Merge pull request #102 from nicoalee/BTP-26-add-git-hooks-and-linter

Btp 26 add git hooks and linter

.eslintignore

@@ -0,0 +1,4 @@
+**/node_modules
+.vscode/*
+api/*.js
+api/*.js.map

.eslintrc.json

@@ -0,0 +1,32 @@
+{
+    "parserOptions": {
+        "ecmaVersion": 12,
+        "sourceType": "module",
+        "parser": "@typescript-eslint/parser"
+    },
+    "plugins": ["@typescript-eslint", "prettier"],
+    "extends": [
+        "eslint:recommended",
+        "plugin:@typescript-eslint/eslint-recommended",
+        "plugin:@typescript-eslint/recommended",
+        "prettier"
+    ],
+    "rules": {
+        "no-console": "error",
+        "no-duplicate-imports": "error",
+        "prettier/prettier": "error",
+        "no-self-compare": "error",
+        "no-use-before-define": "error",
+        "consistent-return": "error",
+        "max-depth": ["error", { "max": 4 }],
+        "max-nested-callbacks": ["error", { "max": 4 }],
+        "eqeqeq": "error",
+        "camelcase": "warn",
+        "default-case": "warn",
+        "dot-notation": "warn",
+        "no-delete-var": "warn",
+        "no-empty": "error",
+        "no-empty-function": "error",
+        "no-floating-decimal": "error"
+    }
+}

.gitignore

@@ -12,7 +12,6 @@ yarn-error.log*
 
 # Editor directories and files
 .idea
-.vscode
 *.suo
 *.ntvs*
 *.njsproj

.husky/pre-commit

@@ -0,0 +1,4 @@
+#!/usr/bin/env sh
+. "$(dirname -- "$0")/_/husky.sh"
+
+npm run lint-staged

.lintstagedrc.json

@@ -0,0 +1,3 @@
+{
+    "**/*.{js,json,ts,vue}": ["npm run style-check", "npm run lint-check"]
+}

.prettierignore

@@ -0,0 +1,2 @@
+node_modules
+ui/node_modules

.prettierrc.json

@@ -0,0 +1,10 @@
+{
+    "tabWidth": 4,
+    "singleQuote": true,
+    "trailingComma": "es5",
+    "printWidth": 120,
+    "semi": true,
+    "bracketSpacing": true,
+    "bracketSameLine": false,
+    "arrowParens": "always"
+}

.vscode/extensions.json

@@ -0,0 +1,3 @@
+{
+    "recommendations": ["esbenp.prettier-vscode", "dbaeumer.vscode-eslint", "vue.volar"]
+}

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "eslint.validate": ["javascript", "vue", "typescript"],
+    "editor.defaultFormatter": "dbaeumer.vscode-eslint",
+    "editor.codeActionsOnSave": {
+        "source.fixAll.eslint": true
+    }
+}

README.md

@@ -24,25 +24,26 @@ A video demonstration of how to use ezBIDS can be found [here](https://www.youtu
 
 Users do not need to organize their uploaded data in any specific manner, so long as the data is non-anonymized. The uploaded data can contain any number of sub-folders, and users and may compress (e.g. zip, tar) their upload directory if users so choose. ezBIDS permits two types of data uploads:
 
-1. **DICOM files** - Only DICOMs should be included in the upload. No specific organizational structure is required. 
-2. **dcm2niix generated output (i.e. NIfTI, json, bval, and bvec) files** - Only these files (no DICOMs) should be included in the upload. We strongly recommend that the dcm2niix output not be anonymized (i.e. include *-ba n* in the dcm2niix command), in which case, no specific organizational structure is required.
+1. **DICOM files** - Only DICOMs should be included in the upload. No specific organizational structure is required.
+2. **dcm2niix generated output (i.e. NIfTI, json, bval, and bvec) files** - Only these files (no DICOMs) should be included in the upload. We strongly recommend that the dcm2niix output not be anonymized (i.e. include _-ba n_ in the dcm2niix command), in which case, no specific organizational structure is required.
 
-Should users feel the need to anonymize their data before uploading, we strongly recommend that subjects (and sessions) be organized into subject (and session) folders, with explicit labeling of the subject (and session) IDs (e.g. */MRI_data/sub-01/ses-01/DICOMS*). Failure to do so for non-anonymized data will result in additional work.
+Should users feel the need to anonymize their data before uploading, we strongly recommend that subjects (and sessions) be organized into subject (and session) folders, with explicit labeling of the subject (and session) IDs (e.g. _/MRI_data/sub-01/ses-01/DICOMS_). Failure to do so for non-anonymized data will result in additional work.
 
 ### Backend Workflow
-*(optional reading, if interested in the backend API workflow)*
+
+_(optional reading, if interested in the backend API workflow)_
 
 1. Uploading Data
 
-When a user starts uploading data, ezBIDS will create a new *session* using `(post)/session` API. A session organize each ezBIDS upload/conversion process. For each session, a new DB/session collection is created with the mongo ID as session ID, and create a unique working directory using the sessionID on the backend server where all uploaded data is stored. When all files are successfully uploaded, client makes `(patch)/session/uploaded/:session_id` API call and set the session state to "uploaded" to let the ezBIDS handler knows that the session is ready to being preprocessing.
+When a user starts uploading data, ezBIDS will create a new _session_ using `(post)/session` API. A session organize each ezBIDS upload/conversion process. For each session, a new DB/session collection is created with the mongo ID as session ID, and create a unique working directory using the sessionID on the backend server where all uploaded data is stored. When all files are successfully uploaded, client makes `(patch)/session/uploaded/:session_id` API call and set the session state to "uploaded" to let the ezBIDS handler knows that the session is ready to being preprocessing.
 
