MetaExplainer - Implementation

Conda cheat sheet

Install conda from: https://docs.conda.io/en/latest/miniconda.html

• It is better to make sure that we all use the same conda environment, so the below steps can help do so

• Make sure you have cmake installed on your system before you run the next command

• conda env create -f setup/environment_edited.yml

  replicates the ENV_NAME conda environment

• conda activate ENV_NAME

  activates the environment

• conda env list

  to list all packages installed in that environment. You need to activate the environment before running this command

• conda search PackageName

  searches for PackageName in the environment. You need to activate the environment before running this command

• Run anaconda with zsh: https://stackoverflow.com/questions/31615322/zsh-conda-pip-installs-command-not-found

• To convert a notebook to a Python script, run the below command and replace notebook name in argument: jupyter nbconvert --to script <notebook>

• To use the heals1.0 environment in your jupyter notebook; run the below:
  conda install nb_conda
conda install ipykernel
python -m ipykernel install --user --name heals1.0 You probably wouldn't need the first command if you already have nb_conda installed in the environment where jupyter is running from.

Package install

• To install pyMetamap, follow instructions at: https://github.com/AnthonyMRios/pymetamap

Git cheat sheet

• git clone https://github.com/XXXX

  clones a repo

• If there a task I need to accomplish, it is usually better to create a branch from master, checkout that branch, modify the code on my local machine, and push the branch to github. Then on github request a new pull request. Somoeone else needs to merge the new branch to the master branch. Here are the detailed steps.

  1. git checkout master switches to the master branch

  2. git pull gets the recent updates

  3. git checkout -b BRANCH_NAME creates a new branch

  4. modify the code locally

  5. git add . adds the modification to the stageing area of BRANCH_NAME

  6. git commit -m "nice message" commits the changes to BRANCH_NAME

  7. git push or git push --set-upstream origin BRANCH_NAME pushes the changes to github repo

  8. on github, choose the branch then click on New pull request. Nice tuotrial about pull request.

• git branch -a lists all local branches

• git branch -d BRANCH_NAME deletes a branch locally

• git checkout -- <file> to discard changes in working directory

• update branch based on master

  • git checkout BRANCH_NAME

  • git merge origin/develop

  • git push origin BRANCH_NAME

• git reset FILENAME resets or removes file from git add before commit

• git restore FILENAME restores file and discards local changes in the working directory

UI:

Things to know

• Dependencies and project structure are handled by the package manager for nodejs called yarn

  • To install yarn, run below:
    • conda install -c conda-forge nodejs
      • This will install the latest version of nodejs, and is necessary for the project to build, as the version that comes by default is often very out of date.
      • If it doesn't install the latest version of nodejs - try conda install nodejs -c conda-forge --repodata-fn=repodata.json or `conda upgrade -c conda-forge nodejs'
    • conda install -c conda-forge yarn
      • This will install yarn

• The dependencies are in the package.json as well as the yarn.lock files. You should not have to touch them, as these are for the package manager

How to build UI

• After installing nodejs and yarn, change directory to ui/dash-board

  • to set up project, run README under ui/dashboard directory

Package

• For Metamap support, follow the below steps:
  • Download pymetamap and copy into eaas/eaascode/utils. Follow instructions from: https://github.com/AnthonyMRios/pymetamap
  • Download metamap 2020 version and install locally using these instructions: https://metamap.nlm.nih.gov/Installation.shtml