SL-LAIDLAW/Metallaxis

View on GitHub
add TE information to interactive SVG + show description of genes + only get annotation for genes, not transcripts or exons #91
Sean LAIDLAW authored 157719a8
errored00:01:26
An engine encountered an error
E10 Error

We had trouble running the tailor engine.

The engine's output shown below may indicate the cause of the error.

If not, please contact us so we can investigate further.

1
git clone
2
codeclimate validate-config
View output
codeclimate validate-config
No errors or warnings found in .codeclimate.json.
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codeclimate prepare
View output
codeclimate prepare
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builder pull-engines
View output
determining required images
docker pull codeclimate/codeclimate-bandit:b866
b866: Pulling from codeclimate/codeclimate-bandit
a0e0ef996968: Pulling fs layer
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124b11ffd9dc: Verifying Checksum
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Digest: sha256:b831294279e697e4402c0bd94153247577b1e1297055bac81a8e2922b4dedba5
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-bandit:b866
docker pull codeclimate/codeclimate-editorconfig:b855
b855: Pulling from codeclimate/codeclimate-editorconfig
a073c86ecf9e: Pulling fs layer
0e28711eb56d: Pulling fs layer
e460dd483fdd: Pulling fs layer
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cb4230eeef73: Waiting
a073c86ecf9e: Verifying Checksum
a073c86ecf9e: Download complete
e460dd483fdd: Download complete
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54992f8503df: Verifying Checksum
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0e28711eb56d: Verifying Checksum
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c2238fe48590: Download complete
cb4230eeef73: Download complete
b65d797fb447: Verifying Checksum
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b85108c1334c: Verifying Checksum
b85108c1334c: Download complete
0e28711eb56d: Pull complete
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Digest: sha256:6d2c4a9632c2f4d3d5c7ea8aa58739fb07a6276a39847a8c00276e38cf1de302
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-editorconfig:b855
docker pull codeclimate/codeclimate-gofmt:b105
b105: Pulling from codeclimate/codeclimate-gofmt
f56be85fc22e: Pulling fs layer
85791d961cd3: Pulling fs layer
d694b5ae8c79: Pulling fs layer
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aa6e1b1410c0: Waiting
ae888a17dd15: Waiting
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6937c3ea65cb: Waiting
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f56be85fc22e: Verifying Checksum
f56be85fc22e: Download complete
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aa6e1b1410c0: Verifying Checksum
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f56be85fc22e: Pull complete
ae888a17dd15: Verifying Checksum
ae888a17dd15: Download complete
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d694b5ae8c79: Verifying Checksum
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d694b5ae8c79: Pull complete
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aa6e1b1410c0: Pull complete
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Digest: sha256:a56a4c3d42dfe13655556c67636b78f1a127533350ff232a39dea0f17e32b9b7
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-gofmt:b105
docker pull codeclimate/codeclimate-golint:b89
b89: Pulling from codeclimate/codeclimate-golint
9d48c3bd43c5: Pulling fs layer
7f94eaf8af20: Pulling fs layer
9fe9984849c1: Pulling fs layer
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b357234f8796: Waiting
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9d48c3bd43c5: Verifying Checksum
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b357234f8796: Download complete
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b357234f8796: Pull complete
83039f8453a9: Pull complete
Digest: sha256:d50485f9f9db1f5e67f3effe3b562f40512670ef691c84c719c3d03408bf2e8a
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-golint:b89
docker pull codeclimate/codeclimate-pep8:b25
b25: Pulling from codeclimate/codeclimate-pep8
ab6db1bc80d0: Pulling fs layer
bf17e9a1c113: Pulling fs layer
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328f3a57c882: Pulling fs layer
43b5f16a0c84: Pulling fs layer
a9696c7f4cd8: Waiting
51b9219e6e44: Waiting
328f3a57c882: Waiting
43b5f16a0c84: Waiting
e3c7e34cb08c: Waiting
0de813e89c33: Waiting
4f8d95c214b1: Verifying Checksum
4f8d95c214b1: Download complete
bf17e9a1c113: Verifying Checksum
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ab6db1bc80d0: Verifying Checksum
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a9696c7f4cd8: Verifying Checksum
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bf17e9a1c113: Pull complete
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e3c7e34cb08c: Verifying Checksum
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Digest: sha256:75f70c714bc5f9e65359d45469a1fe7c1b181a15aee8fbabec7e23c65b19d447
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-pep8:b25
docker pull codeclimate/codeclimate-shellcheck:b684
b684: Pulling from codeclimate/codeclimate-shellcheck
c19324d1d971: Pulling fs layer
b9d55d77164a: Pulling fs layer
8f50218ab73b: Pulling fs layer
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40c725c46ebc: Waiting
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93181916221c: Waiting
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c19324d1d971: Download complete
b9d55d77164a: Verifying Checksum
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c19324d1d971: Pull complete
9e528ae5c4ee: Verifying Checksum
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Digest: sha256:e0b2536aefdfd2c58c796ab66fea38b8c8b0389ce41a9bbfcd59ccd54b530acc
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-shellcheck:b684
docker pull codeclimate/codeclimate-sonar-python:b10
b10: Pulling from codeclimate/codeclimate-sonar-python
709515475419: Pulling fs layer
d1c225ed7c34: Pulling fs layer
887f300163b6: Pulling fs layer
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8fe915fa1948: Waiting
65145a386a45: Waiting
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Digest: sha256:7904831e83e5474cba8a95726a691787d74d669d74a8721f114057ebb4a8943d
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-sonar-python:b10
docker pull codeclimate/codeclimate-stylelint:b1017
b1017: Pulling from codeclimate/codeclimate-stylelint
5d20c808ce19: Pulling fs layer
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371e3eac71b2: Verifying Checksum
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Digest: sha256:4fef77bcf58e92656c2d4734c1e0e5bb9140eb3aa730a05d83ae51dc33cb0463
