fe8f67102fea3744fedf652e4c15339390902ca70c5a31c4f547fa23da697cc"}, + {file = "notebook-7.0.6.tar.gz", hash = "sha256:ec6113b06529019f7f287819af06c97a2baf7a95ac21a8f6e32192898e9f9a58"}, ] [package.dependencies] @@ -2346,7 +2222,6 @@ test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4 name = "notebook-shim" version = "0.2.3" description = "A shim layer for notebook traits and config" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2364,7 +2239,6 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync" name = "numpy" version = "1.26.1" description = "Fundamental package for array computing in Python" -category = "main" optional = false python-versions = "<3.13,>=3.9" files = [ @@ -2406,7 +2280,6 @@ files = [ name = "oauth2client" version = "4.1.3" description = "OAuth 2.0 client library" -category = "main" optional = false python-versions = "*" files = [ @@ -2425,7 +2298,6 @@ six = ">=1.6.1" name = "oauthlib" version = "3.2.2" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2442,7 +2314,6 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"] name = "openpyxl" version = "3.1.2" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2457,7 +2328,6 @@ et-xmlfile = "*" name = "overrides" version = "7.4.0" description = "A decorator to automatically detect mismatch when overriding a method." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2469,7 +2339,6 @@ files = [ name = "packaging" version = "23.2" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2481,7 +2350,6 @@ files = [ name = "pandarallel" version = "1.6.5" description = "An easy to use library to speed up computation (by parallelizing on multi CPUs) with pandas." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2501,7 +2369,6 @@ doc = ["mkdocs-material"] name = "pandas" version = "1.5.3" description = "Powerful data structures for data analysis, time series, and statistics" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2549,7 +2416,6 @@ test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] name = "pandocfilters" version = "1.5.0" description = "Utilities for writing pandoc filters in python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -2561,7 +2427,6 @@ files = [ name = "parso" version = "0.8.3" description = "A Python Parser" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2577,7 +2442,6 @@ testing = ["docopt", "pytest (<6.0.0)"] name = "pathspec" version = "0.11.2" description = "Utility library for gitignore style pattern matching of file paths." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2589,7 +2453,6 @@ files = [ name = "pdoc" version = "12.3.1" description = "API Documentation for Python Projects" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2609,7 +2472,6 @@ dev = ["black", "hypothesis", "mypy", "pytest", "pytest-cov", "pytest-timeout", name = "pexpect" version = "4.8.0" description = "Pexpect allows easy control of interactive console applications." -category = "main" optional = false python-versions = "*" files = [ @@ -2620,23 +2482,10 @@ files = [ [package.dependencies] ptyprocess = ">=0.5" -[[package]] -name = "pickleshare" -version = "0.7.5" -description = "Tiny 'shelve'-like database with concurrency support" -category = "main" -optional = false -python-versions = "*" -files = [ - {file = "pickleshare-0.7.5-py2.py3-none-any.whl", hash = "sha256:9649af414d74d4df115d5d718f82acb59c9d418196b7b4290ed47a12ce62df56"}, - {file = "pickleshare-0.7.5.tar.gz", hash = "sha256:87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca"}, -] - [[package]] name = "platformdirs" version = "3.11.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2652,7 +2501,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co name = "pluggy" version = "1.3.0" description = "plugin and hook calling mechanisms for python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2666,14 +2514,13 @@ testing = ["pytest", "pytest-benchmark"] [[package]] name = "prometheus-client" -version = "0.17.1" +version = "0.18.0" description = "Python client for the Prometheus monitoring system." -category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" files = [ - {file = "prometheus_client-0.17.1-py3-none-any.whl", hash = "sha256:e537f37160f6807b8202a6fc4764cdd19bac5480ddd3e0d463c3002b34462101"}, - {file = "prometheus_client-0.17.1.tar.gz", hash = "sha256:21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091"}, + {file = "prometheus_client-0.18.0-py3-none-any.whl", hash = "sha256:8de3ae2755f890826f4b6479e5571d4f74ac17a81345fe69a6778fdb92579184"}, + {file = "prometheus_client-0.18.0.tar.gz", hash = "sha256:35f7a8c22139e2bb7ca5a698e92d38145bc8dc74c1c0bf56f25cca886a764e17"}, ] [package.extras] @@ -2683,7 +2530,6 @@ twisted = ["twisted"] name = "prompt-toolkit" version = "3.0.39" description = "Library for building powerful interactive command lines in Python" -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -2698,7 +2544,6 @@ wcwidth = "*" name = "protobuf" version = "4.24.4" description = "" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2721,7 +2566,6 @@ files = [ name = "psutil" version = "5.9.6" description = "Cross-platform lib for process and system monitoring in Python." