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NicolasVuillamy 2020-09-09 20:18:21 +02:00
commit f072bc5c8d
16 changed files with 404 additions and 64 deletions
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19
.automation/test/snakemake/README.md Normal file
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@ -0,0 +1,19 @@
# Snakemake test cases
This folder holds the test cases for **Snakemake**.
## Additional Docs
No Additional information is needed for this test case.
## Good Test Cases
The test cases denoted: `LANGUAGE_good_FILE.EXTENSION` are all valid, and should pass successfully when linted.
- **Note:** They are linted utilizing the default linter rules.
## Bad Test Cases
The test cases denoted: `LANGUAGE_bad_FILE.EXTENSION` are **NOT** valid, and should trigger errors when linted.
- **Note:** They are linted utilizing the default linter rules.

11
.automation/test/snakemake/snakemake_bad_1.smk Normal file
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@ -0,0 +1,11 @@
rule all:
input:
file1='result.txt',
rule simulation:
output:
file1="result.txt"
shell:
"""
touch {output}
"""

16
.automation/test/snakemake/snakemake_good_1.smk Normal file
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@ -0,0 +1,16 @@
rule all:
input:
file1="result.txt",
rule simulation:
output:
file1="result.txt",
log:
"logs/simulation.log",
conda:
"envs/simulation.yml"
shell:
"""
touch {output}
"""

0
.github/linters/.snakefmt.toml vendored Normal file
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7
Dockerfile
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@ -10,7 +10,7 @@
FROM borkdude/clj-kondo:2020.07.29 as clj-kondo FROM borkdude/clj-kondo:2020.07.29 as clj-kondo
FROM dotenvlinter/dotenv-linter:2.1.0 as dotenv-linter FROM dotenvlinter/dotenv-linter:2.1.0 as dotenv-linter
FROM mstruebing/editorconfig-checker:2.1.0 as editorconfig-checker FROM mstruebing/editorconfig-checker:2.1.0 as editorconfig-checker
FROM golangci/golangci-lint:v1.30.0 as golangci-lint FROM golangci/golangci-lint:v1.31.0 as golangci-lint
FROM yoheimuta/protolint:v0.26.0 as protolint FROM yoheimuta/protolint:v0.26.0 as protolint
FROM koalaman/shellcheck:v0.7.1 as shellcheck FROM koalaman/shellcheck:v0.7.1 as shellcheck
FROM wata727/tflint:0.19.1 as tflint FROM wata727/tflint:0.19.1 as tflint
@ -44,6 +44,7 @@ LABEL com.github.actions.name="GitHub Super-Linter" \
org.opencontainers.image.version=$BUILD_VERSION \ org.opencontainers.image.version=$BUILD_VERSION \
org.opencontainers.image.authors="GitHub DevOps <github_devops@github.com>" \ org.opencontainers.image.authors="GitHub DevOps <github_devops@github.com>" \
org.opencontainers.image.url="https://github.com/github/super-linter" \ org.opencontainers.image.url="https://github.com/github/super-linter" \
org.opencontainers.image.source="https://github.com/github/super-linter" \
org.opencontainers.image.documentation="https://github.com/github/super-linter" \ org.opencontainers.image.documentation="https://github.com/github/super-linter" \
org.opencontainers.image.vendor="GitHub" \ org.opencontainers.image.vendor="GitHub" \
org.opencontainers.image.description="Lint your code base with GitHub Actions" org.opencontainers.image.description="Lint your code base with GitHub Actions"
@ -90,6 +91,7 @@ RUN apk add --update --no-cache \
krb5-libs \ krb5-libs \
libc-dev libxml2-dev libxml2-utils libgcc \ libc-dev libxml2-dev libxml2-utils libgcc \
libcurl libintl libssl1.1 libstdc++ \ libcurl libintl libssl1.1 libstdc++ \
linux-headers \
make \ make \
musl-dev \ musl-dev \
npm nodejs-current \ npm nodejs-current \
@ -337,6 +339,7 @@ ENV ACTIONS_RUNNER_DEBUG=${ACTIONS_RUNNER_DEBUG} \
OUTPUT_FOLDER=${OUTPUT_FOLDER} \ OUTPUT_FOLDER=${OUTPUT_FOLDER} \
OUTPUT_FORMAT=${OUTPUT_FORMAT} \ OUTPUT_FORMAT=${OUTPUT_FORMAT} \
RUN_LOCAL=${RUN_LOCAL} \ RUN_LOCAL=${RUN_LOCAL} \
SNAKEMAKE_CONFIG_FILE=${SNAKEMAKE_CONFIG_FILE} \
TEST_CASE_RUN=${TEST_CASE_RUN} \ TEST_CASE_RUN=${TEST_CASE_RUN} \
VALIDATE_ALL_CODEBASE=${VALIDATE_ALL_CODEBASE} \ VALIDATE_ALL_CODEBASE=${VALIDATE_ALL_CODEBASE} \
VALIDATE_ANSIBLE=${VALIDATE_ANSIBLE} \ VALIDATE_ANSIBLE=${VALIDATE_ANSIBLE} \
@ -380,6 +383,8 @@ ENV ACTIONS_RUNNER_DEBUG=${ACTIONS_RUNNER_DEBUG} \
VALIDATE_RAKU=${VALIDATE_RAKU} \ VALIDATE_RAKU=${VALIDATE_RAKU} \
VALIDATE_RUBY=${VALIDATE_RUBY} \ VALIDATE_RUBY=${VALIDATE_RUBY} \
VALIDATE_SHELL_SHFMT=${VALIDATE_SHELL_SHFMT} \ VALIDATE_SHELL_SHFMT=${VALIDATE_SHELL_SHFMT} \
VALIDATE_SNAKEMAKE_LINT=${VALIDATE_SNAKEMAKE_LINT} \
VALIDATE_SNAKEMAKE_SNAKEFMT=${VALIDATE_SNAKEMAKE_SNAKEFMT} \
VALIDATE_STATES=${VALIDATE_STATES} \ VALIDATE_STATES=${VALIDATE_STATES} \
VALIDATE_SQL=${VALIDATE_SQL} \ VALIDATE_SQL=${VALIDATE_SQL} \
VALIDATE_TERRAFORM=${VALIDATE_TERRAFORM} \ VALIDATE_TERRAFORM=${VALIDATE_TERRAFORM} \

