diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c700f7d9c9c19e87e26a3451d3fca79a0d99b253..e9c16a1be251d942476c04b279d78e20dfbb4c64 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,7 +1,3 @@
-stages:
- - build
- - test
- - deploy
test-python:
@@ -15,7 +11,6 @@ test-python:
- apt-get update && apt install -y libblas-dev liblapack-dev python3-dev
- pip install -r requirements.txt
- python -m unittest
-# - python setup.py test
parallel:
matrix:
- PYTHON_VERSION: [
@@ -26,47 +21,6 @@ test-python:
]
-test-docker-compose:
- image: docker:24
- needs: []
- # when: delayed
- # start_in: 3 minutes
- stage: test
- retry:
- max: 2
- when: runner_system_failure
- script:
- - apk update && apk upgrade && apk add jq bash curl
- - docker compose version
- - ./test_docker_compose.sh
- after_script:
- - docker compose logs back > log/docker-compose.back.log
- - docker compose logs > log/docker-compose.log
- artifacts:
- when: always
- paths:
- - log
- expire_in: 1 week
-
-
-#test-backend-image:
-# image: docker:24
-# needs:
-# - build-backend
-# stage: test
-# script:
-# - mkdir .eggs jass.egg-info && chmod -R 777 .eggs jass.egg-info
-# - touch data/initTable.hdf5
-# - >
-# docker run
-# -v $(pwd)/data:/data
-# -v $(pwd)/projects:/projects
-# -v $(pwd)/.eggs:/code/.eggs
-# -v $(pwd)/jass.egg-info:/code/jass.egg-info
-# "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG/backend:$CI_COMMIT_SHA"
-# python setup.py test
-
-
pages:
needs: []
image: python:3.9
@@ -82,319 +36,3 @@ pages:
- public
only:
- master
-
-
-.build:
- stage: build
- image: docker:24
- retry:
- max: 2
- when: runner_system_failure
- script:
- - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
- # pull the latest build on master
- - docker pull "$CI_REGISTRY_IMAGE/master/${PATH_TAG}:latest" || true
- # pull the latest build on this branch
- - docker pull "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG/${PATH_TAG}:latest" || true
- # build the image while passing commit SHA and tagging the image with it
- - docker build
- --target ${PATH_TAG}
- --build-arg CI_COMMIT_REF_SLUG
- --build-arg CI_COMMIT_SHA
- --build-arg API_URL
- --cache-from "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG/${PATH_TAG}:latest"
- --cache-from "$CI_REGISTRY_IMAGE/master/${PATH_TAG}:latest"
- --tag "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG/${PATH_TAG}:$CI_COMMIT_SHA"
- --tag "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG/${PATH_TAG}:latest"
- .
- # push image as latest for the current branch
- - docker push "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG/${PATH_TAG}:latest"
- # push image tagged with its sha
- - docker push "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG/${PATH_TAG}:$CI_COMMIT_SHA"
-
-
-build-backend:
- needs: []
- extends: .build
- variables:
- PATH_TAG: backend
- after_script:
- - mkdir .eggs jass.egg-info && chmod -R 777 .eggs jass.egg-info
- - touch data/initTable.hdf5
- - >
- docker run
- -v $(pwd)/data:/data
- -v $(pwd)/projects:/projects
- -v $(pwd)/.eggs:/code/.eggs
- -v $(pwd)/jass.egg-info:/code/jass.egg-info
- "$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG/${PATH_TAG}:$CI_COMMIT_SHA"
- python -m unittest
-
-
-build-client-dev:
- except:
- - master
- needs: []
- extends: .build
- before_script:
- - cd client
- variables:
- PATH_TAG: client-static-serve
- API_URL: "https://jass-${CI_COMMIT_REF_SLUG}.dev.pasteur.cloud/api"
-
-
-build-client-prod:
- only:
- - master
- needs: []
- extends: .build
- before_script:
- - cd client
- variables:
- PATH_TAG: client-static-serve
- API_URL: "https://jass.pasteur.fr/api"
-
-
-
-.deploy:
- stage: deploy
- needs:
- - build-backend
- - build-client-dev
- - test-python
-# - test-backend-image
- image: harbor.pasteur.fr/kube-system/helm-kubectl:3.4.0
- retry:
- max: 2
- when: runner_system_failure
- script:
- # create if missing the shared pvc to save data
- - kubectl apply -n $NAMESPACE -f chart/pvc-shared-data.yaml
- - helm dependency update chart
- # shows some error on first deployment
- - kubectl get secret --namespace "${NAMESPACE}" ${CI_COMMIT_REF_SLUG}-rabbitmq || NO_SECRET=$?
- - >
- if [ $NO_SECRET ]; then
- RABBITMQ_PASSWORD=''
- RABBITMQ_ERLANG_COOKIE=''
- else
- RABBITMQ_PASSWORD=$(kubectl get secret --namespace "${NAMESPACE}" ${CI_COMMIT_REF_SLUG}-rabbitmq -o jsonpath="{.data.rabbitmq-password}" | base64 -d)
- RABBITMQ_ERLANG_COOKIE=$(kubectl get secret --namespace "${NAMESPACE}" ${CI_COMMIT_REF_SLUG}-rabbitmq -o jsonpath="{.data.rabbitmq-erlang-cookie}" | base64 -d)
- fi
- - >
- helm upgrade --install --namespace=${NAMESPACE}
- --set CI_REGISTRY_IMAGE=${CI_REGISTRY_IMAGE}
- --set image.tag=${CI_COMMIT_SHA}
- --set ingress.host.name=${PUBLIC_URL}
- --set registry.username=${DEPLOY_USER}
- --set registry.password=${DEPLOY_TOKEN}
- --set registry.host=${CI_REGISTRY}
- --set imagePullSecrets[0].name="registry-pull-secret-${CI_COMMIT_REF_SLUG}"
- --set rabbitmq.auth.password=$RABBITMQ_PASSWORD
- --set rabbitmq.auth.erlangCookie=$RABBITMQ_ERLANG_COOKIE
- --values ./chart/values.${NAMESPACE}.yaml
- ${CI_COMMIT_REF_SLUG} ./chart/
-
-
-deploy-dev:
- except:
- - master
- stage: deploy
- extends: .deploy
- variables:
- NAMESPACE: "jass-dev"
- PUBLIC_URL: "jass-${CI_COMMIT_REF_SLUG}.dev.pasteur.cloud"
- environment:
- name: "k8sdev-01/jass-dev/${CI_COMMIT_REF_SLUG}"
- url: "https://jass-${CI_COMMIT_REF_SLUG}.dev.pasteur.cloud"
- on_stop: delete-dev-deployment
-
-
-deploy-prod:
- only:
- - master
- stage: deploy
- needs:
- - build-backend
- - build-client-prod
- - test-python
- extends: .deploy
- variables:
- NAMESPACE: "jass-prod"
- PUBLIC_URL: "jass.pasteur.fr"
- environment:
- name: "k8sprod-02/jass-prod/${CI_COMMIT_REF_SLUG}"
- url: "https://jass.pasteur.fr"
-
-
-delete-dev-deployment:
- stage: deploy
- needs: []
- when: manual
- image: harbor.pasteur.fr/kube-system/helm-kubectl:3.4.0
- variables:
- GIT_STRATEGY: none # important to not checkout source when branch is deleted
- NAMESPACE: "jass-dev"
- environment:
- name: "k8sdev-01/jass-dev/${CI_COMMIT_REF_SLUG}"
- action: stop
- retry:
- max: 2
- when: runner_system_failure
- script:
- - echo "Removing $CI_COMMIT_REF_SLUG"
- - helm delete -n ${NAMESPACE} ${CI_COMMIT_REF_SLUG}
- - kubectl delete pvc -lapp.kubernetes.io/name=rabbitmq,app.kubernetes.io/instance=${CI_COMMIT_REF_SLUG}
-
-
-.upload-from-fex-to-somewhere:
- stage: deploy
- needs: []
- when: manual
- image: harbor.pasteur.fr/kube-system/helm-kubectl:3.14.0
- variables:
- FEX_URL: ""
- script:
- - mkdir -p removed added
- - >
- if [[ "$FEX_URL" =~ ^https://dl\.pasteur\.fr/.* ]]; then
- echo "Valid URL: $FEX_URL";
- else
- echo "FEX_URL invalide (FEX_URL=$FEX_URL), please provide a fex url starting with https://dl.pasteur.fr/...";
- exit 1;
- fi
- - wget $FEX_URL
- - ls -lah .
- - export HDF5_FILENAME=$(ls -1 *hdf5 | cut -d'/' -f2)
- - >
- if [ ! $HDF5_FILENAME ]; then
- echo "No hdf5 file fetched, exiting";
- exit 2;
- else
- echo "Valid File: $HDF5_FILENAME";
- fi
- - kubectl apply -f chart/sidekick.yaml -f chart/pvc-shared-data.yaml
- - kubectl wait -f chart/sidekick.yaml --for=condition=Ready --timeout=3600s
- - kubectl cp sidekick:/data/$HDF5_FILENAME ./removed/$HDF5_FILENAME || echo "no older version"
- - kubectl cp ./$HDF5_FILENAME sidekick:/data/$HDF5_FILENAME
- - mv ./$HDF5_FILENAME ./added/
- - kubectl exec sidekick -- ls -lah /data
- - kubectl delete -f chart/sidekick.yaml --force
- artifacts:
- when: always
- paths:
- - added
- - removed
- expire_in: 1 month
-
-
-upload-from-fex-to-dev:
- extends: .upload-from-fex-to-somewhere
- environment:
- name: "k8sdev-01/jass-dev/${CI_COMMIT_REF_SLUG}"
-
-
-upload-from-fex-to-prod:
- extends: .upload-from-fex-to-somewhere
- only:
- - master
- environment:
- name: "k8sprod-02/jass-prod/${CI_COMMIT_REF_SLUG}"
-
-
-.delete-data-from-somewhere:
- stage: deploy
- needs: []
- when: manual
- image: harbor.pasteur.fr/kube-system/helm-kubectl:3.14.0
- variables:
- HDF5_FILENAME: ""
- script:
- - kubectl apply -f chart/sidekick.yaml -f chart/pvc-shared-data.yaml
- - kubectl wait -f chart/sidekick.yaml --for=condition=Ready --timeout=3600s
- - kubectl exec sidekick -- ls -lah /data
- - >
- if [ ! $HDF5_FILENAME ]; then
- echo "No hdf5 file provided, exiting";
- exit 0;
- else
- echo "File to remove: $HDF5_FILENAME";
- fi
- - mkdir removed
- - >
- if [[ "$HDF5_FILENAME" =~ ^[^/]+\.hdf5$ ]]; then
- echo "Valid filename: $HDF5_FILENAME";
- else
- echo "HDF5_FILENAME invalide (HDF5_FILENAME=$HDF5_FILENAME), please provide an hdf5 file in /data";
- fi
- - kubectl cp sidekick:/data/$HDF5_FILENAME ./removed/$HDF5_FILENAME
- - kubectl exec sidekick -- rm -f /data/$HDF5_FILENAME
- - kubectl delete -f chart/sidekick.yaml --force
- artifacts:
- when: always
- paths:
- - removed
- expire_in: 1 month
-
-
-delete-data-from-dev:
- extends: .delete-data-from-somewhere
- environment:
- name: "k8sdev-01/jass-dev/${CI_COMMIT_REF_SLUG}"
-
-
-delete-data-from-prod:
- extends: .delete-data-from-somewhere
- only:
- - master
- environment:
- name: "k8sprod-02/jass-prod/${CI_COMMIT_REF_SLUG}"
-
-
-.log-fetcher:
- stage: deploy
- needs: []
- when: manual
- image: harbor.pasteur.fr/kube-system/helm-kubectl:3.12.0
- variables:
- GIT_STRATEGY: none # don't need to checkout sources
- LAST_ROWS_COUNT: "400" # you can override it when triggering the job
- CHART_LOCATION: "chart"
- script:
- - kubectl -n ${NAMESPACE} get quota
- - mkdir logs
- - |
- for POD in $(kubectl -n ${NAMESPACE} get po -l="app.kubernetes.io/instance=${CI_COMMIT_REF_SLUG}" --output=jsonpath='{.items[*].metadata.name}'); do
- echo "************************************************************"
- echo "************************************************************"
- echo "* ${POD}";
- echo "************************************************************"
- kubectl -n ${NAMESPACE} logs $POD --tail ${LAST_ROWS_COUNT} > logs/${POD}.log
- cat logs/${POD}.log
- done
- - echo "Check Job artifacts to download or browse log files. See "Job artifacts">"Browse" on right panel"
- artifacts:
- when: always
- paths:
- - logs
- expire_in: 1 month
-
-
-log-fetcher-in-dev:
- except:
- - master
- extends: .log-fetcher
- variables:
- NAMESPACE: "jass-dev"
- environment:
- name: "k8sdev-01/${NAMESPACE}/${CI_COMMIT_REF_SLUG}"
-
-
-log-fetcher-in-prod:
- only:
- - master
- extends: .log-fetcher
- variables:
- NAMESPACE: "jass-prod"
- environment:
- name: "k8sprod-02/${NAMESPACE}/${CI_COMMIT_REF_SLUG}"
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index b00f3d65e8dddefb9ded18e07ec4b8c9eebd3dcc..0000000000000000000000000000000000000000
--- a/Dockerfile
+++ /dev/null
@@ -1,37 +0,0 @@
-FROM python:3.10-bullseye as backend
-
-ENV JASS_DATA_DIR '/data'
-ENV JASS_PROJECTS_DIR '/projects'
-
-EXPOSE 8080
-
-CMD ["uvicorn", "jass.server:app", "--host", "0.0.0.0", "--port", "8080"]
-
-RUN addgroup --gid 1000 kiwi \
- && adduser --disabled-password --gecos '' --uid 1000 --gid 1000 kiwi \
- && apt-get update \
- && apt-get install -y \
- nano \
- wget \
- rsync \
- && rm -rf /var/lib/apt/lists/* \
- && pip install --upgrade pip setuptools \
- && mkdir /code \
- && mkdir ${JASS_DATA_DIR} \
- && chown kiwi:kiwi ${JASS_DATA_DIR} \
- && mkdir ${JASS_PROJECTS_DIR} \
- && chown kiwi:kiwi ${JASS_PROJECTS_DIR}
-WORKDIR /code
-
-COPY requirements*.txt /code/
-RUN pip install -r requirements.txt \
- && pip3 install -U watchdog[watchmedo]
-
-COPY ./*-entrypoint.sh /
-RUN chmod a+x /*-entrypoint.sh
-ENTRYPOINT ["/docker-entrypoint.sh"]
-
-COPY . /code/
-RUN pip install -e .
