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Feature/k8s support #1069
Feature/k8s support #1069
Commits on May 6, 2024
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Commits on May 7, 2024
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Commits on May 8, 2024
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Commits on May 9, 2024
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Commits on May 10, 2024
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Commits on May 15, 2024
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Commits on May 16, 2024
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Commits on May 17, 2024
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Commits on May 20, 2024
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Commits on May 24, 2024
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Update input/output working example (md5sum)
- Test command: ```sh funnel task create examples/md5sum.json ``` [no ci]
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Commits on May 30, 2024
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Update docker.go to implement ContainerEngine interface
- Can be used in HPC environment with unique docker setups (e.g. exadocker) as well as future command templating efforts. [no ci]
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Commits on May 31, 2024
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Update docker and kin-openapi to compatible versions
- github.com/docker/docker versions above v24.0.9 resulted in `panic: Can't connect docker client`: ``` ➜ go test tests/auth/auth_test.go --- FAIL: TestBasicAuthFail (0.01s) panic: Can't connect docker client [recovered] panic: Can't connect docker client FAIL command-line-arguments 0.673s FAIL ``` - This error appears to be originating from [util/dockerutil/docker.go](https://github.com/ohsu-comp-bio/funnel/blob/f5acbabe85d28f45f2f86db959c4d7bc929334a4/util/dockerutil/docker.go#L28). - github.com/getkin/kin-openapi versions above v0.112.0 resulted in type errors: v0.113.0: ``` ➜ go test util/openapi2proto/main.go util/openapi2proto/main.go:54:38: invalid operation: p.Value.AdditionalProperties != nil (mismatched types openapi3.AdditionalProperties and untyped nil) util/openapi2proto/main.go:55:24: cannot use p.Value.AdditionalProperties (variable of type openapi3.AdditionalProperties) as *openapi3.SchemaRef value in argument to getType FAIL command-line-arguments [build failed] FAIL ``` v0.123.0 (latest): ``` ➜ go test util/openapi2proto/main.go util/openapi2proto/main.go:43:7: cannot convert "integer" (untyped string constant) to type *openapi3.Types util/openapi2proto/main.go:45:7: cannot convert "boolean" (untyped string constant) to type *openapi3.Types util/openapi2proto/main.go:47:7: cannot convert "number" (untyped string constant) to type *openapi3.Types util/openapi2proto/main.go:49:7: cannot convert "object" (untyped string constant) to type *openapi3.Types util/openapi2proto/main.go:54:38: invalid operation: p.Value.AdditionalProperties != nil (mismatched types openapi3.AdditionalProperties and untyped nil) util/openapi2proto/main.go:55:24: cannot use p.Value.AdditionalProperties (variable of type openapi3.AdditionalProperties) as *openapi3.SchemaRef value in argument to getType util/openapi2proto/main.go:60:7: cannot convert "array" (untyped string constant) to type *openapi3.Types util/openapi2proto/main.go:72:17: cannot use p.Value.Type (variable of type *openapi3.Types) as string value in return statement util/openapi2proto/main.go:84:32: invalid operation: param.Schema.Value.Type != "" (mismatched types *openapi3.Types and untyped string) util/openapi2proto/main.go:175:17: resp.Get undefined (type *openapi3.Responses has no field or method Get) util/openapi2proto/main.go:175:17: too many errors FAIL command-line-arguments [build failed] FAIL ```
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Commits on Jun 1, 2024
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Commits on Jun 18, 2024
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Commits on Jun 20, 2024
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Update Base64Encode test to match Github Actions test
- TODO: investigate why this is necessary...
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Commits on Jun 21, 2024
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Revert glob output change based on TesOutput spec
- Wildcards in outputs will be uploaded to a directory, with no special handling for the filename. ```yaml tesOutput: properties: url: description: |- URL at which the TES server makes the output accessible after the task is complete. When tesOutput.path contains wildcards, it must be a directory; see `tesOutput.path_prefix` for details on how output URLs are constructed in this case. ```
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Commits on Jul 23, 2024
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Commits on Jul 24, 2024
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Commits on Jul 25, 2024
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Commits on Jul 26, 2024
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Commits on Jul 27, 2024
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Commits on Jul 31, 2024
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Commits on Sep 10, 2024
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Update K8s support and documentation
- Update docker images to use quay.io/ohsu-comp-bio/funnel
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Commits on Sep 17, 2024
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Commits on Sep 18, 2024
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Commits on Sep 19, 2024
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