From 281b328ad75ae231bc1b5c9a7bd3e061ba9c03c3 Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Fri, 17 May 2024 05:06:55 -0700 Subject: [PATCH 1/8] initial mkdocs setup --- .gitignore | 3 + docs/getting_started.md | 74 +++++++++++++ docs/index.md | 12 ++ docs/reference/fileformats/fileformat.md | 1 + docs/reference/fileformats/maf.md | 1 + docs/reference/helper_modules/extract.md | 1 + docs/reference/helper_modules/load.md | 1 + .../helper_modules/process_functions.md | 1 + .../helper_modules/process_mutation.md | 1 + docs/reference/helper_modules/transform.md | 1 + docs/reference/helper_modules/validate.md | 1 + .../consortium_to_public.md | 1 + .../database_to_staging.md | 1 + .../main_pipeline_steps/input_to_database.md | 1 + docs/tutorials/local_file_validation.md | 20 ++++ mkdocs.yml | 104 ++++++++++++++++++ setup.cfg | 8 ++ 17 files changed, 232 insertions(+) create mode 100644 docs/getting_started.md create mode 100644 docs/index.md create mode 100644 docs/reference/fileformats/fileformat.md create mode 100644 docs/reference/fileformats/maf.md create mode 100644 docs/reference/helper_modules/extract.md create mode 100644 docs/reference/helper_modules/load.md create mode 100644 docs/reference/helper_modules/process_functions.md create mode 100644 docs/reference/helper_modules/process_mutation.md create mode 100644 docs/reference/helper_modules/transform.md create mode 100644 docs/reference/helper_modules/validate.md create mode 100644 docs/reference/main_pipeline_steps/consortium_to_public.md create mode 100644 docs/reference/main_pipeline_steps/database_to_staging.md create mode 100644 docs/reference/main_pipeline_steps/input_to_database.md create mode 100644 docs/tutorials/local_file_validation.md create mode 100644 mkdocs.yml diff --git a/.gitignore b/.gitignore index 326c8535..eb16f1b9 100644 --- a/.gitignore +++ b/.gitignore @@ -26,3 +26,6 @@ data_guide.out Genie.Rproj build/ dist/ + +# MkDocs output +docs_site/ diff --git a/docs/getting_started.md b/docs/getting_started.md new file mode 100644 index 00000000..8415254c --- /dev/null +++ b/docs/getting_started.md @@ -0,0 +1,74 @@ +# Getting Started + +## Dependencies + +This package contains both R, Python and cli tools. These are tools or packages you will need, to be able to reproduce these results: + +- Python >=3.8 or <3.10 + - `pip install -r requirements.txt` +- [bedtools](https://bedtools.readthedocs.io/en/latest/content/installation.html) +- R 4.2.2 + - `renv::install()` + - Follow instructions [here](https://r-docs.synapse.org/#note-for-windows-and-mac-users) to install synapser +- [Java > 8](https://www.java.com/en/download/) + - For mac users, it seems to work better to run `brew install java` +- [wget](https://www.gnu.org/software/wget/) + - For mac users, have to run `brew install wget` + +## Installation + +### PyPi + +The [aacrgenie](https://pypi.org/project/aacrgenie/) package is available from PyPI. It can be installed or upgraded with pip. + +``` +pip install aacrgenie +``` + +### Local + +Source code and development versions are available on Github. Installing from source: + +``` +git clone https://github.com/Sage-Bionetworks/Genie.git +cd Genie +``` + +Install the packages locally. + +``` +pip install -e . +pip install -r requirements.txt +pip install -r requirements-dev.txt +``` + +You can stay on the main branch to get the latest stable release or check out the develop branch or a tagged revision: + +``` +git checkout +``` + + +## Configuration + +Configure the Synapse client to authenticate to Synapse. + +1. Create a Synapse [Personal Access token (PAT)](https://help.synapse.org/docs/Managing-Your-Account.2055405596.html#ManagingYourAccount-PersonalAccessTokens). +1. Add a `~/.synapseConfig` file with the following information: + + ``` + [authentication] + authtoken = + ``` + +1. OR set