-
-USER kiwi
diff --git a/client/.dockerignore b/client/.dockerignore
deleted file mode 100644
index de70a21c18deb656ffc5d46bafa23326da93a06e..0000000000000000000000000000000000000000
--- a/client/.dockerignore
+++ /dev/null
@@ -1,6 +0,0 @@
-node_modules/
-dist/
-.nuxt/
-.dockerignore
-Dockerfile
-yarn-error.log
diff --git a/client/.editorconfig b/client/.editorconfig
deleted file mode 100644
index 5d126348471c348decba17143ce128130c9f4104..0000000000000000000000000000000000000000
--- a/client/.editorconfig
+++ /dev/null
@@ -1,13 +0,0 @@
-# editorconfig.org
-root = true
-
-[*]
-indent_style = space
-indent_size = 2
-end_of_line = lf
-charset = utf-8
-trim_trailing_whitespace = true
-insert_final_newline = true
-
-[*.md]
-trim_trailing_whitespace = false
diff --git a/client/.env b/client/.env
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/client/.eslintrc.js b/client/.eslintrc.js
deleted file mode 100644
index 137da5039e9fb64eaaabb3b600368a3566c79d7f..0000000000000000000000000000000000000000
--- a/client/.eslintrc.js
+++ /dev/null
@@ -1,24 +0,0 @@
-module.exports = {
- root: true,
- env: {
- browser: true,
- node: true
- },
- parserOptions: {
- parser: '@babel/eslint-parser',
- requireConfigFile: false
- },
- extends: [
- '@nuxtjs',
- 'plugin:nuxt/recommended',
- 'prettier'
- ],
- plugins: [
- ],
- // add your custom rules here
- rules: {
- "no-unused-vars": "off",
- 'no-console': 'off',
- 'vue/valid-v-slot': 'off'
- }
-}
diff --git a/client/.gitignore b/client/.gitignore
deleted file mode 100644
index a28235008d0117da4a3de4486f4c012c1f680f6d..0000000000000000000000000000000000000000
--- a/client/.gitignore
+++ /dev/null
@@ -1,90 +0,0 @@
-# Created by .ignore support plugin (hsz.mobi)
-### Node template
-# Logs
-/logs
-*.log
-npm-debug.log*
-yarn-debug.log*
-yarn-error.log*
-
-# Runtime data
-pids
-*.pid
-*.seed
-*.pid.lock
-
-# Directory for instrumented libs generated by jscoverage/JSCover
-lib-cov
-
-# Coverage directory used by tools like istanbul
-coverage
-
-# nyc test coverage
-.nyc_output
-
-# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
-.grunt
-
-# Bower dependency directory (https://bower.io/)
-bower_components
-
-# node-waf configuration
-.lock-wscript
-
-# Compiled binary addons (https://nodejs.org/api/addons.html)
-build/Release
-
-# Dependency directories
-node_modules/
-jspm_packages/
-
-# TypeScript v1 declaration files
-typings/
-
-# Optional npm cache directory
-.npm
-
-# Optional eslint cache
-.eslintcache
-
-# Optional REPL history
-.node_repl_history
-
-# Output of 'npm pack'
-*.tgz
-
-# Yarn Integrity file
-.yarn-integrity
-
-# dotenv environment variables file
-#.env we need this for docker-compose
-
-# parcel-bundler cache (https://parceljs.org/)
-.cache
-
-# next.js build output
-.next
-
-# nuxt.js build output
-.nuxt
-
-# Nuxt generate
-dist
-
-# vuepress build output
-.vuepress/dist
-
-# Serverless directories
-.serverless
-
-# IDE / Editor
-.idea
-
-# Service worker
-sw.*
-
-# macOS
-.DS_Store
-
-# Vim swap files
-*.swp
diff --git a/client/.husky/.gitignore b/client/.husky/.gitignore
deleted file mode 100644
index 31354ec1389994b5f6708c7d915fdcc6bb76ba6e..0000000000000000000000000000000000000000
--- a/client/.husky/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-_
diff --git a/client/.husky/common.sh b/client/.husky/common.sh
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/client/.husky/pre-commit b/client/.husky/pre-commit
deleted file mode 100755
index eb6e8c1c015b2d5424071a25745ae31c7f993f9a..0000000000000000000000000000000000000000
--- a/client/.husky/pre-commit
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-. "$(dirname "$0")/_/husky.sh"
-. "$(dirname "$0")/common.sh"
-
-yarn lint-staged
diff --git a/client/.prettierrc b/client/.prettierrc
deleted file mode 100644
index b2095be81e4e40b736dfc9b3559d0250e4becd02..0000000000000000000000000000000000000000
--- a/client/.prettierrc
+++ /dev/null
@@ -1,4 +0,0 @@
-{
- "semi": false,
- "singleQuote": true
-}
diff --git a/client/Dockerfile b/client/Dockerfile
deleted file mode 100644
index 2e20df2d3b3cd15d0fe492b46764c3dd17b7c5ca..0000000000000000000000000000000000000000
--- a/client/Dockerfile
+++ /dev/null
@@ -1,35 +0,0 @@
-#################################################
-# container shipping client source and dependencies
-#################################################
-FROM node:16.20-alpine3.18 as client-base-container
-
-ARG API_URL
-
-RUN mkdir /client \
- && cd /client
-
-WORKDIR /client
-
-COPY package.json /client/
-COPY yarn.lock /client/
-
-RUN yarn install
-
-COPY . /client
-
-#################################################
-# container that will generate the client
-#################################################
-FROM client-base-container as client-static-build
-
-ARG API_URL
-
-RUN yarn run generate
-
-#################################################
-# container that will serve the client
-#################################################
-FROM nginxinc/nginx-unprivileged:stable-alpine as client-static-serve
-
-COPY --from=client-static-build /client/dist /usr/share/nginx/html
-COPY --from=client-static-build /client/nginx.conf /etc/nginx/conf.d/default.conf
diff --git a/client/README.md b/client/README.md
deleted file mode 100644
index 26f3720082164c9a6109234723d595764a54ae87..0000000000000000000000000000000000000000
--- a/client/README.md
+++ /dev/null
@@ -1,73 +0,0 @@
-# my-nuxt-app
-
-## Build Setup
-
-```bash
-# install dependencies
-$ yarn install
-
-# serve with hot reload at localhost:3000
-$ yarn dev
-
-# serve client and connect to a remote backend instance
-$ API_URL='https://jass-BRANCH.dev.pasteur.cloud/api' yarn dev
-
-
-# build for production and launch server
-$ yarn build
-$ yarn start
-
-# generate static project
-$ yarn generate
-```
-
-For detailed explanation on how things work, check out the [documentation](https://nuxtjs.org).
-
-## Special Directories
-
-You can create the following extra directories, some of which have special behaviors. Only `pages` is required; you can delete them if you don't want to use their functionality.
-
-### `assets`
-
-The assets directory contains your uncompiled assets such as Stylus or Sass files, images, or fonts.
-
-More information about the usage of this directory in [the documentation](https://nuxtjs.org/docs/2.x/directory-structure/assets).
-
-### `components`
-
-The components directory contains your Vue.js components. Components make up the different parts of your page and can be reused and imported into your pages, layouts and even other components.
-
-More information about the usage of this directory in [the documentation](https://nuxtjs.org/docs/2.x/directory-structure/components).
-
-### `layouts`
-
-Layouts are a great help when you want to change the look and feel of your Nuxt app, whether you want to include a sidebar or have distinct layouts for mobile and desktop.
-
-More information about the usage of this directory in [the documentation](https://nuxtjs.org/docs/2.x/directory-structure/layouts).
-
-
-### `pages`
-
-This directory contains your application views and routes. Nuxt will read all the `*.vue` files inside this directory and setup Vue Router automatically.
-
-More information about the usage of this directory in [the documentation](https://nuxtjs.org/docs/2.x/get-started/routing).
-
-### `plugins`
-
-The plugins directory contains JavaScript plugins that you want to run before instantiating the root Vue.js Application. This is the place to add Vue plugins and to inject functions or constants. Every time you need to use `Vue.use()`, you should create a file in `plugins/` and add its path to plugins in `nuxt.config.js`.
-
-More information about the usage of this directory in [the documentation](https://nuxtjs.org/docs/2.x/directory-structure/plugins).
-
-### `static`
-
-This directory contains your static files. Each file inside this directory is mapped to `/`.
-
-Example: `/static/robots.txt` is mapped as `/robots.txt`.
-
-More information about the usage of this directory in [the documentation](https://nuxtjs.org/docs/2.x/directory-structure/static).
-
-### `store`
-
-This directory contains your Vuex store files. Creating a file in this directory automatically activates Vuex.
-
-More information about the usage of this directory in [the documentation](https://nuxtjs.org/docs/2.x/directory-structure/store).
diff --git a/client/assets/css/global.css b/client/assets/css/global.css
deleted file mode 100644
index a039ea84e835b06176f7a87676f9f2cb60b29fa0..0000000000000000000000000000000000000000
--- a/client/assets/css/global.css
+++ /dev/null
@@ -1,239 +0,0 @@
-/* FONT CALLS */
-
-@font-face {
- font-family: 'BrandonGrotesqueReg';
- src: local('BrandonGrotesqueReg'),
- url(~assets/fonts/brandon_reg-webfont.ttf) format('truetype');
- font-weight: normal;
- font-style: normal;
-}
-
-@font-face {
- font-family: 'BrandonGrotesqueBld';
- src: local('BrandonGrotesqueBld'),
- url(~assets/fonts/brandon_bld-webfont-webfont.ttf) format('truetype');
- font-weight: normal;
- font-style: normal;
-}
-
-@font-face {
- font-family: 'BrandonGrotesqueBlk';
- src: local('BrandonGrotesqueBlk'),
- url(~assets/fonts/brandon_blk-webfont.ttf) format('truetype');
- font-weight: normal;
- font-style: normal;
-}
-
-@font-face {
- font-family: 'PlayfairDisplayBld';
- src:
- local('PlayfairDisplayBld'),
- url(~assets/fonts/playfairdisplay-bold-webfont.ttf) format('truetype');
- font-weight: normal;
- font-style: normal;
-}
-
-@font-face {
- font-family: 'PlayfairDisplayReg';
- src: local('PlayfairDisplayReg'),
- url(~assets/fonts/playfairdisplay-regular-webfont.ttf) format('truetype');
- font-weight: normal;
- font-style: normal;
-}
-
-/* FONT DETAILS */
-
-* {
- font-family: 'BrandonGrotesqueReg', sans-serif;
- font-size: 18px;
-}
-
-h1 {
- font-family: 'PlayfairDisplayReg', sans-serif;
- text-transform: capitalize;
- font-size: 30px;
-}
-
-h2 {
- font-family: 'PlayfairDisplayBld', sans-serif;
- font-size: 24px;
-}
-
-h3 {
- text-align: center;
- font-size: 28px;
-}
-
-h4 {
- font-size: 22px;
-}
-
-/* WEBSITE HEADER */
-
-.logo {
- font-family: 'PlayfairDisplayReg', sans-serif;
- font-size: 50px;
-}
-
-.logo a {
- color: black;
- text-decoration: none;
-}
-
-.logo a:hover {
- color: black;
- text-decoration: none;
-}
-
-/* MAIN PAGE */
-.main_title {
- font-family: 'PlayfairDisplayReg', sans-serif;
- font-size: 50px;
- text-transform: capitalize;
- text-align: center;
- padding: 20px;
-}
-
-.main-intro {
- text-align: justify;
- font-family: 'BrandonGrotesqueReg', sans-serif;
- font-size: 18px;
- line-height: 1.5;
-}
-
-.card-title {
- font-family: 'PlayfairDisplayReg', sans-serif;
- font-size: 25px;
-}
-
-button,
-input,
-select,
-textarea {
- font-size: 100%;
- margin: 0;
- max-width: 100%;
- vertical-align: baseline;
-}
-
-button,
-input {
- line-height: normal;
-}
-
-button[disabled],
-input[disabled] {
- cursor: default;
-}
-
-a.button {
- font-family: 'Montserrat', sans-serif;
- color: #eee;
- text-transform: uppercase;
- font-size: 13px;
- border: 1px solid #eee;
- border-radius: 15px;
- display: inline-block;
- padding: 2px 15px;
- -webkit-transition: all .4s ease;
- -moz-transition: all .4s ease;
- -ms-transition: all .4s ease;
- -o-transition: all .4s ease;
- transition: all .4s ease;
-}
-
-a.button:hover {
- color: #30343e;
- background: #eee;
- -webkit-transition: all .4s ease;
- -moz-transition: all .4s ease;
- -ms-transition: all .4s ease;
- -o-transition: all .4s ease;
- transition: all .4s ease;
-}
-
-a.button.blue {
- color: #35a9f5;
- border-color: #35a9f5;
-}
-
-a.button.blue.active {
- background: #35a9f5;
- color: #eee;
-}
-
-a.button.blue:hover {
- color: #30343e;
- border-color: #30343e;
-}
-
-/* Buttons */
-button,
-input[type="submit"],
-input[type="button"],
-input[type="reset"] {
- background: #fff;
- cursor: pointer;
- display: inline-block;
- font-size: 15px;
- padding: 6px 20px;
- margin: 5px 5px 5px 0;
- color: rgba(59, 127, 224, 1);
- border: 1px solid rgba(59, 127, 224, 1);
- border-radius: 30px;
- -webkit-appearance: button;
- -webkit-transition: all 400ms ease;
- -moz-transition: all 400ms ease;
- -o-transition: all 400ms ease;
- transition: all 400ms ease;
-}
-
-button::-moz-focus-inner,
-input::-moz-focus-inner {
- border: 0;
- padding: 0;
-}
-
-button:hover,
-button:focus,
-input[type="submit"]:hover,
-input[type="button"]:hover,
-input[type="reset"]:hover,
-input[type="submit"]:focus,
-input[type="button"]:focus,
-input[type="reset"]:focus {
- opacity: 1;
- color: #FFF;
- background: rgba(59, 127, 224, 1);
- -webkit-transition: all 400ms ease;
- -moz-transition: all 400ms ease;
- -o-transition: all 400ms ease;
- transition: all 400ms ease;
- outline: none;
-}
-
-button:active,
-input[type="submit"]:active,
-input[type="button"]:active,
-input[type="reset"]:active {
- opacity: 1;
- color: #FFF;
- background: rgba(59, 127, 224, 1);
- -webkit-transition: all 400ms ease;
- -moz-transition: all 400ms ease;
- -o-transition: all 400ms ease;
- transition: all 400ms ease;
-}
-
-.v-tab--active {
- font-family: 'BrandonGrotesqueBlk', sans-serif;
-}
-
-.footer-column {
- border-left: 1px solid #2d96fa;
- padding-left: 30px;
-}
-
-.footer-text {
- font-size: 12px;
-}
diff --git a/client/assets/fonts/brandon_bld-webfont-webfont.ttf b/client/assets/fonts/brandon_bld-webfont-webfont.ttf
deleted file mode 100755
index 351267a2ac6a3878934b201e986a2ab4c39509ef..0000000000000000000000000000000000000000
Binary files a/client/assets/fonts/brandon_bld-webfont-webfont.ttf and /dev/null differ
diff --git a/client/assets/fonts/brandon_blk-webfont.ttf b/client/assets/fonts/brandon_blk-webfont.ttf
deleted file mode 100755
index b00888e1bc84b3cb319370407ade6e9287194772..0000000000000000000000000000000000000000
Binary files a/client/assets/fonts/brandon_blk-webfont.ttf and /dev/null differ
diff --git a/client/assets/fonts/brandon_reg-webfont.ttf b/client/assets/fonts/brandon_reg-webfont.ttf
deleted file mode 100755
index b3cf32c00568382854f0ad9d87ac2e0eab586411..0000000000000000000000000000000000000000
Binary files a/client/assets/fonts/brandon_reg-webfont.ttf and /dev/null differ
diff --git a/client/assets/fonts/playfairdisplay-bold-webfont.ttf b/client/assets/fonts/playfairdisplay-bold-webfont.ttf
deleted file mode 100755
index 317673b9d266478a00f9a387f27d010cc1dfea61..0000000000000000000000000000000000000000
Binary files a/client/assets/fonts/playfairdisplay-bold-webfont.ttf and /dev/null differ
diff --git a/client/assets/fonts/playfairdisplay-regular-webfont.ttf b/client/assets/fonts/playfairdisplay-regular-webfont.ttf
deleted file mode 100755
index de22c163f4ca5d6d41291ef9dd96e2af732446ca..0000000000000000000000000000000000000000
Binary files a/client/assets/fonts/playfairdisplay-regular-webfont.ttf and /dev/null differ
diff --git a/client/assets/variables.scss b/client/assets/variables.scss
deleted file mode 100644
index 2d8fdba7151a5b463e91c98107eda4798d4a6e78..0000000000000000000000000000000000000000
--- a/client/assets/variables.scss
+++ /dev/null
@@ -1,9 +0,0 @@
-// Ref: https://github.com/nuxt-community/vuetify-module#customvariables
-//
-// The variables you want to modify
-// $font-size-root: 20px;
-
-@import '~/assets/css/global.css';
-
-$body-font-family: 'BrandonGrotesqueReg';
-$tabs-item-max-width: 180px;
diff --git a/client/components/AnalysisCard.vue b/client/components/AnalysisCard.vue
deleted file mode 100644
index b685d02f7ce1060bbaa48562c141d0a94ca0ffff..0000000000000000000000000000000000000000
--- a/client/components/AnalysisCard.vue
+++ /dev/null
@@ -1,88 +0,0 @@
-<template>
- <v-card :elevation=0 :class="myClass">
- <v-col
- cols="12"
- sm="8"
- offset-sm="2"
- lg="6"
- offset-lg="3">
- <v-card-title class="card-title">
- {{ title }}
- </v-card-title>
- <v-row>
- <v-col
- cols="12"
- sm="5"
- md="4">
- <v-img
- class="mx-auto"
- height="200"
- width="200"
- :src='myImg'>
- </v-img>
- </v-col>
- <v-col
- cols="12"
- sm="7"
- md="8">
- <v-card-text class="card-text">
- {{ description }}
- </v-card-text>
- </v-col>
- <v-col
- cols="12"
- md="8"
- offset-md="2">
- <v-card-actions class="card-actions">
- <v-card-text class="card-text"> {{ shortBtn }}</v-card-text>
- <v-btn :to="link" class="card-button" :style="myStyle">
- {{ shortDesc }}
- </v-btn>
- </v-card-actions>
- </v-col>
- </v-row>
- </v-col>
- </v-card>
-</template>
-
-<script>
-export default {
- name: "AnalysisCard",
- props: {
- title: { type: String, default: '' },
- description: { type: String, default: '' },
- shortBtn: { type: String, default: '' },
- shortDesc: { type: String, default: '' },
- link: { type: String, default: '' },
- myStyle: { type: Object, default() { return {} } },
- myClass: { type: String, default: '' },
- myImg: { type: String, default: '' }
- }
-}
-</script>
-
-<style scoped>
-.card-title {
- word-break: unset;
-}
-
-.card-text {
- font-size: 18px;
- text-align: justify;
-}
-
-.card-actions {
- background: white;
- border-radius: 3px;
- box-shadow: 1px 1px 5px #aeaeae;
- margin: 0 auto;
- padding: 20px;
-}
-
-.card-button {
- color: #fff;
- margin: 0 auto;