6
README.md
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@ -75,6 +75,7 @@ Developers on **GitHub** can call the **GitHub Action** to lint their code base
| **Raku** | [Raku](https://raku.org) | | **Raku** | [Raku](https://raku.org) |
| **Ruby** | [RuboCop](https://github.com/rubocop-hq/rubocop) | | **Ruby** | [RuboCop](https://github.com/rubocop-hq/rubocop) |
| **Shell** | [Shellcheck](https://github.com/koalaman/shellcheck) / [executable bit check] / [shfmt](https://github.com/mvdan/sh) | | **Shell** | [Shellcheck](https://github.com/koalaman/shellcheck) / [executable bit check] / [shfmt](https://github.com/mvdan/sh) |
| **Snakemake** | [snakefmt](https://github.com/snakemake/snakefmt/) / [snakemake --lint](https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html#best-practices) |
| **SQL** | [sql-lint](https://github.com/joereynolds/sql-lint) | | **SQL** | [sql-lint](https://github.com/joereynolds/sql-lint) |
| **Terraform** | [tflint](https://github.com/terraform-linters/tflint) / [terrascan](https://github.com/accurics/terrascan) | | **Terraform** | [tflint](https://github.com/terraform-linters/tflint) / [terrascan](https://github.com/accurics/terrascan) |
| **TypeScript** | [eslint](https://eslint.org/) / [standard js](https://standardjs.com/) | | **TypeScript** | [eslint](https://eslint.org/) / [standard js](https://standardjs.com/) |
@ -197,6 +198,7 @@ But if you wish to select or exclude specific linters, we give you full control
| **PYTHON_FLAKE8_CONFIG_FILE** | `.flake8` | Filename for [flake8 configuration](https://flake8.pycqa.org/en/latest/user/configuration.html) (ex: `.flake8`, `tox.ini`) | | **PYTHON_FLAKE8_CONFIG_FILE** | `.flake8` | Filename for [flake8 configuration](https://flake8.pycqa.org/en/latest/user/configuration.html) (ex: `.flake8`, `tox.ini`) |
| **PYTHON_BLACK_CONFIG_FILE** | `.python-black` | Filename for [black configuration](https://github.com/psf/black/blob/master/docs/compatible_configs.md) (ex: `.isort.cfg`, `pyproject.toml`) | | **PYTHON_BLACK_CONFIG_FILE** | `.python-black` | Filename for [black configuration](https://github.com/psf/black/blob/master/docs/compatible_configs.md) (ex: `.isort.cfg`, `pyproject.toml`) |
| **RUBY_CONFIG_FILE** | `.ruby-lint.yml` | Filename for [rubocop configuration](https://docs.rubocop.org/rubocop/configuration.html) (ex: `.ruby-lint.yml`, `.rubocop.yml`) | | **RUBY_CONFIG_FILE** | `.ruby-lint.yml` | Filename for [rubocop configuration](https://docs.rubocop.org/rubocop/configuration.html) (ex: `.ruby-lint.yml`, `.rubocop.yml`) |
| **SNAKEMAKE_CONFIG_FILE** | `.snakefmt.toml` | Filename for [Snakemake configuration](https://github.com/snakemake/snakefmt#configuration) (ex: `pyproject.toml`, `.snakefmt.toml`) |
| **TYPESCRIPT_ES_CONFIG_FILE** | `.eslintrc.yml` | Filename for [eslint configuration](https://eslint.org/docs/user-guide/configuring#configuration-file-formats) (ex: `.eslintrc.yml`, `.eslintrc.json`) | | **TYPESCRIPT_ES_CONFIG_FILE** | `.eslintrc.yml` | Filename for [eslint configuration](https://eslint.org/docs/user-guide/configuring#configuration-file-formats) (ex: `.eslintrc.yml`, `.eslintrc.json`) |
| **VALIDATE_ALL_CODEBASE** | `true` | Will parse the entire repository and find all files to validate across all types. **NOTE:** When set to `false`, only **new** or **edited** files will be parsed for validation. | | **VALIDATE_ALL_CODEBASE** | `true` | Will parse the entire repository and find all files to validate across all types. **NOTE:** When set to `false`, only **new** or **edited** files will be parsed for validation. |
| **VALIDATE_ANSIBLE** | `true` | Flag to enable or disable the linting process of the Ansible language. | | **VALIDATE_ANSIBLE** | `true` | Flag to enable or disable the linting process of the Ansible language. |
@ -242,10 +244,12 @@ But if you wish to select or exclude specific linters, we give you full control
| **VALIDATE_RAKU** | `true` | Flag to enable or disable the linting process of the Raku language. | | **VALIDATE_RAKU** | `true` | Flag to enable or disable the linting process of the Raku language. |
| **VALIDATE_RUBY** | `true` | Flag to enable or disable the linting process of the Ruby language. | | **VALIDATE_RUBY** | `true` | Flag to enable or disable the linting process of the Ruby language. |
| **VALIDATE_SHELL_SHFMT** | `true` | Flag to enable or disable the linting process of Shell scripts. (Utilizing: shfmt) | | **VALIDATE_SHELL_SHFMT** | `true` | Flag to enable or disable the linting process of Shell scripts. (Utilizing: shfmt) |
| **VALIDATE_SNAKEMAKE_LINT** | `true` | Flag to enable or disable the linting process of Snakefiles. (Utilizing: snakemake --lint) |
| **VALIDATE_SNAKEMAKE_SNAKEFMT** | `true` | Flag to enable or disable the linting process of Snakefiles. (Utilizing: snakefmt) |
| **VALIDATE_STATES** | `true` | Flag to enable or disable the linting process for AWS States Language. | | **VALIDATE_STATES** | `true` | Flag to enable or disable the linting process for AWS States Language. |
| **VALIDATE_SQL** | `true` | Flag to enable or disable the linting process of the SQL language. | | **VALIDATE_SQL** | `true` | Flag to enable or disable the linting process of the SQL language. |
| **VALIDATE_TERRAFORM** | `true` | Flag to enable or disable the linting process of the Terraform language. | | **VALIDATE_TERRAFORM** | `true` | Flag to enable or disable the linting process of the Terraform language. |
| **VALIDATE_TERRAFORM_TERRASCAN** | `true` | Flag to enable or disable the linting process of the Terraform language for security related issues. | | **VALIDATE_TERRAFORM_TERRASCAN** | `true` | Flag to enable or disable the linting process of the Terraform language for security related issues. |
| **VALIDATE_TSX** | `true` | Flag to enable or disable the linting process for tsx files (Utilizing: eslint) | | **VALIDATE_TSX** | `true` | Flag to enable or disable the linting process for tsx files (Utilizing: eslint) |
| **VALIDATE_TYPESCRIPT_ES** | `true` | Flag to enable or disable the linting process of the Typescript language. (Utilizing: eslint) | | **VALIDATE_TYPESCRIPT_ES** | `true` | Flag to enable or disable the linting process of the Typescript language. (Utilizing: eslint) |
| **VALIDATE_TYPESCRIPT_STANDARD** | `true` | Flag to enable or disable the linting process of the Typescript language. (Utilizing: standard) | | **VALIDATE_TYPESCRIPT_STANDARD** | `true` | Flag to enable or disable the linting process of the Typescript language. (Utilizing: standard) |