an environmental variable + + ``` + export SYNAPSE_AUTH_TOKEN= + ``` + +1. Confirm you can log in to synapse in your terminal. + + ```shell + synapse login + ``` \ No newline at end of file diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 00000000..404ce2d3 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,12 @@ +![genie banner](https://raw.githubusercontent.com/Sage-Bionetworks/Genie/master/genie_banner.png) + +# AACR Project GENIE + +[![PyPi](https://img.shields.io/pypi/v/aacrgenie.svg?style=for-the-badge&label=PyPi&logo=PyPi)](https://pypi.org/project/aacrgenie) +[![Docker Automated](https://img.shields.io/docker/automated/sagebionetworks/genie.svg?style=for-the-badge&logo=docker)](https://hub.docker.com/r/sagebionetworks/genie) +[![GitHub CI](https://img.shields.io/github/actions/workflow/status/Sage-Bionetworks/Genie/ci.yml?branch=develop&style=for-the-badge&logo=github)](https://github.com/Sage-Bionetworks/Genie) + + +## Introduction + +This repository documents code used to gather, QC, standardize, and analyze data uploaded by institutes participating in AACR's Project GENIE (Genomics, Evidence, Neoplasia, Information, Exchange). \ No newline at end of file diff --git a/docs/reference/fileformats/fileformat.md b/docs/reference/fileformats/fileformat.md new file mode 100644 index 00000000..35baa97a --- /dev/null +++ b/docs/reference/fileformats/fileformat.md @@ -0,0 +1 @@ +::: genie.example_filetype_format \ No newline at end of file diff --git a/docs/reference/fileformats/maf.md b/docs/reference/fileformats/maf.md new file mode 100644 index 00000000..d02b0bf2 --- /dev/null +++ b/docs/reference/fileformats/maf.md @@ -0,0 +1 @@ +::: genie_registry.maf \ No newline at end of file diff --git a/docs/reference/helper_modules/extract.md b/docs/reference/helper_modules/extract.md new file mode 100644 index 00000000..d87bdd1d --- /dev/null +++ b/docs/reference/helper_modules/extract.md @@ -0,0 +1 @@ +::: genie.extract \ No newline at end of file diff --git a/docs/reference/helper_modules/load.md b/docs/reference/helper_modules/load.md new file mode 100644 index 00000000..a14133ec --- /dev/null +++ b/docs/reference/helper_modules/load.md @@ -0,0 +1 @@ +::: genie.load \ No newline at end of file diff --git a/docs/reference/helper_modules/process_functions.md b/docs/reference/helper_modules/process_functions.md new file mode 100644 index 00000000..a4045053 --- /dev/null +++ b/docs/reference/helper_modules/process_functions.md @@ -0,0 +1 @@ +::: genie.process_functions \ No newline at end of file diff --git a/docs/reference/helper_modules/process_mutation.md b/docs/reference/helper_modules/process_mutation.md new file mode 100644 index 00000000..4033aa55 --- /dev/null +++ b/docs/reference/helper_modules/process_mutation.md @@ -0,0 +1 @@ +::: genie.process_mutation \ No newline at end of file diff --git a/docs/reference/helper_modules/transform.md b/docs/reference/helper_modules/transform.md new file mode 100644 index 00000000..d60f9d95 --- /dev/null +++ b/docs/reference/helper_modules/transform.md @@ -0,0 +1 @@ +::: genie.transform \ No newline at end of file diff --git a/docs/reference/helper_modules/validate.md b/docs/reference/helper_modules/validate.md new file mode 100644 index 00000000..e8af6277 --- /dev/null +++ b/docs/reference/helper_modules/validate.md @@ -0,0 +1 @@ +::: genie.validate \ No newline at end of file diff --git a/docs/reference/main_pipeline_steps/consortium_to_public.md b/docs/reference/main_pipeline_steps/consortium_to_public.md new file mode 100644 index 00000000..4bdaa4ec --- /dev/null +++ b/docs/reference/main_pipeline_steps/consortium_to_public.md @@ -0,0 +1 @@ +::: genie.consortium_to_public \ No newline at end of file diff --git a/docs/reference/main_pipeline_steps/database_to_staging.md b/docs/reference/main_pipeline_steps/database_to_staging.md