smaht-dac · B3rse · Dec 4, 2023 · Oct 19, 2023 · Oct 31, 2023 · Oct 31, 2023
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,4 +1,4 @@
-# portal-pipeline-utils GA Workflow
+# smaht-pipeline-utils GA Workflow
 
 name: CI
 
@@ -17,7 +17,7 @@ on:
 jobs:
   # This workflow contains a single job called "test"
   test:
-    name: Test portal-pipeline-utils with Python ${{ matrix.python_version }}
+    name: Test smaht-pipeline-utils with Python ${{ matrix.python_version }}
 
     # The type of runner that the job will run on
     runs-on: ubuntu-22.04
@@ -33,7 +33,7 @@ jobs:
         with:
           python-version: ${{ matrix.python_version }}
 
-      - name: Test portal-pipeline-utils
+      - name: Test smaht-pipeline-utils
         run: |
           make configure
           make build

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -4,8 +4,6 @@ Change Log
 ==========
 
 
-3.0.0
+0.0.1
 =====
-* 2023-10-10
-* Added this CHANGELOG.rst file.
-* Upgrade to Python 3.11.
+* Initial release
diff --git a/LOG.md b/LOG.md
diff --git a/README.md b/README.md
@@ -2,25 +2,25 @@
 
 Utilities for deploying pipelines and interfacing with portal infrastructure.
 
-For more information on available commands and how to contribute and deploy pipelines within the infrastructure check the extended [*documentation*](https://portal-pipeline-utils.readthedocs.io/en/latest/ "portal-pipeline-utils documentation").
+For more information on available commands and how to contribute and deploy pipelines within the infrastructure check the extended [*documentation*](https://smaht-pipeline-utils.readthedocs.io/en/latest/ "smaht-pipeline-utils documentation").
 
 ## Install
 
 The software is python based. To install the software and the required packages, we recommend using a fresh virtual environment.
 Please refer to `pyproject.toml` for the supported Python versions.
 
-The package is available on [*pypi*](https://pypi.org/project/portal-pipeline-utils "portal-pipeline-utils pypi"):
+The package is available on [*pypi*](https://pypi.org/project/smaht-pipeline-utils "smaht-pipeline-utils pypi"):
 
-    pip install portal-pipeline-utils
+    pip install smaht-pipeline-utils
 
 To install from source:
 
-    git clone https://github.com/dbmi-bgm/portal-pipeline-utils.git
-    cd portal-pipeline-utils
+    git clone https://github.com/smaht-dac/smaht-pipeline-utils.git
+    cd smaht-pipeline-utils
     make configure
     make update
     make build
 
-To check that the software is correctly installed, try to run `pipeline_utils`. If installed from source, this command may fail with a bash “command not found” error, try `poetry run pipeline_utils` instead.
+To check that the software is correctly installed, try to run `smaht_pipeline_utils`. If installed from source, this command may fail with a bash “command not found” error, try `poetry run smaht_pipeline_utils` instead.
 
 See `make info` for details on make targets.
diff --git a/docs/conf.py b/docs/conf.py
@@ -17,12 +17,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'portal-pipeline-utils'
-copyright = '2021, HMS DBMI'
-author = 'Michele Berselli, CGAP & SMaHT Team'
+project = 'smaht-pipeline-utils'
+copyright = '2023, HMS DBMI'
+author = 'Michele Berselli, SMaHT Team'
 
 # The full version, including alpha/beta/rc tags
-release = '2.1.0'
+release = '0.0.1'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/contribute_pipeline.rst b/docs/contribute_pipeline.rst
@@ -177,4 +177,4 @@ Example
 Examples
 --------
 
-Real examples of implemented pipeline modules can be found linked as submodules in our main pipeline repository for the CGAP project here: https://github.com/dbmi-bgm/cgap-pipeline-main.
+Real examples of implemented pipeline modules can be found linked as submodules in our main pipeline repository for the SMaHT project here: https://github.com/smaht-dac/main-pipelines.
diff --git a/docs/deploy_pipeline.rst b/docs/deploy_pipeline.rst
@@ -55,37 +55,37 @@ by running a test command:
 More information on how to setup Docker can be found in the
 `AWS Documentation <https://docs.aws.amazon.com/AmazonECS/latest/developerguide/docker-basics.html>`_.
 