- text-transform: none;
-}
-</style>
-
diff --git a/client/components/Heatmap.js b/client/components/Heatmap.js
deleted file mode 100644
index c40d42e36f0b0d37b794214476ac0af7e75f6106..0000000000000000000000000000000000000000
--- a/client/components/Heatmap.js
+++ /dev/null
@@ -1,124 +0,0 @@
-import Plotly from 'plotly.js-dist';
-const d3 = require("d3");
-
-const trace1 = {
- x: [],
- y: [],
- type: 'scatter',
-};
-const plotHeatMapSize = 1100;
-
-export default {
- display: 'Scatter',
- data: {
- data: [trace1],
- attr: { displayModeBar: false },
- layout: {
- plot_bgcolor: '#d3d3d3',
- paper_bgcolor: '#d3d3d3',
- },
- },
- makePlot(parent, selectedChr, selectedRegion) {
- const layout = {
- title: "Z score Heatmap",
- autosize: false,
- width: plotHeatMapSize,
- font: {
- size: 8
- },
- margin: {
- l: 90,
- r: 50,
- b: 60,
- t: 30,
- pad: 4
- },
- xaxis: {
- showticklabels: true,
- ticks: '',
- side: 'bottom',
- fixedrange: true,
- type: 'category'
- },
- yaxis: {
- ticks: '',
- fixedrange: true,
- ticksuffix: ' '
- },
- showlegend: false
- };
-
- const why = this;
- const idProject = parent.project.id;
-
- d3.csv(process.env.API_URL + "/projects/" + idProject + "/heatmap/" + selectedChr + "/" + selectedRegion).then(
- function (allRows) {
- const cols = [];
- const lines = [];
-
- for (const valeur in allRows[0]) {
- if ((valeur !== "") && (valeur !== 'ID')) {
- cols.push(valeur);
- }
- }
-
- const arr = [];
- let row = allRows[0];
-
- for (let i = 0; i < allRows.length; i++) {
- row = allRows[i];
- arr.push([]);
- lines[i] = row.ID;
- arr[i].push(new Array(cols));
- for (let j = 0; j < cols.length; j++) {
- arr[i][j] = row[cols[j]];
- }
- }
-
- const data = [
- {
- z: arr,
- x: cols,
- y: lines,
- type: 'heatmap',
- colorscale: [
- ['-1', '#4A6FE3'],
- ['-0.9', '#5F7BE1'],
- ['-0.8', '#7086E1'],
- ['-0.7', '#8091E1'],
- ['-0.6', '#8F9DE1'],
- ['-0.5', '#9DA8E2'],
- ['-0.4', '#ABB4E2'],
- ['-0.3', '#B9BFE3'],
- ['-0.2', '#C7CBE3'],
- ['-0.1', '#D5D7E3'],
- ['0', '#E2E2E2'],
- ['0.1', '#E4D3D6'],
- ['0.2', '#E6C4C9'],
- ['0.3', '#E6B4BD'],
- ['0.4', '#E5A5B1'],
- ['0.5', '#E495A5'],
- ['0.6', '#E28699'],
- ['0.7', '#DF758D'],
- ['0.8', '#DB6581'],
- ['0.9', '#D75376'],
- ['1', '#D33F6A']
- ],
- transforms: [{
- type: 'filter',
- target: 'y',
- operation: '!=',
- value: 'PVALmin'
- }]
- }
- ];
-
- why.data.data = data;
- why.data.layout = layout;
-
- Plotly.newPlot('divHeatPlot', why.data.data, why.data.layout, { displayModeBar: false });
- parent.submanhattan.makePlot(parent, selectedChr, selectedRegion);
- }
- );
- }
-}
diff --git a/client/components/Manhattan.js b/client/components/Manhattan.js
deleted file mode 100644
index 2218a041c7e094ca79abe2fa8874d64518e9b25e..0000000000000000000000000000000000000000
--- a/client/components/Manhattan.js
+++ /dev/null
@@ -1,345 +0,0 @@
-import Plotly from 'plotly.js-dist';
-const d3 = require("d3");
-
-const chromosomes = [
- "chr1",
- "chr2",
- "chr3",
- "chr4",
- "chr5",
- "chr6",
- "chr7",
- "chr8",
- "chr9",
- "chr10",
- "chr11",
- "chr12",
- "chr13",
- "chr14",
- "chr15",
- "chr16",
- "chr17",
- "chr18",
- "chr19",
- "chr20",
- "chr21",
- "chr22"
-];
-
-const color = ['orangered', '#4287f5'];
-
-let trace1 = {
- x: [],
- y: [],
- type: 'scatter',
-};
-
-const tableLines = [];
-
-export default {
- display: 'Scatter',
- data: {
- data: [trace1],
- attr: { displayModeBar: false },
- layout: {
- plot_bgcolor: '#d3d3d3',
- paper_bgcolor: '#d3d3d3',
- },
- datarows: []
- },
- updateTrace() {
- trace1 = {
- x: [1, 2, 3, 4],
- y: [10, 15, 13, 17],
- type: 'scatter',
- };
-
- this.data.data = [trace1];
- },
- makePlot(parent) {
- const plotHeatMapSize = 1100;
- const why = this;
- const idProject = parent.project.id;
-
- d3.csv(process.env.API_URL + "/projects/" + idProject + "/genome")
- .then((rows) => {
- why.data.datarows = rows;
- const dataplot = chromosomes.map((chr) => {
- const rowsFiltered = rows.filter((row) => {
- return (row.CHR === chr);
- });
- const xvar = unpack(rowsFiltered, 'Region');
- const yvar = unpackLog(rowsFiltered, 'JOSTmin');
- return {
- name: chr,
- x: xvar,
- y: yvar,
- text: unpackText(rowsFiltered),
- hovertemplate: '%{text}',
- mode: 'markers',
- showlegend: false,
- type: 'scatter',
- marker: {
- color: 'red'
- }
- }
- });
-
- why.data.data = dataplot;
-
- const layout = {
- title: "Joint test association results by regions",
- width: plotHeatMapSize,
- hovermode: 'closest',
- showLink: false,
- modeBarButtonsToRemove: [],
- font: {
- size: 8
- },
- margin: {
- l: 80,
- r: 50,
- b: 60,
- t: 30,
- pad: 4
- },
- xaxis: {
- showgrid: true,
- showticklabels: true,
- tickmode: "array",
- tickvals: [
- 'Region67',
- 'Region206',
- 'Region339',
- 'Region461',
- 'Region577',
- 'Region688',
- 'Region793',
- 'Region890',
- 'Region974',
- 'Region1053',
- 'Region1138',
- 'Region1221',
- 'Region1293',
- 'Region1352',
- 'Region1405',
- 'Region1457',
- 'Region1507',
- 'Region1555',
- 'Region1598',
- 'Region1637',
- 'Region1668',
- 'Region1692'
- ],
- ticktext: [
- '1',
- '2',
- '3',
- '4',
- '5',
- '6',
- '7',
- '8',
- '9',
- '10',
- '11',
- '12',
- '13',
- '14',
- '15',
- '16',
- '17',
- '18',
- '19',
- '20',
- '21',
- '22'
- ],
- tickfont: {
- family: 'Arial, sans-serif',
- size: 12,
- color: 'black',
- },
- title: "chromosome",
- side: 'bottom',
- type: 'category',
- range: [0, '1704'],
- },
- yaxis: {
- range: [0, '2.3'],
- title: "-log(Pvalue)",
- type: 'log',
- tickfont: {
- family: 'Arial, sans-serif',
- size: 10,
- color: 'black'
- }
- },
- };
-
- why.data.layout = layout
-
- let k = 1;
- let i;
- let j;
- const markerOffset = 0.04;
-
- for (i = 0; i < dataplot.length; i++) {
-
- k = 1 - k;
- dataplot[i].marker.color = color[k];
-
- for (j = 0; j < dataplot[i].x.length; j++) {
- const dict = {
- "type": 'line',
- "xref": 'x',
- "yref": 'y',
- "x0": dataplot[i].x[j],
- "y0": 0.01,
- "x1": dataplot[i].x[j],
- "y1": offsetSignal(dataplot[i].y[j], markerOffset),
- "line": {
- color: dataplot[i].marker.color,
- width: 0.3
- }
- };
-
- tableLines.push(dict);
- }
- }
-
- const update = {
- shapes: tableLines
- };
-
- const suggestiveline = -Math.log10(1e-5);
- const suggestivelineColor = "orange";
-
- const genomewideline = -Math.log10(5e-8);
- const genomewidelineColor = "green";
-
- const datmp = dataplot[0];
- const tbx = datmp.x;
- const d = tbx[0];
-
- const datmp2 = dataplot[dataplot.length - 1];
- const tbx2 = datmp2.x
- const e = tbx2[tbx2.length - 1];
-
- const trace1 = {
- x: [d, e],
- y: [suggestiveline, suggestiveline],
- mode: 'lines+markers+text',
- name: '1e-5',
- textposition: 'top',
- type: 'scatter',
- showlegend: true,
- marker: {
- color: suggestivelineColor
- }
- };
-
- const trace2 = {
- x: [d, e],
- y: [genomewideline, genomewideline],
- mode: 'lines+markers+text',
- name: '5e-8',
- textposition: 'top',
- type: 'scatter',
- showlegend: true,
- marker: {
- color: genomewidelineColor
- }
- };
-
- why.data.layout.shapes = tableLines;
- why.data.data.push(trace1);
- why.data.data.push(trace2);
-
- Plotly.newPlot('divWholeStatPlot', why.data.data, why.data.layout, { displayModeBar: false });
- parent.$refs.divWholeStatPlot.on('plotly_click', function (data) {
- parent.isready2 = true;
- why.reactOnClick(data);
- Plotly.update('divWholeStatPlot', why.data.layout);
-
- const selectedChr = data.points.map(function (d) {
- return d.data.name;
-
- });
-
- const selectedRegion = data.points[0].x;
- parent.heatmap.makePlot(parent, selectedChr, selectedRegion);
-
- });
-
- });
- },
- reactOnClick(data) {
- let updaterange = data.points[0].x.split("Region");
- const tmp = Number(updaterange[1]) + 10;
- updaterange = "Region" + tmp;
- const selectRectangle = {
- "type": 'rect',
- // x-reference is assigned to the x-values
- "xref": 'x',
- // y-reference is assigned to the plot paper [0,1]
- "yref": 'paper',
- "x0": data.points[0].x,
- "y0": 0,
- "x1": updaterange,
- "y1": 1,
- "fillcolor": '#d3d3d3',
- "opacity": 0.6,
- "line": {
- width: 0
- }
- };
-
- if (tableLines[tableLines.length - 1].type === 'rect') {
- tableLines.pop();
- }
-
- tableLines.push(selectRectangle);
- this.data.layout.shapes = tableLines;
- }
-};
-
-// ---------------------------------------------------------------------------------------------------------------------------
-
-function offsetSignal(signal, markerOffset) {
- let result = 0;
- if (Math.abs(signal) > markerOffset) {
- if (signal > 0) {
- result = signal - markerOffset;
- }
- else {
- result = signal + markerOffset;
- }
- }
- return result;
-}
-
-// ---------------------------------------------------------------------------------------------------------------------------
-
-function unpack(rows, key) {
- return rows.map((row) => { return row[key]; });
-}
-
-// ---------------------------------------------------------------------------------------------------------------------------
-
-function unpackLog(rows, key) {
- return rows.map((row) => { return -Math.log10(row[key]); });
-}
-
-// ---------------------------------------------------------------------------------------------------------------------------
-
-function unpackText(rows) {
- return rows.map(function (row) {
- const rsid = row.snp_ids;
- const pos = row.MiddlePosition / 1000000;
- const chr = row.CHR;
- const pval = row.JOSTmin;
- const text = 'rsid: ' + rsid + '<br>' + 'pos: ' + chr + ':' + pos.toFixed(2) + '<br>-log(Pvalue): ' + pval + '<extra></extra>';
- return text;
- });
-}
diff --git a/client/components/PhenotypeCard.vue b/client/components/PhenotypeCard.vue
deleted file mode 100644
index cd38dab76ba49d68143066941292a9c90fe5cc2c..0000000000000000000000000000000000000000
--- a/client/components/PhenotypeCard.vue
+++ /dev/null
@@ -1,71 +0,0 @@
-<template>
- <span style="padding:8px;font-size:16px;">
- <v-dialog
- persistent
- width=500>
- <template #activator="{ on }">
- <v-chip medium
- color="white"
- text-color="#298e49"
- v-on="on">
- <v-icon left
- style="font-size:20px;">
- mdi-information
- </v-icon>
- {{ phe.full_name }}
- </v-chip>
- </template>
-
- <template #default="dialog">
- <v-card width="500" elevation="6">
- <v-toolbar
- color="#298e49"
- dark>Phenotype: {{ phe.full_name }}
- </v-toolbar>
-
- <v-card-text style="padding-top:12px;">
- <p>
- <b>Consortium:</b> {{ phe.consortium }}
- </p>
- <p>
- <b>Id:</b> {{ phe.id }}
- </p>
- <p>
- <b>Outcome:</b> {{ phe.outcome }}
- </p>
- <p>
- <b>Ref:</b> {{ phe.ref }}
- </p>
- <p>
- <b>Ref_link:</b> <a target="_blank" :href="phe.ref_link">{{ phe.ref_link }}</a>
- </p>
- </v-card-text>
- <v-card-actions>
- <v-btn
- color="#B0E8C2"
- depressed
- @click="dialog.value = false">
- <v-icon left>
- mdi-close
- </v-icon>
- Close
- </v-btn>
- </v-card-actions>
- </v-card>
- </template>
- </v-dialog>
- </span>
-</template>
-
-<script>
-export default {
- props: {
- phe: {
- type: Object,
- default() {
- return {}
- }
- }
- }
-}
-</script>
diff --git a/client/components/ShareLink.vue b/client/components/ShareLink.vue
deleted file mode 100644
index c1751d683d7ebe564b217949b1378a913bbbb965..0000000000000000000000000000000000000000
--- a/client/components/ShareLink.vue
+++ /dev/null
@@ -1,46 +0,0 @@
-<template>
- <v-speed-dial v-model="dialShare" absolute top right direction="left" open-on-hover>
- <template #activator>
- <v-btn fab bottom small color="primary">
- <v-icon v-if="dialShare">mdi-close</v-icon>
- <v-icon v-else>mdi-share-variant</v-icon>
- </v-btn>
- </template>
- <v-btn dark fab bottom color="blue darken-7" small :href="`https://www.linkedin.com/shareArticle?mini=true&url=${pageUrl}`" target="_blank">
- <v-icon>mdi-linkedin</v-icon>
- </v-btn>
- <v-btn dark fab bottom color="blue" small :href="`https://www.facebook.com/sharer/sharer.php?u=${pageUrl}`" target="_blank">
- <v-icon>mdi-facebook</v-icon>
- </v-btn>
- <v-btn dark fab bottom color="green" small :href="`https://wa.me/?text=Checkout%20this%20page.%20${pageUrl}`" target="_blank">
- <v-icon>mdi-whatsapp</v-icon>
- </v-btn>
- <v-btn dark fab bottom color="primary" small :href="`mailto:?subject=JASS analysis&body=Here is an analysis computed in JASS: ${pageUrl}`" target="_blank" title="Send by mail">
- <v-icon>mdi-email</v-icon>
- </v-btn>
- <v-btn dark fab bottom color="primary" small title="Copy to clipboard" @click="copySign()">
- <v-icon>mdi-clipboard</v-icon>
- </v-btn>
- </v-speed-dial>
-</template>
-
-<script>
-export default {
- props: {
- pageUrl: {
- type: String,
- default: ''
- }
- },
- data() {
- return {
- dialShare: false
- }
- },
- methods: {
- copySign() {
- navigator.clipboard.writeText(this.pageUrl);
- }
- }
-}
-</script>
diff --git a/client/components/SubManhattan.js b/client/components/SubManhattan.js
deleted file mode 100644
index abe578dedcb895779fa52060e626411b23abd25a..0000000000000000000000000000000000000000
--- a/client/components/SubManhattan.js
+++ /dev/null
@@ -1,123 +0,0 @@
-import Plotly from 'plotly.js-dist';
-const d3 = require("d3");
-
-const color = ['red', 'blue'];
-
-const trace1 = {
- x: [],
- y: [],
- type: 'scatter',
-};
-const plotHeatMapSize = 1100;
-
-export default {
- display: 'Scatter',
- data: {
- data: [trace1],
- attr: { displayModeBar: false },
- layout: {
- plot_bgcolor: '#d3d3d3',
- paper_bgcolor: '#d3d3d3',
- },
- },
- makePlot(parent, selectedChr, selectedRegion) {
- const why = this;
- const numberColor = (selectedChr + 1) % 2;
- const idProject = parent.project.id;
-
- d3.csv(process.env.API_URL + "/projects/" + idProject + "/manhattan/" + selectedChr + "/" + selectedRegion)
- .then((allRows) => {
- const regions = [];
-
- for (let i = 0; i < 2000; i++) {
- regions[i] = "Region" + i;
- }
-
- const data = regions.map((region) => {
- const rowsFiltered = allRows.filter((row) => {
- return (row.Region === region);
- });
-
- return {
- name: region,
- x: unpack(rowsFiltered, 'snp_ids'),
- y: unpackLog(rowsFiltered, 'JASS_PVAL'),
- text: unpack(rowsFiltered, 'Region'),
- mode: 'markers',
- type: 'scatter',
- marker: {
- color: color[numberColor]
- }
- }
- });
-
- const titleplot = "Joint test association results for locus " + selectedRegion + " on " + selectedChr;
-
- const layout = {
- title: titleplot,
- width: plotHeatMapSize,
- hovermode: 'closest',
- font: {
- size: 8
- },
- margin: {
- l: 90,
- r: 90,
- b: 10,
- t: 100,
- pad: 4
- },
- xaxis: {
- showticklabels: false,
- ticks: '',
- side: 'top',
- type: 'category',
- range: [-0.5, allRows.length]
- },
- yaxis: {
- title: "-log(Pvalue)",
- ticks: '',
- ticksuffix: ' ',
- fixedrange: true,
- },
- };
-
- why.data.data = data;
- why.data.layout = layout;
-
- Plotly.newPlot('divLocalStatPlot', why.data.data, why.data.layout, { displayModeBar: false });
-
- parent.$refs.divLocalStatPlot.on('plotly_relayout',
- function (eventdata) {
- const update = {
- 'xaxis.range': [eventdata['xaxis.range[0]'],
- eventdata['xaxis.range[1]']]
- }
- Plotly.relayout('divHeatPlot', update);
- });
- });
- }
-}
-
-function unpack(rows, key) {
- return rows.map((row) => { return row[key]; });
-}
-
-// ---------------------------------------------------------------------------------------------------------------------------
-
-function unpackLog(rows, key) {
- return rows.map((row) => { return -Math.log10(row[key]); });
-}
-
-// ---------------------------------------------------------------------------------------------------------------------------
-
-function unpackText(rows) {
- return rows.map((row) => {
- const rsid = row.snp_ids;
- const pos = row.MiddlePosition / 1000000;
- const chr = row.CHR;
- const pval = row.JOSTmin;
- const text = 'rsid: ' + rsid + '<br>' + 'pos: ' + chr + ':' + pos.toFixed(2) + '<br>-log(Pvalue): ' + pval + '<extra></extra>';
- return text;
- });
-}
diff --git a/client/layouts/default.vue b/client/layouts/default.vue
deleted file mode 100644
index 3a662520e9938b33f45330b0653f93e44fb4f943..0000000000000000000000000000000000000000
--- a/client/layouts/default.vue
+++ /dev/null
@@ -1,229 +0,0 @@
-<template>
- <v-app dark>
- <v-app-bar density="compact" style="background-color:white;">
- <v-img
- class="shrink"
- max-width="auto"
- contain
- src="/institut_pasteur_logo_2020.png">
- </v-img>
- <v-divider vertical class="mx-4"></v-divider>
- <a style="text-decoration: none; color: #272727;" href="/">
- <h1 class="logo subheading">JASS</h1>
- </a>
- <v-spacer></v-spacer>
- <v-img
- class="shrink d-none d-md-flex"
- max-width="auto"
- contain
- src="/pasteur-img.png">
- </v-img>
- </v-app-bar>
-
- <v-tabs fixed-tabs dark>
- <span class="hidden-xs-only" style="width:280px"></span>
-
- <v-tab v-for="(item, i) in items"
- :key="i"
- :to="item.to" v-text="item.title">
- </v-tab>
-
- <v-tab to="/workload" style="max-width:280px;margin-right: inherit;margin-left: auto;">
- Workload
- <v-progress-linear
- :value="activeTask / (activeTask + pendingTask) * 100"
- :background-color="(activeTask == 0) && (pendingTask == 0) ? '#fffb' : undefined"
- :buffer-value="activeTask === null ? 0 : 100"
- height="20"
- :stream="activeTask === null"
- :striped="activeTask !== null"
- color="rgb(45, 150, 250)"
- :title="'Task: ' + activeTask + ' running and ' + pendingTask + ' pending.'"