new file mode 100644 index 00000000..91975bb7 --- /dev/null +++ b/docs/reference/main_pipeline_steps/database_to_staging.md @@ -0,0 +1 @@ +::: genie.database_to_staging \ No newline at end of file diff --git a/docs/reference/main_pipeline_steps/input_to_database.md b/docs/reference/main_pipeline_steps/input_to_database.md new file mode 100644 index 00000000..5e3c3cc9 --- /dev/null +++ b/docs/reference/main_pipeline_steps/input_to_database.md @@ -0,0 +1 @@ +::: genie.input_to_database \ No newline at end of file diff --git a/docs/tutorials/local_file_validation.md b/docs/tutorials/local_file_validation.md new file mode 100644 index 00000000..c40e139b --- /dev/null +++ b/docs/tutorials/local_file_validation.md @@ -0,0 +1,20 @@ +# Local File Validation + +One of the features of the `aacrgenie` package is that is provides a local validation tool that GENIE data contributors and install and use to validate their files locally prior to uploading to Synapse. + +``` +pip install aacrgenie +genie -v +``` + +This will install all the necessary components for you to run the validator locally on all of your files, including the Synapse client. Please view the help to see how to run to validator. + +``` +genie validate -h +``` + +Validate a file + +``` +genie validate data_clinical_supp_SAGE.txt SAGE +``` diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 00000000..defa2142 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,104 @@ +# Project +site_name: AACR Project GENIE Repository Documentation +site_description: >- + This repository documents code used to gather, QC, standardize, and analyze data + uploaded by institutes participating in AACR's Project GENIE (Genomics, Evidence, + Neoplasia, Information, Exchange). +site_dir: docs_site + +# Repository +repo_url: https://github.com/Sage-Bionetworks/Genie +repo_name: AACR Project GENIE + +# Navigation +nav: + - Home: index.md + - Getting Started: getting_started.md + - Tutorials: + - Local File Validation: tutorials/local_file_validation.md + - Reference: + - Main Pipeline Steps: + - Input to Database: reference/main_pipeline_steps/input_to_database.md + - Database to Staging: reference/main_pipeline_steps/database_to_staging.md + - Consortium to Public: reference/main_pipeline_steps/consortium_to_public.md + - Fileformats: + - Fileformat: reference/fileformats/fileformat.md + - maf: reference/fileformats/maf.md + - Helper modules: + - process_functions: reference/helper_modules/process_functions.md + - validate: reference/helper_modules/validate.md + - extract: reference/helper_modules/extract.md + - load: reference/helper_modules/load.md + - transform: reference/helper_modules/transform.md + - process_mutation: reference/helper_modules/process_mutation.md + +# Theme configuration +theme: + name: material + features: + - navigation.instant + - navigation.tabs + - search.highlight + - search.share + - toc.integrate + - content.tabs.link + - navigation.indexes + - navigation.sections + palette: + - media: "(prefers-color-scheme: light)" + scheme: default + primary: green + accent: green + toggle: + icon: material/weather-night + name: Switch to dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + primary: green + accent: green + toggle: + icon: material/weather-sunny + name: Switch to light mode + # Enable the color mode toggle + features: + - content.code.copy + - navigation.sections + - navigation.tabs + - navigation.top + - navigation.tracking + - navigation.instant + - header.autohide + - content.action.edit + - content.tabs.link + - content.tabs + - search.highlight + - search.share + - search.suggest + - toc.integrate +plugins: +- search +- autorefs +- mkdocstrings: + default_handler: python + handlers: + python: + options: + members_order: source + show_if_no_docstring: False + show_root_heading: True + show_category_heading: True + docstring_style: google + docstring_section_style: spacy + filters: + - "!