3
TEMPLATES/.python-lint
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@ -127,7 +127,8 @@ disable=print-statement,
next-method-defined, next-method-defined,
dict-items-not-iterating, dict-items-not-iterating,
dict-keys-not-iterating, dict-keys-not-iterating,
dict-values-not-iterating dict-values-not-iterating,
import-error
# Enable the message, report, category or checker with the given id(s). You can # Enable the message, report, category or checker with the given id(s). You can
# either give multiple identifier separated by comma (,) or put this option # either give multiple identifier separated by comma (,) or put this option

0
TEMPLATES/.snakefmt.toml Normal file
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2
dependencies/Pipfile vendored
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@ -10,6 +10,8 @@ black = "*"
cfn-lint = "*" cfn-lint = "*"
flake8 = "*" flake8 = "*"
pylint = "*" pylint = "*"
snakefmt = "*"
snakemake = "*"
yamllint = "*" yamllint = "*"
yq = "*" yq = "*"

249
dependencies/Pipfile.lock generated vendored
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@ -1,7 +1,7 @@
{ {
"_meta": { "_meta": {
"hash": { "hash": {
"sha256": "1f2a4e188bcf058f78905dbe7c959b9a801148e39a69e86d6a795b45a65b7af9" "sha256": "db425ed57eee9f33aae7341acbde447b5170e9cbdb3bd360794c4ce4f3944c5c"
}, },
"pipfile-spec": 6, "pipfile-spec": 6,
"requires": { "requires": {
@ -16,6 +16,13 @@
] ]
}, },
"default": { "default": {
"amply": {
"hashes": [
"sha256:6e5d53af62772790ba82a989a3de72b8ce5c1cd809613c06f7cb061f7ec34dc8",
"sha256:c93da6113cac809487abc6565f41e37b9b8a5d469dcfaf4443d8d35befb181af"
],
"version": "==0.1.2"
},
"appdirs": { "appdirs": {
"hashes": [ "hashes": [
"sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41", "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41",
@ -35,14 +42,16 @@
"sha256:2f4078c2a41bf377eea06d71c9d2ba4eb8f6b1af2135bec27bbbb7d8f12bb703", "sha256:2f4078c2a41bf377eea06d71c9d2ba4eb8f6b1af2135bec27bbbb7d8f12bb703",
"sha256:bc58d83eb610252fd8de6363e39d4f1d0619c894b0ed24603b881c02e64c7386" "sha256:bc58d83eb610252fd8de6363e39d4f1d0619c894b0ed24603b881c02e64c7386"
], ],
"markers": "python_version >= '3.5'",
"version": "==2.4.2" "version": "==2.4.2"
}, },
"attrs": { "attrs": {
"hashes": [ "hashes": [
"sha256:0ef97238856430dcf9228e07f316aefc17e8939fc8507e18c6501b761ef1a42a", "sha256:26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594",
"sha256:2867b7b9f8326499ab5b0e2d12801fa5c98842d2cbd22b35112ae04bf85b4dff" "sha256:fce7fc47dfc976152e82d53ff92fa0407700c21acd20886a13777a0d20e655dc"
], ],
"version": "==20.1.0" "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==20.2.0"
}, },
"aws-sam-translator": { "aws-sam-translator": {
"hashes": [ "hashes": [
@ -54,25 +63,32 @@
}, },
"black": { "black": {
"hashes": [ "hashes": [
"sha256:1c02557aa099101b9d21496f8a914e9ed2222ef70336404eeeac8edba836fbea", "sha256:1b30e59be925fafc1ee4565e5e08abef6b03fe455102883820fe5ee2e4734e0b",
"sha256:70b62ef1527c950db59062cda342ea224d772abdf6adc58b86a45421bab20a6b" "sha256:c2edb73a08e9e0e6f65a0e6af18b059b8b1cdd5bef997d7a0b181df93dc81539"
], ],
"index": "pypi", "index": "pypi",
"version": "==20.8b1" "version": "==19.10b0"
}, },
"boto3": { "boto3": {
"hashes": [ "hashes": [
"sha256:4196b418598851ffd10cf9d1606694673cbfeca4ddf8b25d4e50addbd2fc60bf", "sha256:2ab73b0c400ab8c7df84bee7564ef8a0813021da28dd7a05fcbffb77a8ae9de9",
"sha256:69ad8f2184979e223e12ee3071674fdf910983cf9f4d6f34f7ec407b089064b5" "sha256:bb2222fa02fcd09b39e581e532d4f013ea850742d8cd46e9c10a21028b6d2ef5"
], ],
"version": "==1.14.54" "version": "==1.14.56"
}, },
"botocore": { "botocore": {
"hashes": [ "hashes": [
"sha256:6fe05837646447d61acdaf1e3401b92cd9309f00b19c577a50d0ade7735a3403", "sha256:5a72e1758f3c89c663d74eb733d313f69d059ab4fd571ad41829d666e3367392",
"sha256:9e493a21e6a8d45c631eb2952ae8e1d0a31b9984546d4268ea10c0c33e2435ce" "sha256:73fd22d70611fdcfbb44d1e5f77f7edf8a45a58e6286d50963cc19f9cf9e3e67"
], ],
"version": "==1.17.54" "version": "==1.17.56"
},
"certifi": {
"hashes": [
"sha256:5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3",
"sha256:8fc0819f1f30ba15bdb34cceffb9ef04d99f420f68eb75d901e9560b8749fc41"
],
"version": "==2020.6.20"
}, },
"cfn-lint": { "cfn-lint": {
"hashes": [ "hashes": [
@ -82,13 +98,58 @@
"index": "pypi", "index": "pypi",
"version": "==0.35.1" "version": "==0.35.1"
}, },
"chardet": {
"hashes": [
"sha256:84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae",