- class="hidden-xs-only ml-2">
- <small>
- {{ textProgressBar }}
- </small>
- </v-progress-linear>
- </v-tab>
- </v-tabs>
-
- <v-main>
- <v-container fluid>
- <Nuxt />
- </v-container>
- </v-main>
- </v-app>
-</template>
-
-<script>
-export default {
- data() {
- return {
- activeTask: null,
- pendingTask: null,
- clipped: false,
- drawer: false,
- fixed: false,
- items: [
- {
- icon: 'mdi-checkbox-blank-circle',
- title: 'Home',
- to: '/'
- },
- {
- icon: 'mdi-checkbox-blank-circle',
- title: 'GWAS',
- to: '/gwas'
- },
- {
- icon: 'mdi-checkbox-blank-circle',
- title: 'Citations',
- to: '/citations'
- },
- {
- icon: 'mdi-checkbox-blank-circle',
- title: 'Credits',
- to: '/credits'
- }
- ],
- miniVariant: false,
- right: true,
- rightDrawer: false,
- title: 'Vuetify.js',
- footer: {
- col1: [
- {
- label: "THE INSTITUT PASTEUR",
- url: 'https://www.pasteur.fr/en/institut-pasteur',
- },
- {
- label: 'OUR MISSIONS',
- url: 'https://www.pasteur.fr/en/our-missions',
- },
- {
- label: 'SUPPORT US',
- url: 'https://www.pasteur.fr/en/support-us',
- },
- {
- label: 'MEDICAL CENTER',
- url: 'https://www.pasteur.fr/en/medical-center',
- },
- {
- label: 'THE RESEARCH JOURNAL',
- url: 'https://www.pasteur.fr/en/research-journal',
- },
- ],
- col2: [
- { label: 'DONATE', url: 'https://don.pasteur.fr/' },
- { label: 'PRESS AREA', url: 'https://www.pasteur.fr/en/press-area' },
- { label: 'LEGAL NOTICE', url: 'LEGAL NOTICE' },
- {
- label: 'CREDITS',
- url: '/credits',
- },
- ],
- col3: [
- {
- icon: 'mdi-facebook',
- url: 'https://www.facebook.com/InstitutPasteur',
- },
- {
- icon: 'mdi-twitter',
- url: 'https://twitter.com/GGSPasteur',
- },
- {
- icon: 'mdi-linkedin',
- url: 'https://www.linkedin.com/company/institut-pasteur',
- },
- {
- icon: 'mdi-youtube',
- url: 'https://www.youtube.com/user/institutpasteurvideo',
- },
- {
- icon: 'mdi-instagram',
- url: 'https://www.instagram.com/institutpasteur/?hl=fr',
- },
- ],
- },
- }
- },
- computed: {
- textProgressBar() {
- if (this.activeTask === null)
- return ''
- if (this.pendingTask === 0) {
- if (this.activeTask === 0) {
- return 'no load';
- }
- return this.activeTask + " running";
- }
- return this.activeTask + " + " + this.pendingTask;
- },
- },
- created() {
- this.$store.dispatch('fetchTables');
- this.getQueueStatus();
- },
- methods: {
- async getQueueStatus() {
- if (this.isready)
- return;
- await this.$axios.$get('/queue_status').then((function (resultStatus) {
- this.activeTask = resultStatus.active;
- this.pendingTask = resultStatus.reserved;
- setTimeout(this.getQueueStatus, 5000);
- }).bind(this)).catch((function () {
- setTimeout(this.getQueueStatus, 10000);
- }).bind(this));
- },
- }
-}
-</script>
-
-<style>
-header.v-toolbar {
- flex-grow: 0;
-}
-
-footer {
- .footer-text {
- font-size: 12px !important;
- }
-
- .v-list-item-group .v-list-item--active {
- background-color: rgba(0, 0, 0, 0);
- color: #FFF;
- }
-
- .v-list-item--dense,
- .v-list--dense .v-list-item {
- min-height: 30px;
- }
-}
-
-.v-list-group.v-list-group--default {
- .v-list-group__header {
- min-height: 32px;
-
- >.v-list-item__icon {
- margin-bottom: 6px;
- margin-top: 6px;
- }
- }
-
- .v-list-item__content {
- .v-list-item__title {
- white-space: normal;
- }
- }
-}
-
-#app-bar-title {
- color: black;
- text-decoration: inherit;
-
- >h1 {
- text-transform: uppercase;
- }
-}
-</style>
diff --git a/client/layouts/error.vue b/client/layouts/error.vue
deleted file mode 100644
index 3858c352762b196b51e1eb410dd7f70a5343fd12..0000000000000000000000000000000000000000
--- a/client/layouts/error.vue
+++ /dev/null
@@ -1,46 +0,0 @@
-<template>
- <div class="errorPage">
- <h1 v-if="error.statusCode === 404">
- {{ pageNotFound }}
- </h1>
- <h1 v-else>
- {{ otherError }}
- </h1>
- <NuxtLink to="/">
- Home page
- </NuxtLink>
- </div>
-</template>
-
-<script>
-export default {
- layout: 'empty',
- props: {
- error: {
- type: Object,
- default: null
- }
- },
- data() {
- return {
- pageNotFound: '404 Not Found',
- otherError: 'An error occurred'
- }
- },
- head() {
- const title =
- this.error.statusCode === 404 ? this.pageNotFound : this.otherError
- return {
- title
- }
- }
-}
-</script>
-
-<style scoped>
-.errorPage {
- display: flex;
- flex-flow: column wrap;
- align-items: center;
-}
-</style>
diff --git a/client/nginx.conf b/client/nginx.conf
deleted file mode 100644
index 6aed38e437e15252a5a9cf06a38437af7bdf5bf7..0000000000000000000000000000000000000000
--- a/client/nginx.conf
+++ /dev/null
@@ -1,44 +0,0 @@
-server {
- listen 8080;
- server_name localhost;
-
- #access_log /var/log/nginx/host.access.log main;
-
- location / {
- root /usr/share/nginx/html;
- index index.html index.htm;
- try_files $uri $uri/ /index.html /;
- }
-
- #error_page 404 /404.html;
-
- # redirect server error pages to the static page /50x.html
- #
- error_page 500 502 503 504 /50x.html;
- location = /50x.html {
- root /usr/share/nginx/html;
- }
-
- # proxy the PHP scripts to Apache listening on 127.0.0.1:80
- #
- #location ~ \.php$ {
- # proxy_pass http://127.0.0.1;
- #}
-
- # pass the PHP scripts to FastCGI server listening on 127.0.0.1:9000
- #
- #location ~ \.php$ {
- # root html;
- # fastcgi_pass 127.0.0.1:9000;
- # fastcgi_index index.php;
- # fastcgi_param SCRIPT_FILENAME /scripts$fastcgi_script_name;
- # include fastcgi_params;
- #}
-
- # deny access to .htaccess files, if Apache's document root
- # concurs with nginx's one
- #
- #location ~ /\.ht {
- # deny all;
- #}
-}
\ No newline at end of file
diff --git a/client/nuxt.config.js b/client/nuxt.config.js
deleted file mode 100644
index 43c2eac5c286960d466f5220a0917d4ce755d151..0000000000000000000000000000000000000000
--- a/client/nuxt.config.js
+++ /dev/null
@@ -1,118 +0,0 @@
-import colors from 'vuetify/es5/util/colors'
-
-export default {
- // Disable server-side rendering: https://go.nuxtjs.dev/ssr-mode
- ssr: false,
-
- // Target: https://go.nuxtjs.dev/config-target
- target: 'static',
-
- // Global page headers: https://go.nuxtjs.dev/config-head
- head: {
- titleTemplate: '%s - Joint Analysis of Summary Statistics',
- title: 'JASS',
- htmlAttrs: {
- lang: 'en'
- },
- meta: [
- { charset: 'utf-8' },
- { name: 'viewport', content: 'width=device-width, initial-scale=1' },
- { hid: 'description', name: 'description', content: '' },
- { name: 'format-detection', content: 'telephone=no' }
- ],
- script: [
- {
- defer: true,
- 'data-domain': "jass.pasteur.fr",
- src: "https://plausible.pasteur.cloud/js/script.js"
- }
- ],
- link: [
- { rel: 'icon', type: 'image/x-icon', href: '/favicon.ico' }
- ]
- },
-
- // Global CSS: https://go.nuxtjs.dev/config-css
- css: [
- '~/assets/css/global.css'
- ],
-
- // Plugins to run before rendering page: https://go.nuxtjs.dev/config-plugins
- plugins: [
- { src: '~/plugins/sanitizedHtml.js', mode: 'client' },
- ],
-
- // Auto import components: https://go.nuxtjs.dev/config-components
- components: true,
-
- // Modules for dev and build (recommended): https://go.nuxtjs.dev/config-modules
- buildModules: [
- // https://go.nuxtjs.dev/eslint
- '@nuxtjs/eslint-module',
- // https://go.nuxtjs.dev/stylelint
- '@nuxtjs/stylelint-module',
- // https://go.nuxtjs.dev/vuetify
- '@nuxtjs/vuetify',
- '@nuxtjs/dotenv',
- ],
-
- // Modules: https://go.nuxtjs.dev/config-modules
- modules: [
- // https://go.nuxtjs.dev/axios
- '@nuxtjs/axios',
- '@nuxtjs/markdownit'
- ],
-
- // Axios module configuration: https://go.nuxtjs.dev/config-axios
- axios: {
- baseURL: process.env.API_URL || "http://0.0.0.0:8080/api",
- progress: false
- },
-
- env: {
- API_URL: process.env.API_URL || "http://0.0.0.0:8080/api",
- },
-
- vuetify: {
- customVariables: ['~/assets/variables.scss'],
- treeShake: true,
- defaultAssets: {
- font: false,
- icons: 'mdi',
- },
- theme: {
- dark: false,
- themes: {
- dark: {
- primary: '#2d96fa',
- accent: colors.grey.darken3,
- secondary: colors.amber.darken3,
- tertiary: '#fff',
- info: colors.teal.lighten1,
- warning: colors.amber.base,
- error: colors.deepOrange.accent4,
- success: colors.green.accent3,
- },
- light: {
- primary: '#2d96fa',
- secondary: '#424242',
- tertiary: '#fff',
- accent: '#82B1FF',
- error: '#FF5252',
- info: '#2196F3',
- success: '#4CAF50',
- warning: '#FFC107',
- },
- },
- },
- },
-
- // https://nuxtjs.org/docs/2.x/configuration-glossary/configuration-router#base
- router: {
- base: process.env.BASE_PATH || '/',
- },
-
- // Build Configuration: https://go.nuxtjs.dev/config-build
- build: {
- }
-}
diff --git a/client/package.json b/client/package.json
deleted file mode 100644
index 9e960dbdab9b5055a3f4539de5464bd47c5ecf9c..0000000000000000000000000000000000000000
--- a/client/package.json
+++ /dev/null
@@ -1,49 +0,0 @@
-{
- "name": "my-nuxt-app",
- "version": "1.0.0",
- "private": true,
- "scripts": {
- "dev": "nuxt",
- "build": "nuxt build",
- "start": "nuxt start",
- "generate": "nuxt generate",
- "lint:js": "eslint --ext \".js,.vue\" --ignore-path .gitignore .",
- "lint:style": "stylelint \"**/*.{vue,css}\" --ignore-path .gitignore",
- "prepare": "husky install",
- "lint": "npm run lint:js && npm run lint:style"
- },
- "lint-staged": {
- "*.{js,vue}": "eslint",
- "*.{css,vue}": "stylelint"
- },
- "dependencies": {
- "@nuxtjs/axios": "^5.13.6",
- "@nuxtjs/markdownit": "^2.0.0",
- "core-js": "^3.35.0",
- "d3": "^7.1.1",
- "dompurify": "^2.4.7",
- "lodash": "^4.17.21",
- "nuxt": "^2.17.3",
- "plotly.js-dist": "^2.28.0",
- "vue-json-to-csv": "^1.1.8",
- "vuetify": "^2.7.1"
- },
- "devDependencies": {
- "@babel/eslint-parser": "^7.23.3",
- "@nuxtjs/dotenv": "^1.4.2",
- "@nuxtjs/eslint-config": "^6.0.1",
- "@nuxtjs/eslint-module": "^3.0.2",
- "@nuxtjs/stylelint-module": "^4.0.0",
- "@nuxtjs/vuetify": "^1.12.1",
- "eslint": "^7.29.0",
- "eslint-config-prettier": "^8.3.0",
- "eslint-plugin-nuxt": "^2.0.0",
- "eslint-plugin-vue": "^7.12.1",
- "husky": "^6.0.0",
- "lint-staged": "^10.5.4",
- "prettier": "^2.3.2",
- "stylelint": "^13.13.1",
- "stylelint-config-prettier": "^8.0.2",
- "stylelint-config-standard": "^22.0.0"
- }
-}
diff --git a/client/pages/citations.vue b/client/pages/citations.vue
deleted file mode 100644
index c061600982b74e2ef3a0e736c7fdd37410a641c1..0000000000000000000000000000000000000000
--- a/client/pages/citations.vue
+++ /dev/null
@@ -1,71 +0,0 @@
-<template>
- <div>
- <h1>Citations</h1>
-
- <h2>When referring to theoretical basis of JASS tests, cite :</h2>
- <cite class="citation">
- <span class="authors">Julienne H, Laville V, McCaw ZR, He Z, Guillemot V, Lasry C, Ziyatdinov A, Nerin C, Vaysse A, Lechat P, Ménager H, Le Goff W, Dube MP, Kraft P, Ionita-Laza I, Vilhjálmsson BJ, Aschard H.</span>
- <span class="title">Multitrait GWAS to connect disease variants and biological mechanisms.</span>
- <span class="journal">PLoS Genet. 2021 Aug 30;17(8):e1009713.</span>
- <a class="doi" href="https://doi.org/10.1371/journal.pgen.1009713" target="_blank">doi: 10.1371/journal.pgen.1009713.</a>
- </cite>
-
- <h2>When using JASS software in publication, cite :</h2>
- <cite class="citation">
- <span class="authors">Julienne H, Lechat P, Guillemot V, Lasry C, Yao C, Araud R, Laville V, Vilhjalmsson B, Ménager H, Aschard H.</span>
- <span class="title">JASS: command line and web interface for the joint analysis of GWAS results.</span>
- <span class="journal">NAR Genom Bioinform. 2020 Mar;2(1):lqaa003.</span>
- <a class="doi" href="https://doi.org/10.1093/nargab/lqaa003" target="_blank">doi: 10.1093/nargab/lqaa003.</a>
- </cite>
-
- <h2>When refereeing to the imputation of summary statistics, cite :</h2>
- <cite class="citation">
- <span class="authors">Julienne H, Shi H, Pasaniuc B, Aschard H.</span>
- <span class="title">RAISS: robust and accurate imputation from summary statistics. Bioinformatics.</span>
- <span class="journal">Bioinformatics. 2019 Nov 1;35(22):4837-4839.</span>