^_" +# Allows external links to open in a new tab +- open-in-new-tab + +markdown_extensions: + - admonition + - pymdownx.details + - pymdownx.superfences + + - toc: + permalink: true + diff --git a/setup.cfg b/setup.cfg index b4550b08..99c821fb 100644 --- a/setup.cfg +++ b/setup.cfg @@ -54,8 +54,16 @@ dev = pre-commit mypy +docs = + mkdocs<=1.6.0 + mkdocs-material<=9.5.23 + mkdocs-open-in-new-tab<=1.0.3 + mkdocstrings<=0.25.1 + mkdocstrings-python<=1.10.2 + [flake8] max-line-length = 88 ignore = # space before : (needed for how black formats slicing) E203 + From 37c491562b56332b7c7bf670f38a9e10137b8e15 Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Fri, 17 May 2024 05:25:02 -0700 Subject: [PATCH 2/8] show all members (functions, attributes, etc) --- mkdocs.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/mkdocs.yml b/mkdocs.yml index defa2142..257e75f0 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -84,8 +84,10 @@ plugins: python: options: members_order: source + members: yes show_if_no_docstring: False show_root_heading: True + show_root_full_path: True show_category_heading: True docstring_style: google docstring_section_style: spacy From b5c9be3317303d45554d38d9170b550ed8078d05 Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Fri, 17 May 2024 11:40:47 -0700 Subject: [PATCH 3/8] finalize initial mkdocs structure --- docs/reference/fileformats/assay.md | 1 + docs/reference/fileformats/bed.md | 1 + docs/reference/fileformats/clinical.md | 1 + docs/reference/fileformats/cna.md | 1 + .../reference/fileformats/mutations_in_cis.md | 1 + .../fileformats/patient_retraction.md | 1 + .../fileformats/sample_retraction.md | 1 + docs/reference/fileformats/seg.md | 1 + .../fileformats/structural_variant.md | 1 + docs/reference/fileformats/vcf.md | 1 + docs/reference/fileformats/workflow.md | 1 + .../helper_modules/create_case_lists.md | 1 + .../helper_modules/dashboard_table_updater.md | 1 + .../consortium_to_public.md | 1 + .../database_to_staging.md | 1 + .../input_to_database.md | 1 + .../input_to_database.md | 0 .../input_to_database}/process_mutation.md | 0 .../input_to_database/to_retract.md | 1 + .../write_invalid_reasons.md | 1 + mkdocs.yml | 38 ++++++++++++++++--- 21 files changed, 50 insertions(+), 6 deletions(-) create mode 100644 docs/reference/fileformats/assay.md create mode 100644 docs/reference/fileformats/bed.md create mode 100644 docs/reference/fileformats/clinical.md create mode 100644 docs/reference/fileformats/cna.md create mode 100644 docs/reference/fileformats/mutations_in_cis.md create mode 100644 docs/reference/fileformats/patient_retraction.md create mode 100644 docs/reference/fileformats/sample_retraction.md create mode 100644 docs/reference/fileformats/seg.md create mode 100644 docs/reference/fileformats/structural_variant.md create mode 100644 docs/reference/fileformats/vcf.md create mode 100644 docs/reference/fileformats/workflow.md create mode 100644 docs/reference/helper_modules/create_case_lists.md create mode 100644 docs/reference/helper_modules/dashboard_table_updater.md create mode 100644 docs/reference/main_pipeline_commands/consortium_to_public.md create mode 100644 docs/reference/main_pipeline_commands/database_to_staging.md create mode 100644 docs/reference/main_pipeline_commands/input_to_database.md rename docs/reference/main_pipeline_steps/{ => input_to_database}/input_to_database.md (100%) rename docs/reference/{helper_modules => main_pipeline_steps/input_to_database}/process_mutation.md (100%) create mode 100644 docs/reference/main_pipeline_steps/input_to_database/to_retract.md create mode 100644 docs/reference/main_pipeline_steps/input_to_database/write_invalid_reasons.md diff --git a/docs/reference/fileformats/assay.md