-We now need to install the ``pipeline_utils`` software to deploy the pipeline components.
+We now need to install the ``smaht_pipeline_utils`` software to deploy the pipeline components.
 
-Install pipeline_utils
-======================
+Install smaht_pipeline_utils
+============================
 
 The software is Python-based.
 To install the software and the required packages, we recommend
 using a fresh virtual environment.
-Please refer to `pyproject.toml <https://github.com/dbmi-bgm/portal-pipeline-utils/blob/main/pyproject.toml>`_ for the supported Python version.
+Please refer to `pyproject.toml <https://github.com/smaht-dac/smaht-pipeline-utils/blob/main/pyproject.toml>`_ for the supported Python version.
 
 We recommend using pyenv to manage virtual environments.
 Instructions for installing and using
 pyenv can be found `here <https://realpython.com/intro-to-pyenv/>`_.
 
-Once the virtual environment is set up and activated, we can proceed to :ref:`install <install>` portal-pipeline-utils software.
+Once the virtual environment is set up and activated, we can proceed to :ref:`install <install>` smaht-pipeline-utils software.
 
 .. code-block:: bash
 
   # Install from source
-  git clone https://github.com/dbmi-bgm/portal-pipeline-utils.git
-  cd portal-pipeline-utils
+  git clone https://github.com/smaht-dac/smaht-pipeline-utils.git
+  cd smaht-pipeline-utils
   make configure
   make update
   make build
   cd ..
 
   # Install from pypi
-  pip install portal-pipeline-utils
+  pip install smaht-pipeline-utils
 
-To check that the software is correctly installed, try to run ``pipeline_utils``.
-If installed from source, this command may fail with a bash "command not found" error, try ``poetry run pipeline_utils`` instead.
+To check that the software is correctly installed, try to run ``smaht_pipeline_utils``.
+If installed from source, this command may fail with a bash "command not found" error, try ``poetry run smaht_pipeline_utils`` instead.
 
 Set Up Credentials and Environmental Variables
 ==============================================
@@ -142,7 +142,7 @@ Example of a key-pair entry:
     }
   }
 
-``<namespace>`` is the namespace for the environment and can be found in the portal health page (e.g., cgap-wolf).
+``<namespace>`` is the namespace for the environment and can be found in the portal health page (e.g., smaht-wolf).
 
 .. _account_vars:
 
@@ -154,21 +154,21 @@ Finally we need to setup the information to identify the target environment to u
 .. code-block:: bash
 
   # Set the namespace of the target environment
-  #   e.g., cgap-wolf
+  #   e.g., smaht-wolf
   export ENV_NAME=
 
   # Set the bucket used to store the worklow description files
-  #   e.g., cgap-biotest-main-application-tibanna-cwls
+  #   e.g., smaht-wolf-application-tibanna-cwls
   export WFL_BUCKET=
 
   # Set the path to the keypair file with the portal credential
   export KEYDICTS_JSON=~/.cgap-keys.json
 
-  # Set up project and institution
-  #   Project and institution need to correspond to metadata present on the portal
-  #   e.g., cgap-core and hms-dbmi
-  export PROJECT=
-  export INSTITUTION=
+  # Set up consortia and submission centers
+  #   consortia and submission_centers need to correspond to metadata present on the portal
+  #   e.g., ['smaht'] and ['smaht_dac']
+  export CONSORTIA=
+  export SUBMISSION_CENTERS=
 
   # If running sentieon code,
   #   specify the address for the server that validate the software license
@@ -188,14 +188,14 @@ by the ``--repos`` argument.
 