- <a class="doi" href="https://doi.org/10.1093/bioinformatics/btz466" target="_blank">doi: 10.1093/bioinformatics/btz466.</a>
- </cite>
-
- <h2>Additional publications tied to JASS</h2>
-
- <cite class="citation">
- <span class="authors">Suzuki, Y., Ménager, H., Brancotte, B., Vernet, R., Nerin, C., Boetto, C., Auvergne, A., Linhard, C., Torchet, R., Lechat, P., Troubat, L., Cho, M.H., Bouzigon, E., Aschard, H., Julienne, H., 2023.</span>
- <span class="title">Trait selection strategy in multi-trait GWAS: Boosting SNPs discoverability.</span>
- <a href="https://doi.org/10.1101/2023.10.27.564319" class="doi">doi.org/10.1101/2023.10.27.564319</a>
- </cite>
-
- <cite class="citation">
- <span class="authors">Troubat, L., Fettahoglu, D., Henches, L., Aschard, H., Julienne, H., 2023.</span>
- <span class="title">Multi-trait GWAS for diverse ancestries: Mapping the knowledge gap.</span>
- <a href="https://doi.org/10.1101/2023.06.23.546248" class="doi">doi.org/10.1101/2023.06.23.546248</a>
- </cite>
-
- <cite class="citation">
- <span class="authors">Auvergne, A., Traut, N., Henches, L., Troubat, L., Frouin, A., Boetto, C., Kazem, S., Julienne, H., Toro, R., Aschard, H., 2023.</span>
- <span class="title">Linking the genetic structure of neuroanatomical phenotypes with psychiatric disorders.</span>
- <a href="https://doi.org/10.1101/2023.11.01.564329" class="doi">doi.org/10.1101/2023.11.01.564329</a>
- </cite>
- </div>
-</template>
-
-<style scoped>
-h1,
-h2 {
- text-align: center;
-}
-
-h1,
-cite {
- margin-bottom: 30px;
-}
-
-cite {
- display: flex;
- flex-flow: column wrap;
- align-items: center;
-}
-
-cite * {
- text-align: center;
-}
-</style>
diff --git a/client/pages/credits.vue b/client/pages/credits.vue
deleted file mode 100644
index 05cb9f2c3792c2344a242280151c1bba2e965316..0000000000000000000000000000000000000000
--- a/client/pages/credits.vue
+++ /dev/null
@@ -1,36 +0,0 @@
-<template>
- <section>
- <h1>Credits</h1>
-
- <v-row>
- <v-col cols="12" sm="12" md="12">
- <div class="credits">
- <p>Contributors to JASS software and website</p>
- <h4>Computation Engine</h4>
- <b>Julienne, H., Ménager, H., Nerin, C., Guillemot, V., Lasry, C.</b>
- <h4>Backend</h4>
- <b>Ménager, H., Nerin, C., Julienne, H., Brancotte, B.</b>
- <h4>Frontend</h4>
- <b>Lechat, P., Malesys, S.</b>
- <h4>UIX Design</h4>
- <b>Torchet, R.</b>
- <h4>Data collection and preparation</h4>
- <b>Julienne, H., Troubat, L.</b>
- <h4>Project Managers</h4>
- <b>Aschard, H., Julienne, H., Chapeaublanc, E.</b>
- </div>
- </v-col>
- </v-row>
- </section>
-</template>
-
-<style scoped>
-h1,
-.credits {
- text-align: center;
-}
-
-h1 {
- margin-bottom: 30px;
-}
-</style>
diff --git a/client/pages/gwas.vue b/client/pages/gwas.vue
deleted file mode 100644
index 1f233e328614cac7ffc2d3daca503e6bcdd5751c..0000000000000000000000000000000000000000
--- a/client/pages/gwas.vue
+++ /dev/null
@@ -1,216 +0,0 @@
-<template>
- <div>
- <div class="header">
- <h1>Genome-wide analysis parameters</h1>
- <p>
- Please select the phenotypes you want to analyze jointly with the Omnibus test. A research box bellow allows you to query our current database. The maximum number of trait that can be analyzed jointly is 64 phenotypes. Computation time for a large number of trait can take up to half an hour.
- </p>
- </div>
-
- <section>
- <h2>Select an ancestry:</h2>
- <div class="init-table-card-list">
- <v-card
- v-for="table in initTables"
- :key="table.tableName"
- class="init-table-card"
- :class="{ 'selected-table': selectedInitTable === table.tableName }"
- :color="selectedInitTable === table.tableName ? 'blue lighten-4' : ''">
- <v-card-title>{{ table.name }}</v-card-title>
- <v-card-text class="row">
- <div
- v-sanitized-html="$md.render(table.desc)"
- class="col-12 pt-0 pb-0 text-justify"
- ></div>
- <div class="col-12 col-md-6 pt-0">
- <strong>{{ table.nb_snps.toLocaleString() }}</strong>
- SNPS
- </div>
- <div class="col-12 col-md-6 pt-0 order-2">
- <strong>{{ table.nb_phenotypes.toLocaleString() }}</strong>
- phenotypes
- </div>
- <div class="col-12 col-md-6 pt-0 order-1">
- assembly: <strong>{{ table.assembly.toLocaleString() }}</strong>
- </div>
- <div class="col-12 col-md-6 pt-0 order-2">
- ancestry: <strong>{{ table.ancestry.toLocaleString() }}</strong>
- </div>
- </v-card-text>
- <v-card-actions class="card-buttons">
- <v-btn class="button" color="primary" @click="selectAncestry(table.tableName)">
- Select this ancestry
- </v-btn>
- </v-card-actions>
- </v-card>
- </div>
- </section>
-
- <section id="phenotypes-section" v-show="phenotypes.length">
- <h2>Select at least two GWASs to be analyzed jointly:</h2>
- <v-data-table
- v-model="selectedRows"
- :headers="headers"
- :items="phenotypes"
- :items-per-page="10"
- item-key="id"
- class="elevation-1"
- :search="search"
- show-select
- checkbox-color="primary"
- unselectable
- @current-items="current = $event"
- @item-selected="bulkSelect">
- <template #top>
- <v-text-field
- v-model="search"
- label="Search"
- class="mx-4">
- </v-text-field>
- </template>
-
- <template v-slot:item.ref="{ item }">
- <a class="ref-link" :href="item.ref_link" target="_blank" rel="noreferrer">{{ item.ref }}</a>
- </template>
- </v-data-table>
- <div class="start-button">
- <v-btn class="button" color="primary" :disabled="selectedRows.length <= 1" @click="runAnalysis()">
- Start analysis
- </v-btn>
- </div>
- </section>
- </div>
-</template>
-
-<script>
-export default {
- data() {
- return {
- selectedInitTable: '',
- headers: [
- { text: 'Outcome', value: 'outcome' },
- { text: 'Full name', value: 'full_name' },
- { text: 'Consortium', value: 'consortium' },
- { text: 'Type', value: 'typ' },
- { text: 'Ref', value: 'ref' },
- ],
- search: '',
- phenotypes: [],
- selectedRows: [],
- }
- },
- computed: {
- initTables() { return this.$store.state.initTables }
- },
- methods: {
- selectAncestry(initTableName) {
- if (this.selectedInitTable === initTableName) return
- this.selectedInitTable = initTableName
- this.$axios.$post('/phenotypes', { initTableName })
- .then(phenotypes => {
- this.phenotypes = phenotypes
- })
- .then(() => {
- // Scroll to the phenotype table after it appeared
- document
- .getElementById("phenotypes-section")
- .scrollIntoView({
- behavior: 'smooth',
- block: 'start',
- inline: 'nearest'
- })
- })
- },
- bulkSelect({ item: b, value }) {
- const { selectedRows, current, shiftKeyOn } = this;
- if (selectedRows.length === 1 && value === true && shiftKeyOn) {
- const [a] = selectedRows;
- let start = current.findIndex((item) => item === a);
- let end = current.findIndex((item) => item === b);
- if (start - end > 0) {
- const temp = start;
- start = end;
- end = temp;
- }
- for (let i = start; i <= end; i++) {
- selectedRows.push(current[i]);
- }
- }
- },
- runAnalysis() {
- const { selectedRows, $axios } = this;
- const phenotypeIds = {
- phenotypeID: selectedRows.map((phenotype) => { return phenotype.id }),
- initTableName: this.selectedInitTable
- };
-
- $axios.$post('/projects', phenotypeIds).then(response => {
- this.$router.push('/projects/' + response.id)
- })
- },
- }
-}
-</script>
-
-<style scoped>
-.header {
- display: flex;
- flex-flow: column wrap;
- align-items: center;
- margin: 30px;
-}
-
-.header h1 {
- text-align: center;
-}
-
-.header p {
- max-width: 80%;
- text-align: center;
-}
-
-section {
- margin: 40px 0;
-}
-
-section h2 {
- margin-bottom: 20px;
- text-align: center;
-}
-
-.init-table-card-list {
- display: flex;
- flex-flow: row wrap;
- gap: 20px;
- justify-content: center;
-}
-
-.init-table-card {
- width: 600px;
-}
-
-.init-table-card .v-card__title {
- word-break: normal;
-}
-
-.init-table-card .v-card__text {
- font-size: 16px;
-}
-
-.card-buttons {
- justify-content: end;
-}
-
-.button {
- text-transform: none;
-}
-
-.start-button {
- text-align: center;
- margin-top: 20px;
-}
-
-.ref-link {
- font-size: inherit;
-}
-</style>
diff --git a/client/pages/index.vue b/client/pages/index.vue
deleted file mode 100644
index 787c76abcdc07306af8398735abd376d72cf4651..0000000000000000000000000000000000000000
--- a/client/pages/index.vue
+++ /dev/null
@@ -1,93 +0,0 @@
-<template>
- <div>
- <h1 class="main_title"> Welcome to JASS v2.1</h1>
- <h3>a web interface for the Joint Analysis of GWAS Summary Statistics</h3>
- <v-row>
- <v-col cols="12" sm="10" offset-sm="1">
- <v-card-text class="main-intro">
- During the past decade, the statistical genetic community discovered and replicated thousands of variant-trait associations in human populations. However, the sample size required to detect additional variants using standard univariate association screening is increasingly prohibitive. Multi-trait GWAS offers a relevant alternative: it can improve statistical power and lead to new insights about gene function and the joint genetic architecture of human phenotypes.
- </v-card-text>
-
- <v-card-text class="main-intro">
- In practice, conducting multi-trait GWAS can become a hurdle due to missing values, heterogeneous data format, and computational cost. JASS (Joint Analysis of Summary Statistics) webserver solves all these practical barriers allowing investigators to conduct multi-trait GWAS interactively. Through this website, you can investigate <b>{{ getTotalPhenotypes.toLocaleString() }}</b> traits spanning several clinical domains and <b>{{ getTotalTables.toLocaleString() }}</b> ancestries. The results page displays genetic correlation matrices between traits, downloadable Manhattan plots and new associations table.
- </v-card-text>
-
- <v-card-text class="main-intro">
- Our databases have been curated and imputed using the python package <a href="https://gitlab.pasteur.fr/statistical-genetics/jass_preprocessing">JASS preprocessing</a> (data QC and harmonization) and <a href="https://gitlab.pasteur.fr/statistical-genetics/raiss">RAISS</a> (imputation of summary statistics). To conduct multi-trait GWAS on your own data refers to the <a href="https://statistical-genetics.pages.pasteur.fr/jass/">JASS python package documentation</a>. A Nextflow pipeline encapsulating summary statistic curation, imputation, and multi-trait GWAS is available <a href="https://gitlab.pasteur.fr/statistical-genetics/jass_suite_pipeline">here</a>.
- </v-card-text>
- </v-col>
- </v-row>
-
- <v-row dense>
- <AnalysisCard
- v-for="analysis in analyses"
- :key="analysis.title"
- :title="analysis.title"
- :description="analysis.description"
- :short-btn="analysis.shortBtn"
- :short-desc="analysis.shortDesc"
- :link="analysis.link"
- :my-style="analysis.myStyle"
- :my-class="analysis.myClass"
- :my-img="analysis.myImg" />
- </v-row>
-
- <v-row>
- <v-col id="team" cols="10" offset="1" md="8" offset-md="2">
- <h2>Team</h2>
- <p>
- Jass is developed at Institut Pasteur by the
- <a href="https://research.pasteur.fr/en/team/statistical-genetics/">Statistical Genetics group</a>
- and the
- <a href="https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/">Biostatistic and Bioinformatic HUB</a>
- </p>
- <p>
- <a href="https://research.pasteur.fr/en/team/statistical-genetics/"> The Statistical Genetics unit</a>, lead by Hugues Aschard, is interested in developping new methods to analyze GWAS data. In particular, in JASS, we leverage publicly available GWAS results to discover new signals and understand pleiotropy. While our team focus mainly on developping the theory behind the tools, we also aim to make our software widely available and to follow high quality software development standards. Hence, our close collaboration with the hub and more specifically with its WINTER group dedicated to web developement. <a href="https://research.pasteur.fr/en/team/hub-winter/">The WINTER group</a> is a software development team focusing mainly on Web technologies for publishing and sharing scientific tools, analysis, data and workflows. We work hand in hand to develop JASS website.