b/docs/reference/fileformats/assay.md new file mode 100644 index 00000000..a506e066 --- /dev/null +++ b/docs/reference/fileformats/assay.md @@ -0,0 +1 @@ +::: genie_registry.assay \ No newline at end of file diff --git a/docs/reference/fileformats/bed.md b/docs/reference/fileformats/bed.md new file mode 100644 index 00000000..4873808a --- /dev/null +++ b/docs/reference/fileformats/bed.md @@ -0,0 +1 @@ +::: genie_registry.bed \ No newline at end of file diff --git a/docs/reference/fileformats/clinical.md b/docs/reference/fileformats/clinical.md new file mode 100644 index 00000000..fc132126 --- /dev/null +++ b/docs/reference/fileformats/clinical.md @@ -0,0 +1 @@ +::: genie_registry.clinical \ No newline at end of file diff --git a/docs/reference/fileformats/cna.md b/docs/reference/fileformats/cna.md new file mode 100644 index 00000000..a17d36fa --- /dev/null +++ b/docs/reference/fileformats/cna.md @@ -0,0 +1 @@ +::: genie_registry.cna \ No newline at end of file diff --git a/docs/reference/fileformats/mutations_in_cis.md b/docs/reference/fileformats/mutations_in_cis.md new file mode 100644 index 00000000..9fd6e694 --- /dev/null +++ b/docs/reference/fileformats/mutations_in_cis.md @@ -0,0 +1 @@ +::: genie_registry.mutationsInCis \ No newline at end of file diff --git a/docs/reference/fileformats/patient_retraction.md b/docs/reference/fileformats/patient_retraction.md new file mode 100644 index 00000000..87ddab89 --- /dev/null +++ b/docs/reference/fileformats/patient_retraction.md @@ -0,0 +1 @@ +::: genie_registry.patientRetraction \ No newline at end of file diff --git a/docs/reference/fileformats/sample_retraction.md b/docs/reference/fileformats/sample_retraction.md new file mode 100644 index 00000000..75d55d07 --- /dev/null +++ b/docs/reference/fileformats/sample_retraction.md @@ -0,0 +1 @@ +::: genie_registry.sampleRetraction \ No newline at end of file diff --git a/docs/reference/fileformats/seg.md b/docs/reference/fileformats/seg.md new file mode 100644 index 00000000..1fcadbda --- /dev/null +++ b/docs/reference/fileformats/seg.md @@ -0,0 +1 @@ +::: genie_registry.seg \ No newline at end of file diff --git a/docs/reference/fileformats/structural_variant.md b/docs/reference/fileformats/structural_variant.md new file mode 100644 index 00000000..4f834231 --- /dev/null +++ b/docs/reference/fileformats/structural_variant.md @@ -0,0 +1 @@ +::: genie_registry.structural_variant \ No newline at end of file diff --git a/docs/reference/fileformats/vcf.md b/docs/reference/fileformats/vcf.md new file mode 100644 index 00000000..ecee8a99 --- /dev/null +++ b/docs/reference/fileformats/vcf.md @@ -0,0 +1 @@ +::: genie_registry.vcf \ No newline at end of file diff --git a/docs/reference/fileformats/workflow.md b/docs/reference/fileformats/workflow.md new file mode 100644 index 00000000..ccdaa040 --- /dev/null +++ b/docs/reference/fileformats/workflow.md @@ -0,0 +1 @@ +::: genie_registry.workflow \ No newline at end of file diff --git a/docs/reference/helper_modules/create_case_lists.md b/docs/reference/helper_modules/create_case_lists.md new file mode 100644 index 00000000..eb26f186 --- /dev/null +++ b/docs/reference/helper_modules/create_case_lists.md @@ -0,0 +1 @@ +::: genie.create_case_lists \ No newline at end of file diff --git a/docs/reference/helper_modules/dashboard_table_updater.md b/docs/reference/helper_modules/dashboard_table_updater.md new file mode 100644 index 00000000..542f8d6d --- /dev/null +++ b/docs/reference/helper_modules/dashboard_table_updater.md @@ -0,0 +1 @@ +::: genie.dashboard_table_updater \ No newline at end of file diff --git a/docs/reference/main_pipeline_commands/consortium_to_public.md b/docs/reference/main_pipeline_commands/consortium_to_public.md new file mode 100644 index 00000000..41adf69b --- /dev/null +++ b/docs/reference/main_pipeline_commands/consortium_to_public.md @@ -0,0 +1 @@ +::: bin.consortium_to_public \ No newline at end of file diff --git a/docs/reference/main_pipeline_commands/database_to_staging.md b/docs/reference/main_pipeline_commands/database_to_staging.md new file mode 100644 index 00000000..fcece6de --- /dev/null +++ b/docs/reference/main_pipeline_commands/database_to_staging.md @@ -0,0 +1 @@ +::: bin.database_to_staging \ No newline at end of file diff --git a/docs/reference/main_pipeline_commands/input_to_database.md b/docs/reference/main_pipeline_commands/input_to_database.md new file mode 100644 index 00000000..4933515b --- /dev/null +++ b/docs/reference/main_pipeline_commands/input_to_database.md @@ -0,0 +1 @@ +::: bin.input_to_database \ No newline at end of file diff --git a/docs/reference/main_pipeline_steps/input_to_database.md b/docs/reference/main_pipeline_steps/input_to_database/input_to_database.md similarity index 100% rename from docs/reference/main_pipeline_steps/input_to_database.md rename to docs/reference/main_pipeline_steps/input_to_database/input_to_database.md diff --git a/docs/reference/helper_modules/process_mutation.md b/docs/reference/main_pipeline_steps/input_to_database/process_mutation.md similarity index 100% rename from docs/reference/helper_modules/process_mutation.md rename to docs/reference/main_pipeline_steps/input_to_database/process_mutation.md diff --git a/docs/reference/main_pipeline_steps/input_to_database/to_retract.md b/docs/reference/main_pipeline_steps/input_to_database/to_retract.md new file mode 100644 index 00000000..aaae692e --- /dev/null +++ b/docs/reference/main_pipeline_steps/input_to_database/to_retract.md @@ -0,0 +1 @@ +::: genie.toRetract \ No newline at end of file diff --git a/docs/reference/main_pipeline_steps/input_to_database/write_invalid_reasons.md b/docs/reference/main_pipeline_steps/input_to_database/write_invalid_reasons.md new file mode 100644 index 00000000..f93d5106 --- /dev/null +++ b/docs/reference/main_pipeline_steps/input_to_database/write_invalid_reasons.md @@ -0,0 +1 @@ +::: genie.write_invalid_reasons \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 257e75f0..602c2ce0 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -16,21 +16,46 @@ nav: - Getting Started: getting_started.md - Tutorials: - Local File Validation: tutorials/local_file_validation.md - - Reference: + - Reference: + # contains reference to all of the technical codebase + - Main Pipeline Commands: + # contains reference to the scripts with the command line args we call to + # run the pipeline + - Input to Database: reference/main_pipeline_commands/input_to_database.md + - Database to Staging: reference/main_pipeline_commands/database_to_staging.md + - Consortium to Public: reference/main_pipeline_commands/consortium_to_public.md - Main Pipeline Steps: - - Input to Database: reference/main_pipeline_steps/input_to_database.md + # contains all code related to input to database step + - Input to Database: + - input_to_database: reference/main_pipeline_steps/input_to_database/input_to_database.md + - validate: reference/main_pipeline_steps/input_to_database/validate.md + - write_invalid_reasons: reference/main_pipeline_steps/input_to_database/write_invalid_reasons.md + - process_mutation: reference/main_pipeline_steps/input_to_database/process_mutation.md + - to_retract: reference/main_pipeline_steps/input_to_database/toRetract.py - Database to Staging: reference/main_pipeline_steps/database_to_staging.md - Consortium to Public: reference/main_pipeline_steps/consortium_to_public.md - Fileformats: - Fileformat: reference/fileformats/fileformat.md - - maf: reference/fileformats/maf.md + - Assay Information: reference/fileformats/assay.md + - Bed: reference/fileformats/bed.md + - Clinical: reference/fileformats/clinical.md + - Cna: reference/fileformats/cna.md + - Maf: reference/fileformats/maf.md + - Mutations In Cis: reference/fileformats/mutations_in_cis.md + - Patient retraction: reference/fileformats/patient_retraction.md + - Sample retraction: reference/fileformats/sample_retraction.md + - Segmented: reference/fileformats/seg.md + - Structural variant: reference/fileformats/structural_variant.md + - Vcf: reference/fileformats/vcf.md + - Workflow: reference/fileformats/workflow.md - Helper modules: - - process_functions: reference/helper_modules/process_functions.md - - validate: reference/helper_modules/validate.md + # contains all code used in more than one step of the pipeline + - create_case_lists: reference/helper_modules/create_case_lists.md + - dashboard_table_updater: reference/helper_modules/dashboard_table_updater.md - extract: reference/helper_modules/extract.md - load: reference/helper_modules/load.md + - process_functions: reference/helper_modules/process_functions.md - transform: reference/helper_modules/transform.md - - process_mutation: reference/helper_modules/process_mutation.md # Theme configuration theme: @@ -84,6 +109,7 @@ plugins: python: options: members_order: source + # shows all functions and attributes even hidden members: yes show_if_no_docstring: False show_root_heading: True From 0c0a85a61fae4dbff88324bb633d8046d3d26766 Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Fri, 17 May 2024 14:36:26 -0700 Subject: [PATCH 4/8] add mkdocs auto-deploy gh actions --- .github/workflows/build_docs.yml | 37 ++++++++++++++++++++++++++++++++ README.md | 5 ++++- docs/index.md | 7 ++++-- 3 files changed, 46 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/build_docs.yml diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml new file mode 100644 index 00000000..a6e4a368 --- /dev/null +++ b/.github/workflows/build_docs.yml @@ -0,0 +1,37 @@ +name: Build Github Pages Docs +on: + push: + branches: + - gen-1109-setup-mkdocs + +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: 3.9 + + - name: Set Cache ID Based on UTC Week Number + run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV + + - name: Cache dependences + uses: actions/cache@v3 + with: + key: mkdocs-material-${{ env.cache_id }} + path: .cache + restore-keys: | + mkdocs-material- + + - name: Install mkdocs and dependencies + run: | + pip install mkdocs mkdocs-material mkdocstrings mkdocstrings-python mkdocs-open-in-new-tab + + - name: Build and deploy mkdocs site to GitHub Pages + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: mkdocs gh-deploy --force \ No newline at end of file diff --git a/README.md b/README.md index 555bb925..ba1a4c36 100644 --- a/README.md +++ b/README.md @@ -6,11 +6,14 @@ [![Docker Automated](https://img.shields.io/docker/automated/sagebionetworks/genie.svg?style=for-the-badge&logo=docker)](https://hub.docker.com/r/sagebionetworks/genie) [![GitHub CI](https://img.shields.io/github/actions/workflow/status/Sage-Bionetworks/Genie/ci.yml?branch=develop&style=for-the-badge&logo=github)](https://github.com/Sage-Bionetworks/Genie) - ## Introduction This repository documents code used to gather, QC, standardize, and analyze data uploaded by institutes participating in AACR's Project GENIE (Genomics, Evidence, Neoplasia, Information, Exchange). +## Documentation + +For more information about the AACR genie repository, [visit the GitHub Pages site.](https://sage-bionetworks.github.io/Genie/) + ## Dependencies This package contains both R, Python and cli tools. These are tools or packages you will need, to be able to reproduce these results: diff --git a/docs/index.md b/docs/index.md index 404ce2d3..cfc23519 100644 --- a/docs/index.md +++ b/docs/index.md @@ -6,7 +6,10 @@ [![Docker Automated](https://img.shields.io/docker/automated/sagebionetworks/genie.svg?style=for-the-badge&logo=docker)](https://hub.docker.com/r/sagebionetworks/genie) [![GitHub