"sha256:fc323ffcaeaed0e0a02bf4d117757b98aed530d9ed4531e3e15460124c106691"
],
"version": "==3.0.4"
},
"click": { "click": {
"hashes": [ "hashes": [
"sha256:d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a", "sha256:d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a",
"sha256:dacca89f4bfadd5de3d7489b7c8a566eee0d3676333fbb50030263894c38c0dc" "sha256:dacca89f4bfadd5de3d7489b7c8a566eee0d3676333fbb50030263894c38c0dc"
], ],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
"version": "==7.1.2" "version": "==7.1.2"
}, },
"configargparse": {
"hashes": [
"sha256:edd17be986d5c1ba2e307150b8e5f5107aba125f3574dddd02c85d5cdcfd37dc"
],
"version": "==1.2.3"
},
"datrie": {
"hashes": [
"sha256:0e3b76676abbae2368cce6bf605bb0ba7cfd11f2c420b96d67959f353d5d423f",
"sha256:25e9e07ecfceaef78d23bde8d7278e4d6f63e1e3dc5ac00ccb4bec3062f0a8e0",
"sha256:2de594d84a2f43a09ddc15316a8afd48aae0fdc456f9279d0940aa59c473d9d5",
"sha256:31e316ba305cdd7b8a42f8e4af5a0a15a628aee270d2f392c41329a709eeda6d",
"sha256:327d9c17efaebc66d1956dca047b76fdd0e5b989d63cb55b9038ec09d8769089",
"sha256:3a3e360a765cc95410898dc222f8585ea1b1bba0538a1af4d8630a5bc3ad6ee7",
"sha256:525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d",
"sha256:53969643e2794c37f024d5edaa42d5e6e2627d9937ddcc18d99128e9df700e4c",
"sha256:651c63325056347b86c5de7ffeea8529230a5787c61ee6dcabc5b6c644bd3252",
"sha256:67603594f5db5c0029b1cf86a08e89cde015fe64cf0c4ae4e539c61114396729",
"sha256:6c9b333035312b79e6e9a10356d033e3d29aadbae6365007f706c854b3a94674",
"sha256:89ff3d41df4f899387aa07b4b066f5da36e3a10b67b8aeae631c950502ff4503",
"sha256:b07bd5fdfc3399a6dab86d6e35c72b1dbd598e80c97509c7c7518ab8774d3fda",
"sha256:b2d80fa687173cb8f8bae224ef00d1ad6bda8f8597bbb1a63f85182c7d91aeb3",
"sha256:b6fd6c7c149b410a87d46072c1c98f6e87ec557802e1d0e09db7b858746e8550",
"sha256:bf5c956c0a9a9d0f07e3c8923746279171096de18a8a51685e22d9817f8755a6",
"sha256:bf9f34f7c63797219b32713b561c4f94e777ff6c22beecfcd6bdf6b6c25b8518",
"sha256:c783e2c1e28964b2b045a951eb9606833a188c4bd4a780da68d22f557e03e429",
"sha256:dbe04704eb41b8440ca61416d3670ca6ddeea847d19731cf121889bac2962d07",
"sha256:e0582435a4adef1a2fce53aeedb656bf769b0f113b524f98be51d3e3d40720cb",
"sha256:e1d704ee4fdc03f02d7dacc4d92052dbd490dba551509fccfd8ee52c9039d4ad",
"sha256:ee7cd8470a982356e104e62148f2dbe2d3e17545cafaa3ada29f2548984f1e89",
"sha256:f61cf2726f04c08828bfb4e7af698b0b16bdf2777c3993d042f2898b8e118f21",
"sha256:f826e843138698501cbf1a21233f724b851b1e475fad532b638ac5904e115f10",
"sha256:fa9f39ac88dc6286672b9dd286fe459646da48133c877a927af24803eaea441e"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==0.8.2"
},
"decorator": { "decorator": {
"hashes": [ "hashes": [
"sha256:41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760", "sha256:41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760",
@ -102,6 +163,7 @@
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@ -112,18 +174,51 @@
"index": "pypi", "index": "pypi",
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@ -139,6 +234,7 @@
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@ -154,6 +250,14 @@
], ],
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@ -178,6 +282,7 @@
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@ -187,12 +292,13 @@
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@ -209,11 +315,36 @@
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"pyflakes": { "pyflakes": {
@ -221,6 +352,7 @@
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}, },
"pylint": { "pylint": {
@ -231,6 +363,14 @@
"index": "pypi", "index": "pypi",
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}, },
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@ -242,6 +382,7 @@
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}, },
"pyyaml": { "pyyaml": {
@ -261,6 +402,13 @@
"markers": "python_version != '3.4'", "markers": "python_version != '3.4'",
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}, },
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@ -287,6 +435,14 @@
], ],
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@ -299,8 +455,32 @@
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@ -308,6 +488,21 @@
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}, },
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@ -334,14 +529,6 @@
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}, },
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@ -373,11 +560,11 @@
}, },
"yq": { "yq": {
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} }
}, },
"develop": {} "develop": {}