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -2750,7 +2594,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "ptyprocess" version = "0.7.0" description = "Run a subprocess in a pseudo terminal" -category = "main" optional = false python-versions = "*" files = [ @@ -2762,7 +2605,6 @@ files = [ name = "pure-eval" version = "0.2.2" description = "Safely evaluate AST nodes without side effects" -category = "main" optional = false python-versions = "*" files = [ @@ -2777,7 +2619,6 @@ tests = ["pytest"] name = "py" version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -2789,7 +2630,6 @@ files = [ name = "pyasn1" version = "0.5.0" description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -2801,7 +2641,6 @@ files = [ name = "pyasn1-modules" version = "0.3.0" description = "A collection of ASN.1-based protocols modules" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -2816,7 +2655,6 @@ pyasn1 = ">=0.4.6,<0.6.0" name = "pycodestyle" version = "2.11.1" description = "Python style guide checker" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2828,7 +2666,6 @@ files = [ name = "pycparser" version = "2.21" description = "C parser in Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -2840,7 +2677,6 @@ files = [ name = "pydantic" version = "1.10.13" description = "Data validation and settings management using python type hints" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2893,7 +2729,6 @@ email = ["email-validator (>=1.0.3)"] name = "pyflakes" version = "3.1.0" description = "passive checker of Python programs" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2905,7 +2740,6 @@ files = [ name = "pygments" version = "2.16.1" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2920,7 +2754,6 @@ plugins = 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python-versions = ">=3.7" files = [ @@ -3090,7 +2897,6 @@ cli = ["click (>=5.0)"] name = "python-json-logger" version = "2.0.7" description = "A python library adding a json log formatter" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3102,7 +2908,6 @@ files = [ name = "pytz" version = "2023.3.post1" description = "World timezone definitions, modern and historical" -category = "main" optional = false python-versions = "*" files = [ @@ -3114,7 +2919,6 @@ files = [ name = "pywin32" version = "306" description = "Python for Window Extensions" -category = "main" optional = false python-versions = "*" files = [ @@ -3138,7 +2942,6 @@ files = [ name = "pywin32-ctypes" version = "0.2.2" description = "A (partial) reimplementation of pywin32 using ctypes/cffi" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3150,7 +2953,6 @@ files = [ name = "pywinpty" version = "2.0.12" description = "Pseudo terminal support for Windows from Python." 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"^1.6.4" -schematic-db = {version = "^0.0.33", extras = ["synapse"]} +schematic-db = {version = "0.0.dev33", extras = ["synapse"]} typing-extensions = "<4.6.0" [tool.poetry.dev-dependencies] From 0bd51e7caa4b99683d319198cad7fc64d5c3367e Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 1 Nov 2023 11:51:34 -0700 Subject: [PATCH 50/51] update synapseclient ver `.lock` and `.toml` are in sync now --- poetry.lock | 123 +++++++++++++++++++++++++++++++++++++++++++++++-- pyproject.toml | 2 +- 2 files changed, 120 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index 53fb47e45..01b0cbde6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -770,6 +770,23 @@ files = [ {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"}, ] +[[package]] +name = "deprecated" +version = "1.2.14" +description = "Python @deprecated decorator to deprecate old python classes, functions or methods." +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "Deprecated-1.2.14-py2.py3-none-any.whl", hash = "sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c"}, + {file = "Deprecated-1.2.14.tar.gz", hash = "sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3"}, +] + +[package.dependencies] +wrapt = ">=1.10,<2" + +[package.extras] +dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"] + [[package]] name = "deprecation" version = "2.1.0" @@ -1479,6 +1496,21 @@ docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alab qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"] testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] +[[package]] +name = "jeepney" +version = "0.8.0" +description = "Low-level, pure Python DBus protocol wrapper." +optional = false +python-versions = ">=3.7" +files = [ + {file = 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hash = "sha256:bf490a1a709baf35d688fe0ecf980ed4de11d2b3e37b51e5442587a75d9957e7"}, +] + [[package]] name = "pywinpty" version = "2.0.12" @@ -3514,6 +3596,21 @@ dev = ["click", "cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyl doc = ["jupytext", "matplotlib (>2)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"] test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] +[[package]] +name = "secretstorage" +version = "3.3.3" +description = "Python bindings to FreeDesktop.org Secret Service API" +optional = false +python-versions = ">=3.6" +files = [ + {file = "SecretStorage-3.3.3-py3-none-any.whl", hash = "sha256:f356e6628222568e3af06f2eba8df495efa13b3b63081dafd4f7d9a7b7bc9f99"}, + {file = "SecretStorage-3.3.3.tar.gz", hash = "sha256:2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77"}, +] + +[package.dependencies] +cryptography = ">=2.0" +jeepney = ">=0.6" + [[package]] name = "send2trash" version = "1.8.2" @@ -3894,11 +3991,29 @@ Jinja2 = ">=2.0" [[package]] name = "synapseclient" -version = "3.1.1.1479" +version = "3.1.1" description = "A client for Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate." optional = false -python-versions = "*" -files = [] +python-versions = ">=3.8" +files = [ + {file = "synapseclient-3.1.1-py3-none-any.whl", hash = "sha256:d9b732b450ee5c69a8d6875058af6739e0e076eb214fa0d05e7ebb21a0106846"}, + {file = "synapseclient-3.1.1.tar.gz", hash = "sha256:ab78a1202725d22c21f92798191c1862e779b2b31c01ff06f59789bb05fa1174"}, +] + +[package.dependencies] +deprecated = ">=1.2.4,<2.0" +keyring = ">=15,<23.5" +"keyrings.alt" = {version = "3.1", markers = "sys_platform == \"linux\""} +requests = ">=2.22.0,<3.0" +urllib3 = ">=1.26.18,<2" + +[package.extras] +boto3 = ["boto3 (>=1.7.0,<2.0)"] +dev = ["black", "flake8 (>=3.7.0,<4.0)", "func-timeout (>=4.3,<5.0)", "pre-commit", "pytest (>=6.0.0,<7.0)", "pytest-mock (>=3.0,<4.0)", "pytest-rerunfailures (>=12.0,<13.0)", "pytest-xdist[psutil] (>=2.2,<3.0.0)"] +docs = ["sphinx (>=4.0,<5.0)", "sphinx-argparse (>=0.2,<0.3)", "sphinx-rtd-theme"] +pandas = ["pandas (>=1.5,<2.1)"] +pysftp = ["pysftp (>=0.2.8,<0.3)"] +tests = ["flake8 (>=3.7.0,<4.0)", "func-timeout (>=4.3,<5.0)", "pytest (>=6.0.0,<7.0)", "pytest-mock (>=3.0,<4.0)", "pytest-rerunfailures (>=12.0,<13.0)", "pytest-xdist[psutil] (>=2.2,<3.0.0)"] [[package]] name = "tabulate" @@ -4362,4 +4477,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.9.0,<3.11" -content-hash = "6449db96309d6925c86fe1ab09681551260635e7fb2987322b811e944292bde6" +content-hash = "69cf42349d444363f351f4b4d37f731cf537e4cfd374dae4b6c8aec6699bf6cf" diff --git a/pyproject.toml b/pyproject.toml index 18ed05187..a7610126e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,7 +54,7 @@ pygsheets = "^2.0.4" PyYAML = "^6.0.0" rdflib = "^6.0.0" setuptools = "^66.0.0" -synapseclient = "^3.0.0" +synapseclient = "^3.1.1" tenacity = "^8.0.1" toml = "^0.10.2" Flask = "^2.0.0" From f14dabf3aba61a5dff00de62e91a5b1ed2135d90 Mon Sep 17 00:00:00 2001 From: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Date: Wed, 1 Nov 2023 14:06:40 -0700 Subject: [PATCH 51/51] re add `pyopenssl` --- poetry.lock | 20 +++++++++++++++++++- pyproject.toml | 1 + 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 01b0cbde6..e5a9d8c6e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2794,6 +2794,24 @@ typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\"" spelling = ["pyenchant (>=3.2,<4.0)"] testutils = ["gitpython (>3)"] +[[package]] +name = "pyopenssl" +version = "23.3.0" +description = "Python wrapper module around the OpenSSL library" +optional = false +python-versions = ">=3.7" +files = [ + {file = "pyOpenSSL-23.3.0-py3-none-any.whl", hash = "sha256:6756834481d9ed5470f4a9393455154bc92fe7a64b7bc6ee2c804e78c52099b2"}, + {file = "pyOpenSSL-23.3.0.tar.gz", hash = "sha256:6b2cba5cc46e822750ec3e5a81ee12819850b11303630d575e98108a079c2b12"}, +] + +[package.dependencies] +cryptography = ">=41.0.5,<42" + +[package.extras] +docs = ["sphinx (!=5.2.0,!=5.2.0.post0,!=7.2.5)", "sphinx-rtd-theme"] +test = ["flaky", "pretend", "pytest (>=3.0.1)"] + [[package]] name = "pyparsing" version = "3.1.1" @@ -4477,4 +4495,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.9.0,<3.11" -content-hash = "69cf42349d444363f351f4b4d37f731cf537e4cfd374dae4b6c8aec6699bf6cf" +content-hash = "9b6667bb6094ab24849d6b47c8923dd8140a29ba14ffa45a0f4be52609b49f9c" diff --git a/pyproject.toml b/pyproject.toml index a7610126e..714512b84 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -71,6 +71,7 @@ pdoc = "^12.2.0" dateparser = "^1.1.4" pandarallel = "^1.6.4" schematic-db = {version = "0.0.dev33", extras = ["synapse"]} +pyopenssl = "^23.0.0" typing-extensions = "<4.6.0" [tool.poetry.dev-dependencies]