- </p>
- </v-col>
- </v-row>
- </div>
-</template>
-
-<script>
-import { mapGetters } from 'vuex'
-import AnalysisCard from "@/components/AnalysisCard.vue"
-
-export default {
- components: {
- AnalysisCard
- },
- data() {
- return {
- analyses: [
- {
- title: 'Genome wide Analysis',
- description: 'Run JASS on a set of phenotypes genome wide, explore result interactively and download results summary or full genome wide results. Can take up to ~30 to run depending on the number of trait selected.',
- shortBtn: 'Browse Genome Wide Analysis',
- shortDesc: 'Run Analysis',
- link: '/gwas',
- myStyle: {
- backgroundColor: '#2D96FA',
- },
- myImg: '/jass19Avrilsmall.jpg'
- }
- ]
- }
- },
- computed: {
- ...mapGetters([
- 'getTotalTables',
- 'getTotalPhenotypes',
- 'getTotalSNP'
- ])
- }
-}
-</script>
-
-<style>
-#team {
- background-color: #f8f8f8;
- margin: 1em auto;
- text-align: center;
-}
-</style>
diff --git a/client/pages/projects/_id.vue b/client/pages/projects/_id.vue
deleted file mode 100644
index 65d5331f376c0703e70abdca3ce433d8d8ae11a9..0000000000000000000000000000000000000000
--- a/client/pages/projects/_id.vue
+++ /dev/null
@@ -1,458 +0,0 @@
-<template>
- <v-container>
- <v-row v-show="!isready"
- class="fill-height"
- align-content="center"
- justify="center">
- <v-col
- class="text-subtitle-1 text-center"
- cols="12">
- <h2>Creating the worktable ! It might take a few minutes </h2>
- </v-col>
- <v-col
- class="text-subtitle-1 text-center"
- cols="12">
- <PhenotypeCard v-for="pheno in phenotypesDict" :key="pheno.id" :phe="pheno" />
- </v-col>
- <v-col cols="12" md="8" lg="6">
- <v-progress-linear
- color="#298e49"
- striped
- rounded
- height="20"
- :value="progress">
- <strong style="color:white; text-transform:capitalize;">{{ progress }} %</strong>
- </v-progress-linear>
- </v-col>
- </v-row>
- <v-row v-show="isready" align="center">
- <v-col cols="12">
- <v-card>
- <ShareLink :page-url="sharedUrl" style="top:-1em" />
- <div class="row" style="text-align:left;padding:12px;margin:0;">
- <h1 style="text-transform:none;">Results for :</h1>
- <PhenotypeCard v-for="pheno in phenotypesDict" :key="pheno.id" :phe="pheno" />
- </div>
- </v-card>
- <v-card style="margin-top:10px; margin-bottom:10px;" outlined tile no-gutter>
- <v-card-title class="text-h5">
- <v-row justify="start" no-gutters>
- <v-col>
- <h4>ANALYSIS PARAMETER SUMMARY</h4>
- <br>
- <b>Number of phenotype included:</b> {{ phenotypes.length }}
- <br>
- <b>Number of SNPs included:</b> {{ metadata.nb_snps }}
- <br>
- <b>Genomic region analyzed:</b> Whole Genome
- <br>
- <b>Test performed:</b> Omnibus
- </v-col>
- <v-col>
- <v-card style="padding:16px">
- Genetic covariance derived with <a href="https://www.nature.com/articles/ng.3406">the LDScore</a>
- The value on the diagonal correspond to the heritability of the trait.
- <div v-if="gencov && 'error' in gencov">
- <v-icon style="margin-top: -8px;" color="error">mdi-alert-octagon</v-icon>
- Computation failure: <v-card-text style="white-space: pre;">{{ gencov.error }}</v-card-text>
- </div>
- <div v-else id="divCorrelationHeat" ref="divCorrelationHeat"><!-- Plotly chart will be drawn inside this DIV --></div>
- </v-card>
- </v-col>
- </v-row>
- </v-card-title>
- </v-card>
-
-
- <v-card style="margin-top:10px; margin-bottom:10px;" outlined tile no-gutter>
- <v-card-title class="text-h5">
- <v-row justify="start" no-gutters>
- <v-col>
- <h4>RESULTS SUMMARY</h4>
- <b>Univariate and multivariate significant regions:</b> <br>
- Not significant Regions: {{ summary.JASSNotSignif.MinUnivNotSignif }}<br>
- Univariate only significant Regions: {{ summary.JASSNotSignif.MinUnivSignif }}<br>
- Multivariate only significant Regions : {{ summary.JASSSignif.MinUnivNotSignif }}<br>
- Univariate and multivariate significant Regions : {{ summary.JASSSignif.MinUnivSignif }}<br>
- </v-col>
-
- <v-col>
- <vue-json-to-csv :json-data="Regions" :csv-title="'LD-independent lead SNPs - ' + project.id">
- <v-btn small color="#298e49" style="color:#fff; text-transform:capitalize;" @click="processExportAllJASSPVAL()">
- Export LD-independent lead SNPs
- </v-btn>
- </vue-json-to-csv>
- <v-btn
- :disabled="status.genome_full_csv != 'READY'"
- small
- color="#298e49"
- style="color:#fff;text-transform:capitalize;"
- @click="genomeFullCsv()">
- Export genome wide summary statistics
- <v-progress-circular
- v-if="status.genome_full_csv != 'READY'"
- :size="15"
- :width="2"
- style="margin-left:5px"
- indeterminate></v-progress-circular>
- </v-btn>
- <v-btn
- :disabled="status.global_manhattan != 'READY'"
- small
- color="#298e49" style="color:#fff;text-transform:capitalize;"
- @click="manhattanPlot()">
- Manhattan Plot
- <v-progress-circular
- v-if="status.global_manhattan != 'READY'"
- :size="15"
- :width="2"
- style="margin-left:5px"
- indeterminate></v-progress-circular>
- </v-btn>
- <v-btn
- :disabled="status.quadrant_plot != 'READY'"
- small color="#298e49" style="color:#fff;text-transform:capitalize;"
- @click="quadranPlot()">
- Quadrant plot
- <v-progress-circular
- v-if="status.quadrant_plot != 'READY'"
- :size="15"
- :width="2"
- style="margin-left:5px"
- indeterminate></v-progress-circular>
- </v-btn>
- <v-btn
- :disabled="status.qq_plot != 'READY'"
- small color="#298e49" style="color:#fff;text-transform:capitalize;"
- @click="qqPlot()">
- QQ plot
- <v-progress-circular
- v-if="status.qq_plot != 'READY'"
- :size="15"
- :width="2"
- style="margin-left:5px"
- indeterminate></v-progress-circular>
- </v-btn>
- <p>Tips : You can share the link of this page with your collaborators. They will have access to the same results.</p>
- </v-col>
- </v-row>
- </v-card-title>
- </v-card>
-
- <v-card style="margin-top:10px; margin-bottom:10px;" outlined tile no-gutter>
- <v-card-title class="text-h5">
-
- <v-row justify="start" no-gutters>
- <v-col>
- <h4>MANATHAN PLOT</h4>
- <p>
- The Omnibus test Manhattan plot by Linkage Desiquilibrium independent regions.
- The p-values displayed corresponds to the p-value of the lead SNPs in the region.
- To zoom in on a region click on one of the points.
- </p>
- <div id="divWholeStatPlot" ref="divWholeStatPlot"><!-- Plotly chart will be drawn inside this DIV --></div>
- </v-col>
-
- </v-row>
- <v-btn small color="#298e49" style="color:#fff;text-transform:capitalize;" @click="show = !show; processShowGJASSPVAL()">
- Show significant lead SNPs by region
- </v-btn>
- <div>
- <transition name="slide-fade">
- <p v-if="show">
- <v-data-table
- :headers="headers"
- :items="significantsRegions"
- :items-per-page="5"
- class="elevation-1"></v-data-table>
- <vue-json-to-csv :json-data="significantsRegions" :csv-title="'Significants regions - ' + project.id">
- <v-btn small color="#298e49" style="color:#fff;">export csv</v-btn>
- </vue-json-to-csv>
- </p>
- </transition>
- </div>
- </v-card-title>
- </v-card>
-
- <v-card v-show="isready2" style="margin-top:10px; margin-bottom:10px;padding:20px;" outlined tile no-gutter>
- <v-row justify="start" no-gutters>
- <v-col>
- <h4 style="text-transform:uppercase;">Omnibus test Manhattan plot by SNPs</h4>
- <p>Zoom in on rejoin by clicking and draging your mouse on the region of interest</p>
- <p>Zoom out by double clicking on the plot</p>
- </v-col>
-
- </v-row>
- <div id="divLocalStatPlot" ref="divLocalStatPlot"><!-- Plotly chart will be drawn inside this DIV --></div>
- <div id="divHeatPlot"><!-- Plotly chart will be drawn inside this DIV --></div>
- </v-card>
- </v-col>
- </v-row>
- <v-row>
-
- </v-row>
- </v-container>
-</template>
-
-<script>
-import VueJsonToCsv from 'vue-json-to-csv';
-import Plotly from 'plotly.js-dist';
-import PhenotypeCard from "@/components/PhenotypeCard.vue";
-import ShareLink from "@/components/ShareLink.vue";
-import manhattan from "../../components/Manhattan.js";
-import heatmap from "../../components/Heatmap.js";
-import submanhattan from "../../components/SubManhattan.js";
-
-const _ = require('lodash');
-const d3 = require("d3");
-
-export default {
- components: {
- VueJsonToCsv,
- PhenotypeCard
- },
- async asyncData({ $axios, params, $auth }) {
- const project = await $axios.$get('/projects/' + params.id,)
- console.log(project);
- const phenotypes = [];
- const outcomes = [];
-
- project.phenotypes.forEach(pheno => {
- phenotypes.push(pheno.id);
- })
-
- project.phenotypes.forEach(pheno => {
- outcomes.push(pheno.outcome);
- })
-
- const phenotypesDict = project.phenotypes;
-
- return {
- project,
- phenotypes,
- outcomes,
- phenotypesDict,
- ShareLink
- }
- },
- data() {
- return {
- phenotypes: null,
- phenotypesDict: null,
- project: null,
- manhattan: null,
- heatmap: null,
- submanhattan: null,
- headers: [],
- significantsRegions: [],
- Regions: [],
- show: false,
- status: null,
- isready: false,
- isready2: false,
- progress: 0,
- gencov: null,
- metadata: { "nb_phenotypes": 0, "nb_snps": 0 },
- summary: {
- "JASSSignif": {
- "MinUnivNotSignif": 0,
- "MinUnivSignif": 0
- },
- "JASSNotSignif": {
- "MinUnivNotSignif": 0,
- "MinUnivSignif": 0
- }
- },
- sharedUrl: ''
- }
- },
- created() {
- this.status = this.getStatus();
- },
- methods: {
- createPlots() {
- const zLine = [];
- const x = this.outcomes.sort();
-
- for (let i = 0; i < x.length; i++) {
- zLine.push([]);
-
- for (let j = 0; j < (this.gencov.length); j++) {
- if (x[i] === this.gencov[j].phenotypeID_A) {
- zLine[i].push(this.gencov[j].gencov);
- }
- }
- const NantoAdd = x.length - zLine[i].length;
-
- for (let j = 0; j < NantoAdd; j++) {
- zLine[i].unshift(NaN);
- }
- }
-
- const dataplot = [
- {
- z: zLine,
- x,
- y: x,
- type: 'heatmap',
- colorscale: [['-1', '#4A6FE3'],
- ['-0.9', '#5F7BE1'],
- ['-0.8', '#7086E1'],
- ['-0.7', '#8091E1'],
- ['-0.6', '#8F9DE1'],
- ['-0.5', '#9DA8E2'],
- ['-0.4', '#ABB4E2'],
- ['-0.3', '#B9BFE3'],
- ['-0.2', '#C7CBE3'],
- ['-0.1', '#D5D7E3'],
- ['0', '#E2E2E2'],
- ['0.1', '#E4D3D6'], ['0.2', '#E6C4C9'],
- ['0.3', '#E6B4BD'], ['0.4', '#E5A5B1'],
- ['0.5', '#E495A5'], ['0.6', '#E28699'],
- ['0.7', '#DF758D'], ['0.8', '#DB6581'],
- ['0.9', '#D75376'], ['1', '#D33F6A']]
- }
- ];
-
- const layout = {
- width: 400,
- margin: { l: 100, r: 100, t: 10, b: 80 },
- xaxis: {
- showgrid: false
- },
- yaxis: {
- showgrid: false,
- showline: true
- }
- };
-
- this.manhattan = manhattan;
- this.heatmap = heatmap;
- this.submanhattan = submanhattan;
-
- manhattan.makePlot(this);
- Plotly.newPlot('divCorrelationHeat', dataplot, layout, { displayModeBar: false });
- },
- createHeatmapPlot() {
- Plotly.newPlot('divWholeStatPlot', manhattan.data.data, manhattan.data.layout);
-
- this.$refs.divWholeStatPlot.on('plotly_click', function (data) {
- manhattan.reactOnClick(data);
- Plotly.update('divWholeStatPlot', manhattan.data.layout);
- });
-
- },
- quadranPlot() {
- const desiredLink = process.env.API_URL + "/projects/" + this.project.id + "/quadrant";
- window.open(desiredLink, '_blank');
- },
- qqPlot() {
- const desiredLink = process.env.API_URL + "/projects/" + this.project.id + "/qqplot";
- window.open(desiredLink, '_blank');
- },
- manhattanPlot() {
- const desiredLink = process.env.API_URL + "/projects/" + this.project.id + "/globalmanhattan";
- window.open(desiredLink, '_blank');
- },
- genomeFullCsv() {
- const desiredLink = process.env.API_URL + "/projects/" + this.project.id + "/genome_full";
- window.open(desiredLink, '_blank');
- },
- processShowGJASSPVAL() {
- this.headers = [{ text: 'CHR', value: 'CHR' },
- { text: 'JOSTmin', value: 'JOSTmin' },
- { text: 'MiddlePosition', value: 'MiddlePosition' },
- { text: 'PVALmin', value: 'PVALmin' },
- { text: 'Region', value: 'Region' },
- { text: 'signif_status', value: 'signif_status' },
- { text: 'snp_ids', value: 'snp_ids' }];
- this.significantsRegions = this.manhattan.data.datarows.filter(function (obj) {
- return obj.signif_status === 'Joint';
- });
- },
- processExportAllJASSPVAL() {
- this.headers = [{ text: 'CHR', value: 'CHR' },
- { text: 'JOSTmin', value: 'JOSTmin' },
- { text: 'MiddlePosition', value: 'MiddlePosition' },
- { text: 'PVALmin', value: 'PVALmin' },
- { text: 'Region', value: 'Region' },
- { text: 'signif_status', value: 'signif_status' },
- { text: 'snp_ids', value: 'snp_ids' }];
- this.Regions = this.manhattan.data.datarows
- },
-
- async getStatus() {
- await this.$axios.$get('/projects/' + this.project.id).then((async function (result) {
- this.progress = result.progress;
- this.sharedUrl = "http://" + window.location.host + "/projects/" + this.project.id;
- this.status = result.status;
-
- if (result.status.metadata === "READY" && !this.isready) {
- await this.$axios.$get('/projects/' + this.project.id + "/gencov").then((async function (result2) {
- this.gencov = result2;
- await this.$axios.$get('/projects/' + this.project.id + "/summary").then((function (result3) {
-
- this.summary = result3;
- this.isready = true;
-
- this.createPlots();
- }).bind(this));
-
- await this.$axios.$get('/projects/' + this.project.id + "/metadata").then((function (result4) {
- this.metadata = result4;
- }).bind(this));
- }).bind(this)).catch(error => {
- this.gencov = { 'error': error.response.data.detail }
- this.isready = true;
- });
- }
-
- let keepFetching = true;
-
- for (const step in result.status) {
- if (result.status[step] !== "READY") {
- keepFetching = true
- break;
- } else {
- keepFetching = false;
- }
- }
-
- if (keepFetching) {
- setTimeout(this.getStatus, 5000);
- }
- }).bind(this)).catch((function () {
- setTimeout(this.getStatus, 10000);
- }).bind(this));
- }
- }
-}
-</script>
-
-<style>
-.fade-enter-active,
-.fade-leave-active {
- transition: opacity .5s;
-}
-
-.fade-enter,
-.fade-leave-to {
- /* .fade-leave-active below version 2.1.8 */
- opacity: 0;
-}
-
-.slide-fade-enter-active {
- transition: all .3s ease;
-}
-
-.slide-fade-leave-active {
- transition: all .8s cubic-bezier(1.0, 0.5, 0.8, 1.0);
-}
-
-.slide-fade-enter,
-.slide-fade-leave-to {
- /* .slide-fade-leave-active below version 2.1.8 */
- transform: translateX(10px);
- opacity: 0;
-}
-</style>
diff --git a/client/pages/workload.vue b/client/pages/workload.vue
deleted file mode 100644
index 5adda2bdd1db766a5c65d9e75dea94a3539c553b..0000000000000000000000000000000000000000
--- a/client/pages/workload.vue
+++ /dev/null
@@ -1,87 +0,0 @@
-<template>
- <v-row>
- <v-col cols=12 style="text-align:center">
- <h1>Server workload</h1>
- </v-col>
-
- <v-col cols=12>
- <v-row>
- <v-col cols=6 style="text-align:right">
- <h4>Compute node:</h4>
- </v-col>
- <v-col cols=6>
- <h4>{{ worker }}</h4>
- </v-col>
- </v-row>
- </v-col>
-
- <v-col cols=12>
- <v-row>
- <v-col cols=6 style="text-align:right">
- <h4>Tasks being processed:</h4>
- </v-col>
- <v-col cols=6>
- <h4>{{ activeTask }}</h4>
- </v-col>
- </v-row>
- </v-col>
-
- <v-col cols=12>
- <v-row>
- <v-col cols=6 style="text-align:right">
- <h4>Pending tasks to be computed</h4>
- </v-col>
- <v-col cols=6>
- <h4>{{ pendingTask }}</h4>
- </v-col>
- </v-row>
- </v-col>
-
- <v-col
- v-if="activeTask === 0"
- style="text-align:center"
- cols=12>
- Your analysis would start right away.