CI](https://img.shields.io/github/actions/workflow/status/Sage-Bionetworks/Genie/ci.yml?branch=develop&style=for-the-badge&logo=github)](https://github.com/Sage-Bionetworks/Genie) - ## Introduction -This repository documents code used to gather, QC, standardize, and analyze data uploaded by institutes participating in AACR's Project GENIE (Genomics, Evidence, Neoplasia, Information, Exchange). \ No newline at end of file +This repository documents code used to gather, QC, standardize, and analyze data uploaded by institutes participating in AACR's Project GENIE (Genomics, Evidence, Neoplasia, Information, Exchange). + +## Additional Documentation + +Visit the [Project Genie Data Portal](genie.synapse.org/) to learn more about our data \ No newline at end of file From 9ab768025fc9425ce3ee2862fa04ab1a4e0263ed Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Fri, 17 May 2024 14:38:44 -0700 Subject: [PATCH 5/8] fix url --- docs/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.md b/docs/index.md index cfc23519..7fab0628 100644 --- a/docs/index.md +++ b/docs/index.md @@ -12,4 +12,4 @@ This repository documents code used to gather, QC, standardize, and analyze data ## Additional Documentation -Visit the [Project Genie Data Portal](genie.synapse.org/) to learn more about our data \ No newline at end of file +Visit the [Project Genie Data Portal](https://genie.synapse.org/) to learn more about our data \ No newline at end of file From f05eea9b236e40c9f189fc8c25b3577c56534330 Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Fri, 17 May 2024 14:51:35 -0700 Subject: [PATCH 6/8] add requirements.txt for mkdocs --- .github/workflows/build_docs.yml | 11 +++++------ docs/requirements.txt | 5 +++++ 2 files changed, 10 insertions(+), 6 deletions(-) create mode 100644 docs/requirements.txt diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index a6e4a368..89317862 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -16,16 +16,15 @@ jobs: with: python-version: 3.9 - - name: Set Cache ID Based on UTC Week Number - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV - - name: Cache dependences uses: actions/cache@v3 with: - key: mkdocs-material-${{ env.cache_id }} - path: .cache + path: ~/.cache/pip + # Unique cache key based on requirements.txt in docs directory + key: ${{ runner.os }}-pip-${{ hashFiles('docs/requirements.txt') }}-mkdocs-deps + # Restore partial cache if exact match is not found restore-keys: | - mkdocs-material- + ${{ runner.os }}-pip- - name: Install mkdocs and dependencies run: | diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 00000000..87b70a6e --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,5 @@ +mkdocs<=1.6.0 +mkdocs-material<=9.5.23 +mkdocs-open-in-new-tab<=1.0.3 +mkdocstrings<=0.25.1 +mkdocstrings-python<=1.10.2 \ No newline at end of file From 9cb9fbb225d16de05affaf78590f02db3a35e37d Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Fri, 17 May 2024 15:12:13 -0700 Subject: [PATCH 7/8] update to main --- .github/workflows/build_docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index 89317862..92eacbc5 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -2,7 +2,7 @@ name: Build Github Pages Docs on: push: branches: - - gen-1109-setup-mkdocs + - main jobs: deploy: From 5a0383192fab68a64ce307d8a2fb12997ef53c6d Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Fri, 17 May 2024 15:12:40 -0700 Subject: [PATCH 8/8] add newline --- .github/workflows/build_docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index 92eacbc5..9aae76fd 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -33,4 +33,4 @@ jobs: - name: Build and deploy mkdocs site to GitHub Pages env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run: mkdocs gh-deploy --force \ No newline at end of file + run: mkdocs gh-deploy --force