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-stylelint:b1017
docker pull codeclimate/codeclimate-swiftlint:b893
b893: Pulling from codeclimate/codeclimate-swiftlint
9ff7e2e5f967: Pulling fs layer
59856638ac9f: Pulling fs layer
6f317d6d954b: Pulling fs layer
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a3db6c87eafe: Waiting
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Digest: sha256:a2aabaa8206e74ba83b90cc7a1829bdcc28a7108207936eeaddeaa8de7513df2
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-swiftlint:b893
docker pull codeclimate/codeclimate-tailor:b767
b767: Pulling from codeclimate/codeclimate-tailor
5040bd298390: Pulling fs layer
fce5728aad85: Pulling fs layer
c42794440453: Pulling fs layer
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0c0da797ba48: Waiting
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Digest: sha256:9529341c65a32f430c6a03d35fcc33e79b7b0722ec95d082639bf24c921fbd9f
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-tailor:b767
docker pull codeclimate/codeclimate-vint:b186
b186: Pulling from codeclimate/codeclimate-vint
f58436d1df4c: Pulling fs layer
a3ed95caeb02: Pulling fs layer
5729e645edd8: Pulling fs layer
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b8e30729d5cd: Pull complete
Digest: sha256:134df01882fc111899aedb027979658d5e801101254d64a2c60daa1d18ba72a8
Status: Downloaded newer image for registry.prod.codeclimate.net/codeclimate/codeclimate-vint:b186
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...
7
bandit
bandit engine documentation
View output
[main]	INFO	profile include tests: None
[main]	INFO	profile exclude tests: None
[main]	INFO	cli include tests: None
[main]	INFO	cli exclude tests: None
[node_visitor]	INFO	Unable to find qualified name for module: setup.py
8
csslint
csslint engine documentation
9
editorconfig
editorconfig engine documentation
View output
.editorconfig file required
10
git-legal
git-legal engine documentation
11
gofmt
gofmt engine documentation
12
golint
golint engine documentation
13
pep8
pep8 engine documentation
View output
icons/ sample_data/ metallaxis/ docs/ app_setup/ setup.py img/
14
shellcheck
shellcheck engine documentation
15
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: Invalid character encountered in file '/code/icons/metallaxis_logo_revised.graffle' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/icons/MyIcon.icns' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/icons/Icon1024.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/icons/Icon128.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/metallaxis/annotation/snpEff.jar' at line 3 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/metallaxis/annotation/SnpSift.jar' at line 3 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/metallaxis/gui/graph_icon.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/metallaxis/gui/about.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/metallaxis/gui/table.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/metallaxis/gui/logo.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/img/interface_window_gene_view.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/img/interface_window_filter.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/img/interface_window_gene_view_zoom.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/img/interface_window_annotation.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/img/interface_window_statistics_pos.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/img/interface_window_statistics.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: 39 files indexed
INFO: ------------------------------------------------------------------------
INFO: EXECUTION SUCCESS
INFO: ------------------------------------------------------------------------
INFO: Total time: 3.012s
INFO: Final Memory: 9M/417M
INFO: ------------------------------------------------------------------------
16
stylelint
stylelint engine documentation
View output
No files to lint with the extensions: ".css", ".scss", ".sass", ".less", ".sss", ".html", ".vue", ".js", ".jsx", ".ts", ".tsx".
See our documentation at https://docs.codeclimate.com/docs/stylelint for more information.
17
swiftlint
swiftlint engine documentation
18
tailor
tailor engine documentation
View output
engine produced invalid output: {:message=>"Invalid JSON", :output=>"Usage: tailor [options] [--] [[file|directory] ...]\n\nPerform static analysis on Swift source files.\n\nInvoking Tailor with at least one file or directory will analyze all Swift files at those paths. If\nno paths are provided, Tailor will analyze all Swift files found in '$SRCROOT' (if defined), which\nis set by Xcode when run in a Build Phase. Tailor may be set up as an Xcode Build Phase\nautomatically with the --xcode option.\n\nOptions:\n -c,--config=<path/to/.tailor.yml>             specify configuration file\n    --debug                                    print ANTLR error messages when parsing error occurs\n    --except=<rule1,rule2,...>                 run all rules except the specified ones\n -f,--format=<xcode|json|cc|html>              select an output format\n -h,--help                                     display help\n    --invert-color                             invert colorized console output\n -l,--max-line-length=<0-999>                  maximum Line length (in characters)\n    --list-files                               display Swift source files to be analyzed\n    --max-class-length=<0-999>                 maximum Class length (in lines)\n    --max-closure-length=<0-999>               maximum Closure length (in lines)\n    --max-file-length=<0-999>                  maximum File length (in lines)\n    --max-function-length=<0-999>              maximum Function length (in lines)\n    --max-name-length=<0-999>                  maximum Identifier name length (in characters)\n    --max-severity=<error|warning (default)>   maximum severity\n    --max-struct-length=<0-999>                maximum Struct length (in lines)\n    --min-name-length=<1-999>                  minimum Identifier name length (in characters)\n    --no-color                                 disable colorized console output\n    --only=<rule1,rule2,...>                   run only the specified rules\n    --purge=<1-999>                            reduce memory usage by clearing DFA cache after\n                                               specified number of files are parsed\n    --show-rules                               show description for each rule\n -v,--version                                  display version\n    --xcode=<path/to/project.xcodeproj>        add Tailor Build Phase Run Script to Xcode Project\n"}