- </v-col>
-
- <v-col
- v-else-if="activeTask > 0"
- style="text-align:center"
- cols=12>
- Your analysis would be queued, and processed as soon as possible.
- </v-col>
-
- <v-col
- v-else
- cols=12>
-
- </v-col>
- </v-row>
-</template>
-
-<script>
-export default {
- data() {
- return {
- activeTask: '_',
- pendingTask: '_',
- worker: '_',
- }
- },
- created() {
- this.getQueueStatus();
- },
- methods: {
- async getQueueStatus() {
- await this.$axios.$get('/queue_status').then((function (resultStatus) {
- this.activeTask = resultStatus.active;
- this.worker = resultStatus.worker;
- this.pendingTask = resultStatus.reserved;
- setTimeout(this.getQueueStatus, 5000);
- }).bind(this)).catch((function () {
- setTimeout(this.getQueueStatus, 10000);
- }).bind(this));
- },
- }
-}
-</script>
diff --git a/client/plugins/sanitizedHtml.js b/client/plugins/sanitizedHtml.js
deleted file mode 100644
index 408c4e3e775339322850fe643803fd6bfec76998..0000000000000000000000000000000000000000
--- a/client/plugins/sanitizedHtml.js
+++ /dev/null
@@ -1,12 +0,0 @@
-import Vue from 'vue'
-import DOMPurify from 'dompurify'
-
-/**
- * Use DOMpurify to sanitize html or markdown strings.
- * This directive should be used instead of the native v-html.
- */
-Vue.directive('sanitized-html', {
- bind: (el, binding) => {
- el.innerHTML = DOMPurify.sanitize(binding.value)
- },
-})
diff --git a/client/static/favicon.ico b/client/static/favicon.ico
deleted file mode 100644
index 301d7859c1af09d1847a7dcbaefdc718e3bcae7e..0000000000000000000000000000000000000000
Binary files a/client/static/favicon.ico and /dev/null differ
diff --git a/client/static/institut_pasteur_logo_2020.png b/client/static/institut_pasteur_logo_2020.png
deleted file mode 100644
index 4a8ed2bc5f2c226b7cf1b54f47b53668de55d392..0000000000000000000000000000000000000000
Binary files a/client/static/institut_pasteur_logo_2020.png and /dev/null differ
diff --git a/client/static/jass19Avrilsmall.jpg b/client/static/jass19Avrilsmall.jpg
deleted file mode 100644
index 9ab7240b257493e8980a295dcbdbcab22c4f2bef..0000000000000000000000000000000000000000
Binary files a/client/static/jass19Avrilsmall.jpg and /dev/null differ
diff --git a/client/static/pasteur-img.png b/client/static/pasteur-img.png
deleted file mode 100644
index 0dcf83deb21a4c6b411fd044bf5712b1a41b4aa6..0000000000000000000000000000000000000000
Binary files a/client/static/pasteur-img.png and /dev/null differ
diff --git a/client/store/index.js b/client/store/index.js
deleted file mode 100644
index bc36da1ca1f0ef7b8905314a05bce736fbfeaa47..0000000000000000000000000000000000000000
--- a/client/store/index.js
+++ /dev/null
@@ -1,62 +0,0 @@
-// Main store for getting and sharing initTables data
-// across components.
-// https://v2.nuxt.com/docs/directory-structure/store
-
-const _ = require('lodash');
-
-export const state = () => ({
- initTables: {}
-})
-
-export const getters = {
- getTotalTables(state) {
- return Object.keys(state.initTables).length
- },
- getTotalPhenotypes(state) {
- return Object.values(state.initTables).reduce((total, table) => {
- if (typeof (table.nb_phenotypes) === 'number') {
- return total + table.nb_phenotypes
- } else {
- return total
- }
- }, 0)
- },
- getTotalSNP(state) {
- return Object.values(state.initTables).reduce((total, table) => {
- if (typeof (table.nb_snps) === 'number') {
- return total + table.nb_snps
- } else {
- return total
- }
- }, 0)
- },
-}
-
-export const mutations = {
- setInitTables(state, initTables) {
- state.initTables = initTables
- }
-}
-
-export const actions = {
- async fetchTables({ commit }) {
- const initTables = []
-
- return await this.$axios.$get('/tables')
- .then((initTableslist) => {
- const initMetaRequests = initTableslist.map(initTableName => {
- return this.$axios
- .$post('/initmeta', { initTableName })
- .then(initMeta => {
- initMeta.tableName = initTableName
- initTables.push(initMeta)
- })
- })
-
- return Promise.all(initMetaRequests)
- })
- .then(() => {
- commit('setInitTables', _.orderBy(initTables, 'name'))
- })
- }
-}
diff --git a/client/stylelint.config.js b/client/stylelint.config.js
deleted file mode 100644
index 9dba5e33b2975252b6ab90667f823deb37a5b009..0000000000000000000000000000000000000000
--- a/client/stylelint.config.js
+++ /dev/null
@@ -1,9 +0,0 @@
-module.exports = {
- extends: [
- 'stylelint-config-standard',
- 'stylelint-config-prettier'
- ],
- // add your custom config here
- // https://stylelint.io/user-guide/configuration
- rules: {}
-}
diff --git a/client/yarn.lock b/client/yarn.lock
deleted file mode 100644
index c6166e2c25e28bfe8c53ba17c3b00cd04a24d786..0000000000000000000000000000000000000000
--- a/client/yarn.lock
+++ /dev/null
@@ -1,10775 +0,0 @@
-# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
-# yarn lockfile v1
-
-
-"@ampproject/remapping@^2.2.0":
- version "2.2.1"
- resolved "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.1.tgz"
- integrity sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg==
- dependencies:
- "@jridgewell/gen-mapping" "^0.3.0"
- "@jridgewell/trace-mapping" "^0.3.9"
-
-"@babel/code-frame@7.12.11":
- version "7.12.11"
- resolved "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.12.11.tgz"
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- dependencies:
- "@babel/highlight" "^7.10.4"
-
-"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.22.13", "@babel/code-frame@^7.23.5":
- version "7.23.5"
- resolved "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.5.tgz"
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- dependencies:
- "@babel/highlight" "^7.23.4"
- chalk "^2.4.2"
-
-"@babel/compat-data@^7.22.6", "@babel/compat-data@^7.23.3", "@babel/compat-data@^7.23.5":
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-
-"@babel/core@>=7.9.0", "@babel/core@^7.12.16", "@babel/core@^7.23.7":
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- dependencies:
- "@ampproject/remapping" "^2.2.0"
- "@babel/code-frame" "^7.23.5"
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- debug "^4.1.0"
- gensync "^1.0.0-beta.2"
- json5 "^2.2.3"
- semver "^6.3.1"
-
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- dependencies:
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- eslint-visitor-keys "^2.1.0"
- semver "^6.3.1"
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- dependencies:
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- graceful-fs "^4.1.2"
- make-dir "^1.0.0"
- pify "^3.0.0"
- sort-keys "^2.0.0"
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- version "20.2.9"
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-
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- version "0.1.0"
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-
-zwitch@^1.0.0:
- version "1.0.5"
- resolved "https://registry.npmjs.org/zwitch/-/zwitch-1.0.5.tgz"
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diff --git a/docker-compose.test.yaml b/docker-compose.test.yaml
deleted file mode 100644
index 8c30f7691ce6711638fcb243144b7bca8b13d7ca..0000000000000000000000000000000000000000
--- a/docker-compose.test.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-version: '3.4'
-services:
- celery:
- volumes:
- - ./jass/test/data_real:/data
- back:
- volumes:
- - ./jass/test/data_real:/data
\ No newline at end of file
diff --git a/docker-compose.yaml b/docker-compose.yaml
deleted file mode 100644
index 69f2b02235cd7d6dcda38b205af546fa3d3ddccd..0000000000000000000000000000000000000000
--- a/docker-compose.yaml
+++ /dev/null
@@ -1,67 +0,0 @@
-version: '3.4'
-services:
- rabbitmq:
- image: rabbitmq:3-alpine
- healthcheck:
- test: ['CMD', 'rabbitmqctl', 'status']
- interval: 30s
- timeout: 15s
- retries: 3
- volumes:
- - ./chart/rabbitmq.conf:/etc/rabbitmq/conf.d/20-jass.conf
- ports:
- - '5672:5672'
- celery:
- build:
- context: .
- image: jass
- # dirty command below waits a little bit for rabbitmq to be
- # up and running before starting celery
- command: ['/bin/sh', '-c', 'sleep 10 && watchmedo auto-restart --directory=/code --pattern=*.py --recursive -- celery -A jass worker --concurrency=1 --max-tasks-per-child=1']
- environment:
- #LC_ALL: en_US.utf-8
- RABBITMQ_HOST: 'rabbitmq'
- WAIT_FOR_DATA_DIR_READY: 1
- volumes:
- - ./projects:/projects
- - ./data:/data
- - ./jass:/code/jass
- depends_on:
- - rabbitmq
- restart: on-failure
- back:
- build:
- context: .
- command: ['watchmedo', 'auto-restart', '--directory=/code', '--pattern=*.py', '--recursive', '--', 'uvicorn', 'jass.server:app', '--host', '0.0.0.0', '--reload', '--port', '8080']
- environment:
- RABBITMQ_HOST: 'rabbitmq'
- volumes:
- - ./projects:/projects
- - ./data:/data
- - ./jass:/code/jass
- ports:
- - '8080:8080'
- depends_on:
- - rabbitmq
- - celery
- front:
- build:
- context: client
- target: client-base-container
- command: /bin/sh -c "yarn install && yarn dev"
- environment:
- HOST: 0.0.0.0
- NODE_ENV: development
-# API_URL: http://172.19.0.1:8000/api
- volumes:
- - ./client:/client
- ports:
- - '3000:3000'
- front-static:
- build:
- context: client
- target: client-static-serve
-# args:
-# API_URL: http://0.0.0.0:8000/api
- ports:
- - '3001:8080'
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
deleted file mode 100644
index a0aa4ac3c8fca432539f876b88042c73ff2e626c..0000000000000000000000000000000000000000
--- a/docker-entrypoint.sh
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/bin/bash
-
-function msg_info {
- echo -e "\033[1;32m$1\033[0m"
-}
-
-function msg_warning {
- echo -e "\033[1;33m$1\033[0m"
-}
-
-function msg_error {
- echo -e "\033[1;31m$1\033[0m"
-}
-
-cd /code
-
-if [ "$1" == "hold_on" ]; then
- msg_info "holding on util you delete /tmp/hold_on"
- touch /tmp/hold_on
- while [ -e "/tmp/hold_on" ]; do
- sleep 1 ;
- echo "holding on" ;
- done
-fi
-
-#if [ "${WAIT_FOR_DATA_DIR_READY}" == "1" ]; then
-# while [ ! -f ${DATA_DIR_READY} ]; do
-# msg_info "Waiting for data dir ot flagged ready with ${DATA_DIR_READY}"
-# sleep 5
-# done
-#else
-# msg_info "Copying file from /code/data to ${JASS_DATA_DIR}"
-# rsync -a /code/data/ ${JASS_DATA_DIR}/
-# export INIT_TABLE_PATH="${JASS_DATA_DIR}/initTable.hdf5"
-# if [ ! -f ${INIT_TABLE_PATH} ]; then
-# msg_info "$INIT_TABLE_PATH missing, downloading it from $INIT_TABLE_URL"
-# wget "${INIT_TABLE_URL}" --output-document=${INIT_TABLE_PATH}
-# else
-# msg_info "$INIT_TABLE_PATH found"
-# fi
-# touch ${DATA_DIR_READY}
-#fi
-
-
-exec "$@"
diff --git a/jass/__init__.py b/jass/__init__.py
index f467725b00ccfe19f921fb8a6fa41d12cfafa082..1f1936152ef05f96cc5a43fe50a4c93359902bd4 100644
--- a/jass/__init__.py
+++ b/jass/__init__.py
@@ -14,4 +14,4 @@ Submodules
util
"""
-from jass.tasks import celery
+#from jass.tasks import celery
diff --git a/jass/__main__.py b/jass/__main__.py
index 39d030fd0ce8f30e592a1ec4170ac38684276795..888bcc2007ebb9ed68e80088c4a29ae5da8c81d6 100644
--- a/jass/__main__.py
+++ b/jass/__main__.py
@@ -77,16 +77,16 @@ def absolute_path_of_the_file(fileName, output_file=False):
return absoluteFilePath
-def serve(args):
- if not os.path.exists('client/dist'):
- print("Application cannot be served unless you build the client.")
- print("To do so, please run :")
- print(" cd client")
- print(" yarn install")
- print(" export BASE_PATH='/webui/'")
- print(" yarn generate")
- exit(1)
- uvicorn.run(app='jass.server:app', host=config["HOST"], port=int(config["PORT"]))
+# def serve(args):
+# if not os.path.exists('client/dist'):
+# print("Application cannot be served unless you build the client.")
+# print("To do so, please run :")
+# print(" cd client")
+# print(" yarn install")
+# print(" export BASE_PATH='/webui/'")
+# print(" yarn generate")
+# exit(1)
+# uvicorn.run(app='jass.server:app', host=config["HOST"], port=int(config["PORT"]))
def w_list_phenotypes(args):
@@ -297,8 +297,8 @@ def get_parser():
subparsers = parser.add_subparsers(dest="action")
subparsers.required = True
- parser_serve = subparsers.add_parser("serve", help="run JASS web server")
- parser_serve.set_defaults(func=serve)
+ # parser_serve = subparsers.add_parser("serve", help="run JASS web server")
+ # parser_serve.set_defaults(func=serve)
# ------- list-phenotypes -------
diff --git a/jass/celeryconfig.py b/jass/celeryconfig.py
deleted file mode 100644
index 4922de85e5d60e4d83e05209da88e9c6355402c1..0000000000000000000000000000000000000000
--- a/jass/celeryconfig.py
+++ /dev/null
@@ -1,26 +0,0 @@
-import os
-
-## Broker settings.
-# broker_url = os.getenv("JASS_RABBITMQ_URL", "amqp://guest:guest@localhost:5672//")
-from jass.config import config
-
-broker_url = "amqp://%(user)s:%(pwd)s@%(host)s:%(port)s//" % dict(
- user=os.getenv('RABBITMQ_USER', 'guest'),
- pwd=os.getenv('RABBITMQ_PASSWORD', 'guest'),
- host=os.getenv('RABBITMQ_HOST', 'localhost'),
- port=os.getenv('RABBITMQ_PORT', '5672'),
-)
-
-## Broker settings.
-# result_backend = os.getenv('JASS_RABBITMQ_URL','amqp://guest2:guest@localhost:5672//')
-# result_backend = "rpc://"
-result_backend = f'file://{config["CELERY_RESULTS_BACKEND_DIR"]}' # if rpc become not a solution
-# List of modules to import when the Celery worker starts.
-# imports = ('myapp.tasks',)
-
-## Using the database to store task state and results.