73
dependencies/package-lock.json generated vendored
View file

@ -2296,37 +2296,68 @@
} }
}, },
"eslint-plugin-jest": { "eslint-plugin-jest": {
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"resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-2.34.0.tgz", "resolved": "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-4.0.1.tgz",
"integrity": "sha512-OMAr+nJWKdlVM9LOqCqh3pQQPwxHAN7Du8DR6dmwCrAmxtiXQnhHJ6tBNtf+cggqfo51SG/FCwnKhXCIM7hnVg==", "integrity": "sha512-u3YEXVJ8jsj7QCJk3om0Y457fy2euEOkkzxIB/LKU3MdyI+FJ2gI0M4aKEaXzwCSfNDiZ13a3lDo5DVozc+XLQ==",
"requires": { "requires": {
"@typescript-eslint/types": "4.0.1",
"@typescript-eslint/visitor-keys": "4.0.1"
}
},
"@typescript-eslint/types": {
"version": "4.0.1",
"resolved": "https://registry.npmjs.org/@typescript-eslint/types/-/types-4.0.1.tgz",
"integrity": "sha512-S+gD3fgbkZYW2rnbjugNMqibm9HpEjqZBZkTiI3PwbbNGWmAcxolWIUwZ0SKeG4Dy2ktpKKaI/6+HGYVH8Qrlg=="
},
"@typescript-eslint/typescript-estree": {
"version": "4.0.1",
"resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-4.0.1.tgz",
"integrity": "sha512-zGzleORFXrRWRJAMLTB2iJD1IZbCPkg4hsI8mGdpYlKaqzvKYSEWVAYh14eauaR+qIoZVWrXgYSXqLtTlxotiw==",
"requires": {
"@typescript-eslint/types": "4.0.1",
"@typescript-eslint/visitor-keys": "4.0.1",
"debug": "^4.1.1", "debug": "^4.1.1",
"eslint-visitor-keys": "^1.1.0", "globby": "^11.0.1",
"glob": "^7.1.6",
"is-glob": "^4.0.1", "is-glob": "^4.0.1",
"lodash": "^4.17.15", "lodash": "^4.17.15",
"semver": "^7.3.2", "semver": "^7.3.2",
"tsutils": "^3.17.1" "tsutils": "^3.17.1"
} }
},
"@typescript-eslint/visitor-keys": {
"version": "4.0.1",
"resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-4.0.1.tgz",
"integrity": "sha512-yBSqd6FjnTzbg5RUy9J+9kJEyQjTI34JdGMJz+9ttlJzLCnGkBikxw+N5n2VDcc3CesbIEJ0MnZc5uRYnrEnCw==",
"requires": {
"@typescript-eslint/types": "4.0.1",
"eslint-visitor-keys": "^2.0.0"
}
},
"eslint-visitor-keys": {
"version": "2.0.0",
"resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-2.0.0.tgz",
"integrity": "sha512-QudtT6av5WXels9WjIM7qz1XD1cWGvX4gGXvp/zBn9nXG02D0utdU3Em2m/QjTnrsk6bBjmCygl3rmj118msQQ=="
} }
} }
}, },
@ -3376,9 +3407,9 @@
"integrity": "sha1-R+Y/evVa+m+S4VAOaQ64uFKcCZo=" "integrity": "sha1-R+Y/evVa+m+S4VAOaQ64uFKcCZo="
}, },
"java-caller": { "java-caller": {
"version": "2.2.2", "version": "2.2.3",
"resolved": "https://registry.npmjs.org/java-caller/-/java-caller-2.2.2.tgz", "resolved": "https://registry.npmjs.org/java-caller/-/java-caller-2.2.3.tgz",
"integrity": "sha512-rK9ghUptfHflb3KDFOMBj/mCai2fp2Y/ebdNPoseQkSG0GySoy+sX8gn3S4tR1H6y0wRLNvRHjWtdjra4i0CGg==", "integrity": "sha512-NHOO3UVafHZaMK8QPgOM5Ge5VGa/7kNVv2OLJefXovcf3dNAo6eZLWa+Eu2lthp5TOYf+s2olzoK67qTgupmaA==",
"requires": { "requires": {
"debug": "^4.1.1", "debug": "^4.1.1",
"fs-extra": "^9.0.1", "fs-extra": "^9.0.1",
@ -4054,9 +4085,9 @@
"integrity": "sha1-0LFF62kRicY6eNIB3E/bEpPvDAM=" "integrity": "sha1-0LFF62kRicY6eNIB3E/bEpPvDAM="
}, },
"npm-groovy-lint": { "npm-groovy-lint": {
"version": "7.5.4", "version": "7.6.1",
"resolved": "https://registry.npmjs.org/npm-groovy-lint/-/npm-groovy-lint-7.5.4.tgz", "resolved": "https://registry.npmjs.org/npm-groovy-lint/-/npm-groovy-lint-7.6.1.tgz",
"integrity": "sha512-ShDRyW0s4z3OXrz2jSfLqiI7n8Iqvh8XtpBUS2vlX4CgL65IBk5rIt2swQOUL/UWUt3BTUg509ACzhD2g3arJA==", "integrity": "sha512-JPbBejvEjH08QlyLGOU+IMcUS8HuIAk8Z/6onL9u3ToTSWzZTlVPYrPpAxem2cpsh6MvwUwgK4QowB3icxkuew==",
"requires": { "requires": {
"amplitude": "^5.1.2", "amplitude": "^5.1.2",
"ansi-colors": "^4.1.1", "ansi-colors": "^4.1.1",
@ -4070,7 +4101,7 @@
"glob": "^7.1.6", "glob": "^7.1.6",
"import-fresh": "^3.2.1", "import-fresh": "^3.2.1",
"ip": "^1.1.5", "ip": "^1.1.5",
"java-caller": "^2.2.2", "java-caller": "^2.2.3",
"optionator": "^0.8.3", "optionator": "^0.8.3",
"semver": "^7.1.3", "semver": "^7.1.3",
"strip-json-comments": "^3.0.1", "strip-json-comments": "^3.0.1",