 2. Preprocessing Data
 
 The backend server polls for uploaded sessions, and when it finds "uploaded" session, it will launch the preprocessing script. It sets the session state to "preprocessing". It basically unzip all zipped files, run dcm2niix and create a `list` file containing all the nifti and sidecar json. analyzer.py uses this to analyze each nifti files and at the end create `ezBIDS_core.json`. When the preprocessing completes, the session state will be set to "analyzed". The preprocessing step then load ezBIDS_core.json json and copy the content to DB/ezBIDS collection (not session collection) under `original` key.
 
 3. User interact with the session via web UI.
 
-Web UI detects the preprocessing completed by polling for session state, and load the content of ezBIDS_core.json via `(get)/download/:session_id/ezBIDS_core.json` API. User then view / correct the content of ezBIDS_core.json. 
+Web UI detects the preprocessing completed by polling for session state, and load the content of ezBIDS_core.json via `(get)/download/:session_id/ezBIDS_core.json` API. User then view / correct the content of ezBIDS_core.json.
 
 4. (optionally) User request for defacing
 
@@ -51,10 +52,10 @@ The backend stores this information as `deface.json` in the workdir and set the
 
 `deface.sh` create the following files under the workdir.
 
-* deface.finished (list the anatomy files defaced successfully) 
-* deface.failed (list the anatomy files that failed defacing)
+-   deface.finished (list the anatomy files defaced successfully)
+-   deface.failed (list the anatomy files that failed defacing)
 
-UI polls these files to determine which files are successfully defaced (or not). When defacing is completed, the status will be set to "defaced". User can then choose if they want to use the defaced version of anatomy file or not (each object will have a field named `defaceSelection` set to either "original" or "defaced" to indicate which image to use). 
+UI polls these files to determine which files are successfully defaced (or not). When defacing is completed, the status will be set to "defaced". User can then choose if they want to use the defaced version of anatomy file or not (each object will have a field named `defaceSelection` set to either "original" or "defaced" to indicate which image to use).
 
 5. Finalize
 
@@ -78,11 +79,13 @@ The API then store this information as `finalized.json` in workdir, and copy the
 Once session status becomes "finished", user will be then allowed to download the final "bids" directory via the download API, or send to other cloud resources
 
 ### Authors
-- [Soichi Hayashi]([email protected])
-- [Daniel Levitas]([email protected])
-- [Franco Pestilli]([email protected])
+
+-   [Soichi Hayashi]([email protected])
+-   [Daniel Levitas]([email protected])
+-   [Franco Pestilli]([email protected])
 
 ### Funding Acknowledgement
+
 brainlife.io is publicly funded and for the sustainability of the project it is helpful to Acknowledge the use of the platform. We kindly ask that you acknowledge the funding below in your code and publications. Copy and past the following lines into your repository when using this code.
 
 [![NSF-BCS-1734853](https://img.shields.io/badge/NSF_BCS-1734853-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1734853)
@@ -93,6 +96,7 @@ brainlife.io is publicly funded and for the sustainability of the project it is
 [![NIH-NIMH-R01MH126699]](https://img.shields.io/badge/NIH_NIMH-R01MH126699-green.svg)](https://grantome.com/grant/NIH/R01-EB029272)
 
 ### Citations
+
 We ask that you the following articles when publishing papers that used data, code or other resources created by the brainlife.io community.
 
 1. Levias, D. et al. **In review**
@@ -107,7 +111,30 @@ npm init vite@latest ui2 -- --template vue-ts
 
 A local development instance of ezBIDS can be launched by first git cloning this repo, then running `./dev.sh` on a docker enabled machine. When everything is built/running, you should be able to reach the dev instance at http://localhost:3000/
 
+Copyright © 2022 brainlife.io at University of Texas at Austin
 
+### Code Styling/Formatting Guide
 
-Copyright © 2022 brainlife.io at University of Texas at Austin
+This repo has a few guardrails in it to ensure that only clean, standardized, and uniform code is committed into the ezBIDS repository. It is suggested that VSCode is used when contributing to ezBIDS to make use of the Prettier VSCode extension for convenience.
+
+There are a few safeguards active:
+
+1. We use husky to run a git precommit hook and lint staged files using esLint
+2. We use husky to run a git precommit hook and run a prettier style check on staged files
+3. A `.vscode/settings.json` file is attached to this repository, which configures VSCode to allow formatting of files on save and on paste.
+
+Make sure that you run npm install to install husky if you have not already.
+
+> You can run `npm run lint-staged` at any time in order to run a style check on the staged files.
+> `lint-staged` makes a call to prettier and eslint to check if there are any files that do not adhere to the code standard.
+> It does NOT overwrite any files.
+
+> NOTE: If you want to skip the hook for whatever reason, you can run `git commit --no-verify ...` 
+
+VS Code Recommendations:
+
+1. Install the Prettier VS Code extension `esbenp.prettier-vscode`. This will allow you to format files based on prettier rules.
+2. Install the eslint VS Code extension `dbaeumer.vscode-eslint`. This will allow you to see lint errors as you're writing code.
+3. Install the Volar extension `vue.volar`. This provides Vue language features.
 
+> Note: The recommended extensions to install for this project should appear as a notification in the bottom right corner of the VSCode screen the very first time you open the project. You can also open the command palette and go to "Show Recommended Extensions." Alternatively, you can directly navigate to `.vscode/extensions.json` and install the listed extensions.