 .. code-block:: bash
 
-  pipeline_utils pipeline_deploy \
+  smaht_pipeline_utils pipeline_deploy \
     --ff-env ${ENV_NAME} \
     --keydicts-json ${KEYDICTS_JSON} \
     --wfl-bucket ${WFL_BUCKET} \
     --account ${AWS_ACCOUNT_NUMBER} \
     --region ${TIBANNA_AWS_REGION} \
-    --project ${PROJECT} \
-    --institution ${INSTITUTION} \
+    --consortia ${CONSORTIA} \
+    --submission-centers ${SUBMISSION_CENTERS} \
     --sentieon-server ${SENTIEON_LICENSE} \
     --post-software \
     --post-file-format \
@@ -214,18 +214,18 @@ The default is set to the ``main`` branch. The ``--local-build`` flag will preve
 
 *Note: we are working to enable more builders with a command line argument for which builder to use to deploy modules from different repositories through AWS CodeBuild.*
 
-Deploying CGAP Pipelines
+Deploying SMaHT Pipelines
 ========================
 
-CGAP pipelines are released as a complete package with a customized set up for automated deployment to the desired environment.
+SMaHT pipelines are released as a complete package with a customized set up for automated deployment to the desired environment.
 To deploy the pipelines run the following steps:
 
 1. Clone the main pipeline repository.
 The submodules will be empty and set to the current commits saved for the main branch.
 
 .. code-block:: bash
 
-  git clone https://github.com/dbmi-bgm/cgap-pipeline-main.git
+  git clone https://github.com/smaht-dac/main-pipelines.git
 
 2. Check out the desired version.
 This will set the submodules to the commits saved for that pipeline release.
@@ -241,7 +241,7 @@ The submodules will be set in detached state on their current commit.
 
   make pull
 
-4. Build pipeline_utils (optional).
+4. Build smaht_pipeline_utils (optional).
 This will build from source the latest version linked for the current release.
 
 .. code-block:: bash

diff --git a/docs/functions.rst b/docs/functions.rst
@@ -2,49 +2,4 @@
 Functions
 =========
 
-Collection of utilities available as functions:
-
-  - :ref:`check_lines <check_lines>`
-
-.. _check_lines:
-
-check_lines
-+++++++++++
-
-*check_lines* function can be used to check that line counts are matching between the output of two steps where lines should not be dropped (i.e., any steps that modify without filtering), or between an output ``bam`` and the input ``fastq`` files.
-Requires uuid for the *MetaWorkflowRun* object to check and ff_key to access the metadata on the portal. The steps to compare are specified as dictionaries, examples below.
-
-.. code-block:: python
-
-    from pipeline_utils.lib import check_lines
-
-    result <bool> = check_lines.check_lines(metawfr_uuid, ff_key, steps=steps_dict, fastqs=fastqs_dict)
-
-    # metawfr_uuid
-    #   -> uuid for MetaWorkflowRun object
-
-    # ff_key
-    #   -> key to authenticate on the portal
-
-    ## steps_dict example
-    # steps_dict = {
-    #     'workflow_add-readgroups-check': {
-    #                         'dependency': 'workflow_bwa-mem_no_unzip-check',
-    #                         'output': 'bam_w_readgroups',
-    #                         'output_match': 'raw_bam',
-    #                         'key': 'Total Reads',
-    #                         'key_match': 'Total Reads'
-    #                         },
-    #     ...
-    # }
-
-    ## fastqs_dict example
-    # fastqs_dict = {
-    #     'workflow_bwa-mem_no_unzip-check': {
-    #                          'output': 'raw_bam',
-    #                          'input_match': ['fastq_R1', 'fastq_R2'],
-    #                          'key': 'Total Reads',
-    #                          'key_match': 'Total Sequences'
-    #                          },
-    #     ...
-    # }
+In development.
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,10 +1,10 @@
-=========================
-Portal Pipeline Utilities
-=========================
+===============================
+SMaHT Portal Pipeline Utilities
+===============================
 
-Documentation for portal-pipeline-utils_, a collection of utilities for deploying pipelines and interfacing with portal infrastructure.
+Documentation for smaht-pipeline-utils_, a collection of utilities for deploying pipelines and interfacing with SMaHT portal infrastructure.
 