4
dependencies/package.json vendored
View file

@ -11,12 +11,12 @@
"eslint": "^7.8.1", "eslint": "^7.8.1",
"eslint-config-airbnb": "^18.2.0", "eslint-config-airbnb": "^18.2.0",
"eslint-config-prettier": "^6.11.0", "eslint-config-prettier": "^6.11.0",
"eslint-plugin-jest": "^23.20.0", "eslint-plugin-jest": "^24.0.0",
"eslint-plugin-prettier": "^3.1.4", "eslint-plugin-prettier": "^3.1.4",
"htmlhint": "^0.14.1", "htmlhint": "^0.14.1",
"jsonlint": "^1.6.3", "jsonlint": "^1.6.3",
"markdownlint-cli": "^0.23.2", "markdownlint-cli": "^0.23.2",
"npm-groovy-lint": "^7.5.4", "npm-groovy-lint": "^7.6.1",
"prettier": "^2.1.1", "prettier": "^2.1.1",
"prettyjson": "^1.2.1", "prettyjson": "^1.2.1",
"sql-lint": "0.0.15", "sql-lint": "0.0.15",

16
docs/disabling-linters.md
View file

@ -48,6 +48,7 @@ For some linters it is also possible to override rules on a case by case level w
- [Raku](#raku) - [Raku](#raku)
- [Ruby](#ruby) - [Ruby](#ruby)
- [Shell](#shell) - [Shell](#shell)
- [Snakemake](#snakemake)
- [SQL](#sql) - [SQL](#sql)
- [Terraform](#terraform) - [Terraform](#terraform)
- [Typescript eslint](#typescript-eslint) - [Typescript eslint](#typescript-eslint)
@ -1120,6 +1121,21 @@ shfmt [supports EditorConfig files for configuration](https://github.com/mvdan/s
--- ---
## Snakemake
- [snakemake --lint](https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html#best-practices)
- [snakefmt](https://github.com/snakemake/snakefmt/)
### snakemake's configuration
- Check the repository's README
### snakefmt configuration
- Check the repository's README
---
## SQL ## SQL
- [SQL](https://www.npmjs.com/package/sql-lint) - [SQL](https://www.npmjs.com/package/sql-lint)

13
lib/buildFileList.sh
View file

@ -484,6 +484,19 @@ function BuildFileList() {
########################################################## ##########################################################
READ_ONLY_CHANGE_FLAG=1 READ_ONLY_CHANGE_FLAG=1
###########################
# Get the SNAKEMAKE files #
###########################
elif [ "${FILE_TYPE}" == "smk" ]; then
################################
# Append the file to the array #
################################
FILE_ARRAY_SNAKEMAKE+=("${FILE}")
##########################################################
# Set the READ_ONLY_CHANGE_FLAG since this could be exec #
##########################################################
READ_ONLY_CHANGE_FLAG=1
##################### #####################
# Get the SQL files # # Get the SQL files #
##################### #####################

