HumanCellAtlas/ingest-broker

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Update README.md #216
prabh-t authored 5b04ea11
complete00:00:17
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Your first build completed successfully!

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1
git clone
2
codeclimate validate-config
View output
codeclimate validate-config
WARNING: missing 'version' key. Please add `version: "2"`
3
codeclimate prepare
View output
codeclimate prepare
4
builder pull-engines
View output
determining required images
docker pull codeclimate/codeclimate-pep8:b25
b25: Pulling from codeclimate/codeclimate-pep8
ab6db1bc80d0: Pulling fs layer
bf17e9a1c113: Pulling fs layer
4f8d95c214b1: Pulling fs layer
0de813e89c33: Pulling fs layer
a9696c7f4cd8: Pulling fs layer
51b9219e6e44: Pulling fs layer
e3c7e34cb08c: Pulling fs layer
328f3a57c882: Pulling fs layer
43b5f16a0c84: Pulling fs layer
51b9219e6e44: Waiting
e3c7e34cb08c: Waiting
43b5f16a0c84: Waiting
0de813e89c33: Waiting
328f3a57c882: Waiting
a9696c7f4cd8: Waiting
bf17e9a1c113: Verifying Checksum
bf17e9a1c113: Download complete
4f8d95c214b1: Verifying Checksum
4f8d95c214b1: Download complete
ab6db1bc80d0: Verifying Checksum
ab6db1bc80d0: Download complete
a9696c7f4cd8: Verifying Checksum
a9696c7f4cd8: Download complete
ab6db1bc80d0: Pull complete
51b9219e6e44: Download complete
bf17e9a1c113: Pull complete
e3c7e34cb08c: Verifying Checksum
e3c7e34cb08c: Download complete
0de813e89c33: Verifying Checksum
0de813e89c33: Download complete
4f8d95c214b1: Pull complete
43b5f16a0c84: Verifying Checksum
43b5f16a0c84: Download complete
328f3a57c882: Verifying Checksum
328f3a57c882: Download complete
0de813e89c33: Pull complete
a9696c7f4cd8: Pull complete
51b9219e6e44: Pull complete
e3c7e34cb08c: Pull complete
328f3a57c882: Pull complete
43b5f16a0c84: Pull complete
Digest: sha256:75f70c714bc5f9e65359d45469a1fe7c1b181a15aee8fbabec7e23c65b19d447
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-pep8:b25
5
structure
View output
12
Parser process id: 12
codeclimate-parser socket not present
waiting 1s...
6
duplication
View output
12
Parser process id: 12
codeclimate-parser socket not present
waiting 1s...
I, [2024-05-07T01:45:50.474500 #1]  INFO -- : Skipping file broker_app.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 83
    response={"message": f'No spreadsheet found for submission with uuid {submission_uuid}'},
                                                                                          ^
SyntaxError: invalid syntax


I, [2024-05-07T01:45:50.509123 #1]  INFO -- : Skipping file ./broker/service/summary_service.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 33
    def summary_for_project(self, project_resource) -> ProjectSummary:
                                                    ^
SyntaxError: invalid syntax


I, [2024-05-07T01:45:50.539823 #1]  INFO -- : Skipping file ./broker/service/spreadsheet_storage/spreadsheet_storage_service.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 21
    submission_dir = f'{self.storage_dir}/{submission_uuid}'
                                                           ^
SyntaxError: invalid syntax


I, [2024-05-07T01:45:50.558993 #1]  INFO -- : Skipping file ./broker/service/spreadsheet_upload_service.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 14
    def __init__(self, ingest_api: IngestApi, storage_service: SpreadsheetStorageService, importer: XlsImporter):
                                 ^
SyntaxError: invalid syntax


I, [2024-05-07T01:45:50.576247 #1]  INFO -- : Skipping file ./broker/common/util/tsv_summary_util.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 10
    def project_summary_to_tsv(project_summary: ProjectSummary):
                                              ^
SyntaxError: invalid syntax


I, [2024-05-07T01:45:50.585801 #1]  INFO -- : Skipping file ./broker/common/entity_summary.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 9
    def __add__(self, other: 'EntitySummary') -> 'EntitySummary':
                           ^
SyntaxError: invalid syntax


I, [2024-05-07T01:45:50.593390 #1]  INFO -- : Skipping file ./broker/common/project_summary.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 17
    def add_submission_summary(self, submission_summary: 'SubmissionSummary') -> 'ProjectSummary':
                                                       ^
SyntaxError: invalid syntax
7
pep8
pep8 engine documentation
View output
broker_app.py generate_summary.py broker/
8
sonar-python
sonar-python engine documentation
View output
INFO: Java 1.8.0_111-internal Oracle Corporation (64-bit)
INFO: Linux 4.4.0-1128-aws amd64
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/usr/src/app/build/libs/sonarlint-core-2.17.0.899.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/usr/src/app/build/libs/sonarlint-cli-2.1.0.566.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
INFO: Index files
INFO: 28 files indexed
INFO: ------------------------------------------------------------------------
INFO: EXECUTION SUCCESS
INFO: ------------------------------------------------------------------------
INFO: Total time: 0.408s
INFO: Final Memory: 6M/295M
INFO: ------------------------------------------------------------------------