-.. _portal-pipeline-utils: https://github.com/dbmi-bgm/portal-pipeline-utils
+.. _smaht-pipeline-utils: https://github.com/smaht-dac/smaht-pipeline-utils
 
 Contents
 ########

diff --git a/docs/install.rst b/docs/install.rst
@@ -9,11 +9,11 @@ PyPI
 
 The package is available on pypi_:
 
-.. _pypi: https://pypi.org/project/portal-pipeline-utils
+.. _pypi: https://pypi.org/project/smaht-pipeline-utils
 
 .. code-block:: bash
 
-    pip install portal-pipeline-utils
+    pip install smaht-pipeline-utils
 
 Source
 ^^^^^^
@@ -23,10 +23,10 @@ To install the latest version from source:
 
 .. code-block:: bash
 
-    git clone https://github.com/dbmi-bgm/portal-pipeline-utils.git
-    cd portal-pipeline-utils
+    git clone https://github.com/smaht-dac/smaht-pipeline-utils.git
+    cd smaht-pipeline-utils
     make configure
     make update
     make build
 
-Please refer to `pyproject.toml <https://github.com/dbmi-bgm/portal-pipeline-utils/blob/main/pyproject.toml>`_ for the supported Python version.
+Please refer to `pyproject.toml <https://github.com/smaht-dac/smaht-pipeline-utils/blob/main/pyproject.toml>`_ for the supported Python version.
diff --git a/docs/pipeline_utils.rst b/docs/pipeline_utils.rst
@@ -1,6 +1,6 @@
-==============
-pipeline_utils
-==============
+====================
+smaht_pipeline_utils
+====================
 
 This is the entry point for a collection of utilities available as commands:
 
@@ -10,7 +10,7 @@ Usage:
 
 .. code-block:: bash
 
-    pipeline_utils [COMMAND] [ARGS]
+    smaht_pipeline_utils [COMMAND] [ARGS]
 
 .. _pipeline_deploy:
 
@@ -24,7 +24,7 @@ Usage:
 
 .. code-block:: bash
 
-    pipeline_utils pipeline_deploy --ff-env FF_ENV --repos REPO [REPO ...] [OPTIONAL ARGS]
+    smaht_pipeline_utils pipeline_deploy --ff-env FF_ENV --repos REPO [REPO ...] [OPTIONAL ARGS]
 
 **Arguments:**
 
@@ -61,10 +61,10 @@ Usage:
     - AWS account to use for deployment
   * - *-\-region*
     - AWS account region to use for deployment
-  * - *-\-project*
-    - Project to use for deployment [cgap-core]
-  * - *-\-institution*
-    - Institution to use for deployment [hms-dbmi]
+  * - *-\-consortia*
+    - List of consortia to use for deployment [smaht]
+  * - *-\-submission-centers*
+    - List of centers to use for deployment [smaht_dac]
   * - *-\-post-software*
     - DEPLOY | UPDATE Software objects (.yaml or .yml)
   * - *-\-post-file-format*

diff --git a/docs/repo.rst b/docs/repo.rst
@@ -56,4 +56,4 @@ Example ``foo_bar`` pipeline:
     ├── PIPELINE
     └── VERSION
 
-Real examples can be found linked as submodules in our pipelines repository for CGAP project here: https://github.com/dbmi-bgm/cgap-pipeline-main.
+Real examples can be found linked as submodules in our pipelines repository for SMaHT project here: https://github.com/smaht-dac/main-pipelines.