37
lib/linter.sh
View file

@ -118,6 +118,9 @@ R_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${R_FILE_NAME}" # Path to the R lint r
# Ruby Vars # Ruby Vars
RUBY_FILE_NAME="${RUBY_CONFIG_FILE:-.ruby-lint.yml}" # Name of the file RUBY_FILE_NAME="${RUBY_CONFIG_FILE:-.ruby-lint.yml}" # Name of the file
RUBY_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${RUBY_FILE_NAME}" # Path to the ruby lint rules RUBY_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${RUBY_FILE_NAME}" # Path to the ruby lint rules
# Snakemake Vars
SNAKEMAKE_FILE_NAME="${SNAKEMAKE_CONFIG_FILE:-.snakefmt.toml}" # Name of the file
SNAKEMAKE_SNAKEFMT_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SNAKEMAKE_FILE_NAME}" # Path to the snakemake lint rules
# SQL Vars # SQL Vars
SQL_FILE_NAME=".sql-config.json" # Name of the file SQL_FILE_NAME=".sql-config.json" # Name of the file
SQL_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SQL_FILE_NAME}" # Path to the SQL lint rules SQL_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SQL_FILE_NAME}" # Path to the SQL lint rules
@ -209,6 +212,8 @@ VALIDATE_RAKU="${VALIDATE_RAKU}" # Boolean t
VALIDATE_RUBY="${VALIDATE_RUBY}" # Boolean to validate language VALIDATE_RUBY="${VALIDATE_RUBY}" # Boolean to validate language
VALIDATE_STATES="${VALIDATE_STATES}" # Boolean to validate language VALIDATE_STATES="${VALIDATE_STATES}" # Boolean to validate language
VALIDATE_SHELL_SHFMT="${VALIDATE_SHELL_SHFMT}" # Boolean to check Shell files against editorconfig VALIDATE_SHELL_SHFMT="${VALIDATE_SHELL_SHFMT}" # Boolean to check Shell files against editorconfig
VALIDATE_SNAKEMAKE_LINT="${VALIDATE_SNAKEMAKE_LINT}" # Boolean to validate Snakefiles
VALIDATE_SNAKEMAKE_SNAKEFMT="${VALIDATE_SNAKEMAKE_SNAKEFMT}" # Boolean to validate Snakefiles
VALIDATE_SQL="${VALIDATE_SQL}" # Boolean to validate language VALIDATE_SQL="${VALIDATE_SQL}" # Boolean to validate language
VALIDATE_TERRAFORM="${VALIDATE_TERRAFORM}" # Boolean to validate language VALIDATE_TERRAFORM="${VALIDATE_TERRAFORM}" # Boolean to validate language
VALIDATE_TERRAFORM_TERRASCAN="${VALIDATE_TERRAFORM_TERRASCAN}" # Boolean to validate language VALIDATE_TERRAFORM_TERRASCAN="${VALIDATE_TERRAFORM_TERRASCAN}" # Boolean to validate language
@ -492,18 +497,21 @@ GetLinterRules() {
# Pull in vars # # Pull in vars #
################ ################
LANGUAGE_NAME="${1}" # Name of the language were looking for LANGUAGE_NAME="${1}" # Name of the language were looking for
debug "Getting linter rules for ${LANGUAGE_NAME}..."
####################################################### #######################################################
# Need to create the variables for the real variables # # Need to create the variables for the real variables #
####################################################### #######################################################
LANGUAGE_FILE_NAME="${LANGUAGE_NAME}_FILE_NAME" LANGUAGE_FILE_NAME="${LANGUAGE_NAME}_FILE_NAME"
LANGUAGE_LINTER_RULES="${LANGUAGE_NAME}_LINTER_RULES" LANGUAGE_LINTER_RULES="${LANGUAGE_NAME}_LINTER_RULES"
debug "Variable names for language file name: ${LANGUAGE_FILE_NAME}, language linter rules: ${LANGUAGE_LINTER_RULES}"
########################## ##########################
# Get the file extension # # Get the file extension #
########################## ##########################
FILE_EXTENSION=$(echo "${!LANGUAGE_FILE_NAME}" | rev | cut -d'.' -f1 | rev) FILE_EXTENSION=$(echo "${!LANGUAGE_FILE_NAME}" | rev | cut -d'.' -f1 | rev)
FILE_NAME=$(echo "${!LANGUAGE_FILE_NAME}" | rev | cut -d'.' -f2 | rev) FILE_NAME=$(basename "${!LANGUAGE_FILE_NAME}" ".${FILE_EXTENSION}")
debug "${LANGUAGE_NAME} language rule file (${!LANGUAGE_FILE_NAME}) has ${FILE_NAME} name and ${FILE_EXTENSION} extension"
############################### ###############################
# Set the secondary file name # # Set the secondary file name #
@ -533,8 +541,10 @@ GetLinterRules() {
######################################## ########################################
eval "${LANGUAGE_LINTER_RULES}=${GITHUB_WORKSPACE}/${LINTER_RULES_PATH}/${!LANGUAGE_FILE_NAME}" eval "${LANGUAGE_LINTER_RULES}=${GITHUB_WORKSPACE}/${LINTER_RULES_PATH}/${!LANGUAGE_FILE_NAME}"
else else
debug " -> Codebase does NOT have file:[${GITHUB_WORKSPACE}/${LINTER_RULES_PATH}/${!LANGUAGE_FILE_NAME}]"
# Check if we have secondary name to check # Check if we have secondary name to check
if [ -n "$SECONDARY_FILE_NAME" ]; then if [ -n "$SECONDARY_FILE_NAME" ]; then
debug "${LANGUAGE_NAME} language rule file has a secondary rules file name to check: ${SECONDARY_FILE_NAME}"
# We have a secondary name to validate # We have a secondary name to validate
if [ -f "${GITHUB_WORKSPACE}/${LINTER_RULES_PATH}/${SECONDARY_FILE_NAME}" ]; then if [ -f "${GITHUB_WORKSPACE}/${LINTER_RULES_PATH}/${SECONDARY_FILE_NAME}" ]; then
info "----------------------------------------------" info "----------------------------------------------"
@ -546,10 +556,11 @@ GetLinterRules() {
eval "${LANGUAGE_LINTER_RULES}=${GITHUB_WORKSPACE}/${LINTER_RULES_PATH}/${SECONDARY_FILE_NAME}" eval "${LANGUAGE_LINTER_RULES}=${GITHUB_WORKSPACE}/${LINTER_RULES_PATH}/${SECONDARY_FILE_NAME}"
fi fi
fi fi
######################################################## ########################################################
# No user default provided, using the template default # # No user default provided, using the template default #
######################################################## ########################################################
debug " -> Codebase does NOT have file:[${LINTER_RULES_PATH}/${!LANGUAGE_FILE_NAME}], using Default rules at:[${!LANGUAGE_LINTER_RULES}]" debug " -> Codebase does NOT have file:[${GITHUB_WORKSPACE}/${LINTER_RULES_PATH}/${!LANGUAGE_FILE_NAME}], nor file:[${GITHUB_WORKSPACE}/${LINTER_RULES_PATH}/${SECONDARY_FILE_NAME}], using Default rules at:[${!LANGUAGE_LINTER_RULES}]"
fi fi
} }
################################################################################ ################################################################################
@ -1848,6 +1859,28 @@ if [ "${VALIDATE_SHELL_SHFMT}" == "true" ]; then
fi fi
fi fi
##################
# SNAKEMAKE LINT #
##################
if [ "${VALIDATE_SNAKEMAKE_LINT}" == "true" ]; then
################################
# Lint the files with snakefmt #
################################
# LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILE_ARRAY"
LintCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" "\(Snakefile|.*\.smk\)\$" "${FILE_ARRAY_SNAKEMAKE[@]}"
fi
######################
# SNAKEMAKE SNAKEFMT #
######################
if [ "${VALIDATE_SNAKEMAKE_SNAKEFMT}" == "true" ]; then
################################
# Lint the files with snakefmt #
################################
# LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILE_ARRAY"
LintCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --diff" "\(Snakefile|.*\.smk\)\$" "${FILE_ARRAY_SNAKEMAKE[@]}"
fi
###################### ######################
# AWS STATES LINTING # # AWS STATES LINTING #
###################### ######################

12
lib/worker.sh
View file

@ -180,19 +180,19 @@ function LintCodebase() {
###################################################### ######################################################
# Make sure we don't lint node modules or test cases # # Make sure we don't lint node modules or test cases #
###################################################### ######################################################
if [[ ${FILE} == *"node_modules"* ]]; then if [[ ${DIR_NAME} == *"node_modules"* ]]; then
# This is a node modules file # This is a node modules file
continue continue
elif [[ ${FILE} == *"${TEST_CASE_FOLDER}"* ]]; then elif [[ ${DIR_NAME} == *"${TEST_CASE_FOLDER}"* ]]; then
# This is the test cases, we should always skip # This is the test cases, we should always skip
continue continue
elif [[ ${FILE} == *".git"* ]]; then elif [[ ${DIR_NAME} == *".git" ]] || [[ ${FILE} == *".git" ]] || [[ ${FILE} == *".git/"* ]]; then
# This is likely the .git folder and shouldn't be parsed # This is likely the .git folder and shouldn't be parsed
continue continue
elif [[ ${FILE} == *".venv"* ]]; then elif [[ ${DIR_NAME} == *".venv"* ]]; then
# This is likely the python virtual environment folder and shouldn't be parsed # This is likely the python virtual environment folder and shouldn't be parsed
continue continue
elif [[ ${FILE} == *".rbenv"* ]]; then elif [[ ${DIR_NAME} == *".rbenv"* ]]; then
# This is likely the ruby environment folder and shouldn't be parsed # This is likely the ruby environment folder and shouldn't be parsed
continue continue
elif [[ ${FILE_TYPE} == "BASH" ]] && ! IsValidShellScript "${FILE}"; then elif [[ ${FILE_TYPE} == "BASH" ]] && ! IsValidShellScript "${FILE}"; then
@ -724,6 +724,8 @@ function RunTestCases() {
TestCodebase "RAKU" "raku" "raku -c" ".*\.\(raku\|rakumod\|rakutest\|pm6\|pl6\|p6\)\$" "raku" TestCodebase "RAKU" "raku" "raku -c" ".*\.\(raku\|rakumod\|rakutest\|pm6\|pl6\|p6\)\$" "raku"
TestCodebase "RUBY" "rubocop" "rubocop -c ${RUBY_LINTER_RULES}" ".*\.\(rb\)\$" "ruby" TestCodebase "RUBY" "rubocop" "rubocop -c ${RUBY_LINTER_RULES}" ".*\.\(rb\)\$" "ruby"
TestCodebase "SHELL_SHFMT" "shfmt" "shfmt -d" ".*\.\(sh\|bash\|dash\|ksh\)\$" "shell_shfmt" TestCodebase "SHELL_SHFMT" "shfmt" "shfmt -d" ".*\.\(sh\|bash\|dash\|ksh\)\$" "shell_shfmt"
TestCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" ".*\.\(smk\)\$" "snakemake"
TestCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --diff" ".*\.\(smk\)\$" "snakemake"
TestCodebase "STATES" "asl-validator" "asl-validator --json-path" ".*\.\(json\)\$" "states" TestCodebase "STATES" "asl-validator" "asl-validator --json-path" ".*\.\(json\)\$" "states"
TestCodebase "SQL" "sql-lint" "sql-lint --config ${SQL_LINTER_RULES}" ".*\.\(sql\)\$" "sql" TestCodebase "SQL" "sql-lint" "sql-lint --config ${SQL_LINTER_RULES}" ".*\.\(sql\)\$" "sql"
TestCodebase "TERRAFORM" "tflint" "tflint -c ${TERRAFORM_LINTER_RULES}" ".*\.\(tf\)\$" "terraform" TestCodebase "TERRAFORM" "tflint" "tflint -c ${TERRAFORM_LINTER_RULES}" ".*\.\(tf\)\$" "terraform"