-# result_backend = 'db+sqlite:///results.db'
-
-# task_annotations = {'tasks.add': {'rate_limit': '10/s'}}
-# task_track_started = True
-task_acks_late = True # needed as worker can be killed by k8s when consuming to much RAM
diff --git a/jass/config.py b/jass/config.py
index 02e0478b7e520db4e16e003d850fdfb6666c3f52..1a2d3084fc0a05ca2dfccb32c00ca65c9220a079 100644
--- a/jass/config.py
+++ b/jass/config.py
@@ -17,8 +17,8 @@ with environment variables:
import os
config = {
- "HOST": "0.0.0.0",
- "PORT": "8080",
+ # "HOST": "0.0.0.0",
+ # "PORT": "8080",
"DATA_DIR": os.path.normpath(
os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "data")
),
@@ -28,16 +28,16 @@ config = {
"INITTABLE_CHUNKSIZE": 100000,
"MIN_SIZE_TO_KEEP_IN_PROJECTS_DIR_IN_MB": int(os.environ.get('MIN_SIZE_TO_KEEP_IN_PROJECTS_DIR_IN_MB', '0')),
}
-if "JASS_HOST" in os.environ:
- config["HOST"] = os.environ["JASS_HOST"]
-if "JASS_PORT" in os.environ:
- config["PORT"] = os.environ["JASS_PORT"]
+# if "JASS_HOST" in os.environ:
+# config["HOST"] = os.environ["JASS_HOST"]
+# if "JASS_PORT" in os.environ:
+# config["PORT"] = os.environ["JASS_PORT"]
if "JASS_DATA_DIR" in os.environ:
config["DATA_DIR"] = os.environ["JASS_DATA_DIR"]
if "JASS_PROJECTS_DIR" in os.environ:
config["PROJECTS_DIR"] = os.environ["JASS_PROJECTS_DIR"]
-config["CELERY_RESULTS_BACKEND_DIR"] = os.environ.get(
- "CELERY_RESULTS_BACKEND_DIR",
- os.path.join(config["PROJECTS_DIR"], "celery_results"),
-)
-os.makedirs(config["CELERY_RESULTS_BACKEND_DIR"], exist_ok=True)
\ No newline at end of file
+# config["CELERY_RESULTS_BACKEND_DIR"] = os.environ.get(
+# "CELERY_RESULTS_BACKEND_DIR",
+# os.path.join(config["PROJECTS_DIR"], "celery_results"),
+#)
+#os.makedirs(config["CELERY_RESULTS_BACKEND_DIR"], exist_ok=True)
\ No newline at end of file
diff --git a/jass/models/phenotype.py b/jass/models/phenotype.py
index d5074302e7c57605eae21e6f731261b72862c197..84b550255f7b30ffdca552bcac7394c2f8016c1e 100644
--- a/jass/models/phenotype.py
+++ b/jass/models/phenotype.py
@@ -5,7 +5,7 @@ import os
import pandas
from pydantic import BaseModel, validator
-from jass.config import config
+#from jass.config import config
from jass.models.inittable import valideInitTableNamePattern
diff --git a/jass/server.py b/jass/server.py
deleted file mode 100644
index d5ed5f36ea9fb89d6eb34ba97ae351ca4b92aa19..0000000000000000000000000000000000000000
--- a/jass/server.py
+++ /dev/null
@@ -1,358 +0,0 @@
-#!/usr/bin/env python3
-import logging
-import os
-import shutil
-import traceback
-from json import JSONDecodeError
-from pathlib import Path
-from typing import List
-
-from starlette.responses import RedirectResponse, JSONResponse
-from tables import HDF5ExtError
-
-from jass import util
-from jass.config import config
-from jass.models.phenotype import Phenotype, get_available_phenotypes, PhenotypeIdList, InitTableNameModel
-from jass.models.inittable import get_inittable_meta, valideInitTableNamePattern
-from jass.models.project import GlobalProject, load_project as project__load_project
-from jass.tasks import create_project, run_project_analysis_if_needed, get_queue_status
-
-from fastapi import FastAPI, HTTPException
-from fastapi.responses import Response, FileResponse
-from fastapi.middleware.cors import CORSMiddleware
-
-app = FastAPI()
-
-app.add_middleware(
- CORSMiddleware,
- allow_origins=["*"],
- allow_methods=["*"],
- allow_headers=["*"],
-)
-
-if os.path.exists('client/dist'):
- app.mount("/webui", util.SinglePageApplication(directory=Path('client/dist')), name="SPA")
-else:
- logging.info("/webui cannot be served as client/dist is missing, please build the client.")
-
-
-def load_project(project_id, *args, **kargs):
- try:
- return project__load_project(project_id=project_id, *args, **kargs)
- except FileNotFoundError:
- raise HTTPException(status_code=404, detail="Project not found")
- except JSONDecodeError as e:
- print(f"Project {project_id} has a corrupted meta.json ({str(e)}), removing it.")
- shutil.rmtree(GlobalProject.get_folder_path_from_id(project_id))
- raise HTTPException(status_code=404, detail="Project invalid, and removed")
-
-
-@app.get("/")
-async def read_index():
- return RedirectResponse(url="/webui/")
-
-
-@app.get("/api/tables", response_model=List[str])
-def inittable_list():
- """List initTables"""
- for filename in os.listdir(config["DATA_DIR"]):
- if (
- filename.endswith(".hdf5")
- and "worktable" not in filename.lower()
- and valideInitTableNamePattern.match(filename)
- ):
- yield filename
-
-
-@app.post("/api/phenotypes", response_model=List[Phenotype])
-def phenotypes_list(init_table_name: InitTableNameModel):
- """List phenotypes"""
- try:
- return get_available_phenotypes(init_table_name.get_init_table_path())
- except FileNotFoundError as e: # initTable does not exists
- raise HTTPException(status_code=404, detail=str(e))
-
-@app.post("/api/initmeta")
-def inittable_meta(init_table_name: InitTableNameModel):
- """Number of phenotype and SNPs"""
- return get_inittable_meta(init_table_name.get_init_table_path())
-
-
-@app.post("/api/projects", response_model=GlobalProject)
-def project_create(phenotype_id_list: PhenotypeIdList):
- return create_project(
- phenotype_id_list.phenotypeID,
- init_table_name=phenotype_id_list.initTableName,
- )
-
-
-@app.get("/api/projects/{project_id}", response_model=GlobalProject)
-def project_detail(project_id: str):
- project = load_project(project_id=project_id)
- run_project_analysis_if_needed(project)
- return project
-
-
-@app.get("/api/projects/{project_id}/progress", response_model = int )
-def project_detail(project_id: str):
- return load_project(project_id=project_id).progress
-
-
-@app.get("/api/projects/{project_id}/unload", response_model=bool)
-def project_detail(project_id: str):
- return load_project(project_id=project_id, flag_as_visited=False).delete_large_files()
-
-
-@app.get("/api/projects/{project_id}/summary")
-def project_detail(project_id: str):
- return load_project(project_id=project_id).get_project_summary_statistics()
-
-
-@app.get("/api/projects/{project_id}/gencov")
-def project_gencov_view(project_id: str):
- try:
- return util.JSONNumpyResponse(load_project(project_id=project_id).get_project_gencov())
- except ValueError as e: # NaN in values
- raise HTTPException(status_code=500, detail=str(e))
- except HDF5ExtError as e: # file corrupted
- raise HTTPException(status_code=500, detail=str(e))
- except Exception as e: # anything else
- traceback.print_exc()
- raise HTTPException(status_code=500, detail=str(e))
-
-
-@app.get("/api/projects/{project_id}/metadata")
-def project_metadata(project_id: str):
- return FileResponse(load_project(project_id=project_id).get_metadata_file_path())
-
-
-@app.get("/api/projects/{project_id}/globalmanhattan")
-def project_get_manhattan(project_id: str):
- return FileResponse(
- load_project(project_id=project_id).get_global_manhattan_plot_path(),
- media_type="image/png",
- )
-
-
-@app.get("/api/projects/{project_id}/quadrant")
-def project_get_quadrant(project_id: str):
- return FileResponse(
- load_project(project_id=project_id).get_quadrant_plot_path(),
- media_type="image/png",
- )
-
-
-@app.get("/api/projects/{project_id}/qqplot")
-def project_get_qq_plot(project_id: str):
- return FileResponse(
- load_project(project_id=project_id).get_qq_plot_path(),
- media_type="image/png",
- )
-
-
-@app.get("/api/projects/{project_id}/genome_full")
-def get_full_sumstat(project_id: str):
- project = load_project(project_id=project_id)
- if not os.path.exists(project.get_csv_path()):
- print("CREATING CSV FILE")
- project.create_csv_file()
- print("CREATED CSV FILE")
- return FileResponse(
- project.get_csv_path(),
- filename=f"genome_full_{project_id}.csv",
- media_type="text/csv",
- )
-
-
-@app.get("/api/projects/{project_id}/genome")
-def get_data_manhattan(project_id: str):
- return Response(
- content=load_project(project_id=project_id).get_project_genomedata(),
- media_type="text/csv",
- headers={"content-disposition": f"attachment; filename=genome_{project_id}.csv"},
- )
-
-
-@app.get("/api/projects/{project_id}/heatmap/{selected_chr}/{selected_region}")
-def get_heatmap(project_id: str, selected_chr: str, selected_region: str):
- print("CHR")
- print(selected_chr)
- print("Region")
- print(selected_region)
- return Response(
- load_project(project_id=project_id).get_project_local_heatmap_data(
- chromosome=selected_chr,
- region=selected_region,
- ),
- media_type="text/csv; charset=utf-8",
- )
-
-
-@app.get("/api/projects/{project_id}/manhattan/{selected_chr}/{selected_region}")
-def get_manhattan(project_id: str, selected_chr: str, selected_region: str):
- return Response(
- load_project(project_id=project_id).get_project_local_manhattan_data(
- chromosome=selected_chr,
- region=selected_region,
- ),
- media_type="text/csv; charset=utf-8",
- )
-
-
-@app.get("/api/queue_status")
-def queue_status():
- return JSONResponse(get_queue_status())
-
-
-
-
-# @blp_inittable.route("")
-# class InitMetaMethodView(MethodView):
-# @blp_inittable.response(200, InittableMetaSchema())
-# def get(self):
-# """Number of phenotype and SNPs"""
-# return get_inittable_meta(os.path.join(config["DATA_DIR"], "initTable.hdf5"))
-
-# @blp_projects.route("")
-# class ProjectCreateMethodView(MethodView):
-# @blp_projects.arguments(ProjectParamsSchema(), location="form")
-# @blp_projects.response(200, ProjectSchema())
-# def post(self, parameters):
-# """List projects"""
-# phenotype_ids = [
-# phenotype_id
-# for ids_with_commas in parameters["phenotypeID"]
-# for phenotype_id in ids_with_commas.split(",")
-# ]
-# phenotypes = list(filter(lambda d: d.id in phenotype_ids, get_phenotypes()))
-# return create_project([p.id for p in phenotypes], get_phenotypes())
-
-
-# @blp_local_projects.route("")
-# class LocalProjectCreateMethodView(MethodView):
-# @blp_projects.arguments(LocalProjectParamsSchema(), location="form")
-# @blp_projects.response(200, ProjectSchema())
-# def post(self, parameters):
-# """List projects"""
-# phenotype_ids = [
-# phenotype_id
-# for ids_with_commas in parameters["phenotypeID"]
-# for phenotype_id in ids_with_commas.split(",")
-# ]
-# phenotypes = list(filter(lambda d: d.id in phenotype_ids, get_phenotypes()))
-# return create_project(
-# [p.id for p in phenotypes],
-# get_phenotypes(),
-# str(parameters["chromosome"]),
-# str(parameters["start"]),
-# str(parameters["end"]),
-# )
-
-
-# @blp_projects.route("/<project_id>")
-# class ProjectDetailMethodView(MethodView):
-# @blp_projects.response(200, ProjectSchema())
-# def get(self, project_id):
-# return load_project(project_id=project_id)
-
-
-# @blp_projects.route("/<project_id>/csv_status")
-# class ProjectCSVStatusMethodView(MethodView):
-# def get(self, project_id):
-# return load_project(project_id=project_id).get_csv_file_generation()
-
-
-
-
-
-
-
-
-
-
-
-
-# @blp_projects.route("/<project_id>/zoom_manhattan")
-# class ProjectZoomManhattanMethodView(MethodView):
-# def get(self, project_id):
-# try:
-# return (
-# load_project(project_id=project_id).get_project_local_manhattan_data(),
-# 200,
-# {"Content-Type": "text/plain; charset=utf-8"},
-# )
-# except FileNotFoundError:
-# status = Project(id=project_id).status
-# # if status == Project.DOES_NOT_EXIST:
-# # return (
-# # f"project {project_id} does not exist",
-# # 404,
-# # {"Content-Type": "text/plain; charset=utf-8"},
-# # )
-# # elif status["worktable"] == Project.CREATING:
-# # return (
-# # "data not ready yet",
-# # 202,
-# # {"Content-Type": "text/plain; charset=utf-8"},
-# # )
-# # else:
-# # abort(500)
-
-
-
-# @blp_projects.route("/<project_id>/zoomplot")
-# class ProjectZoomPlotMethodView(MethodView):
-# def get(self, project_id):
-# try:
-# return send_file(
-# load_project(project_id=project_id).get_zoom_plot_path(), mimetype="image/png"
-# )
-# except FileNotFoundError:
-# status = load_project(project_id=project_id).status
-# # if status == Project.DOES_NOT_EXIST:
-# # return (
-# # f"project {project_id} does not exist",
-# # 404,
-# # {"Content-Type": "text/plain; charset=utf-8"},
-# # )
-# # elif status["worktable"] == Project.CREATING:
-# # return (
-# # "data not ready yet",
-# # 202,
-# # {"Content-Type": "text/plain; charset=utf-8"},
-# # )
-# # else:
-# # abort(500)
-
-
-
-
-
-# class JassApp(Flask):
-# """
-# JassApp builds the JASS Flask application
-# """
-
-# def __init__(self):
-# self.flask_app = Flask(__name__, static_url_path="", static_folder="static")
-# self.flask_app.config["API_TITLE"] = "JASS API"
-# self.flask_app.config["API_VERSION"] = "v2.0"
-# self.flask_app.config["OPENAPI_VERSION"] = "3.0.2"
-# self.flask_app.route("/")(self.redirect_to_index)
-# self.api = Api(self.flask_app)
-
-# def create_app(self):
-# return self.flask_app
-
-# def redirect_to_index(self):
-# return redirect("index.html")
-
-# def register_api_blueprint(self, blp):
-# self.api.register_blueprint(blp, url_prefix=f"/api/{blp.url_prefix}")
-
-
-# jass_app = JassApp()
-# jass_app.register_api_blueprint(blp_phenotypes)
-# jass_app.register_api_blueprint(blp_projects)
-# jass_app.register_api_blueprint(blp_local_projects)
-# jass_app.register_api_blueprint(blp_inittable)
diff --git a/jass/tasks.py b/jass/tasks.py
deleted file mode 100644
index 82e9b9d9c014f7468726cfb268e376099ff9b3cb..0000000000000000000000000000000000000000
--- a/jass/tasks.py
+++ /dev/null
@@ -1,191 +0,0 @@
-import os
-import sys
-import traceback
-from typing import List, Dict
-
-from celery import Celery, group, chain
-from fastapi import HTTPException
-from flask import Flask
-
-import jass.models.project
-from jass.models.project import GlobalProject, Project, ensure_space_in_project_dir
-
-from jass.models.phenotype import Phenotype, get_available_phenotypes
-from jass.config import config
-
-
-def make_celery(app):
- celery = Celery()
- if "CELERY_CONFIG_MODULE" in os.environ:
- celery.config_from_envvar("CELERY_CONFIG_MODULE")
- else:
- celery.config_from_object("jass.celeryconfig")
- celery.conf.update(app.config)
- TaskBase = celery.Task
-
- class ContextTask(TaskBase):
- abstract = True
-
- def __call__(self, *args, **kwargs):
- with app.app_context():
- return TaskBase.__call__(self, *args, **kwargs)
-
- celery.Task = ContextTask
- return celery
-
-
-flask_app = Flask(__name__)
-celery = make_celery(flask_app)
-
-
-@celery.task
-def ensure_space_in_project_dir_task(project_id):
- ensure_space_in_project_dir(except_project_id=project_id)
-
-
-@celery.task
-def create_project_worktable(project_id):
- project = GlobalProject.load(project_id)
- return project.create_worktable_file()
-
-
-@celery.task
-def create_project_global_plot(project_id):
- project = GlobalProject.load(project_id)
- return project.create_global_manhattan_plot()
-
-
-@celery.task
-def create_project_quadrant_plot(project_id):
- project = GlobalProject.load(project_id)
- return project.create_quadrant_plot()
-
-
-@celery.task
-def create_project_local_plot(project_id):
- project = GlobalProject.load(project_id)
- return project.create_local_plot()
-
-
-@celery.task
-def create_project_qq_plot(project_id):
- project = GlobalProject.load(project_id)
- return project.create_qq_plot()
-
-
-@celery.task
-def create_project_csv_file(project_id):
- project = GlobalProject.load(project_id)
- return project.create_csv_file()
-
-
-@celery.task
-def create_project_metadata_file(project_id):
- project = GlobalProject.load(project_id)
- return project.create_project_metadata_file()
-
-
-@celery.task
-def dummy_task():
- print("This task to nothing, but help the chain to have a valid status")
-
-
-def get_queue_status():
- inspect = celery.control.inspect()
- workers = set()
- ret = {'active': 0, 'reserved': 0}
- for k in ['active', 'reserved']:
- try:
- for worker, queue in getattr(inspect, k)().items():
- ret[k] += len(queue)
- workers.add(worker)
- except (
- AttributeError, # when no worker
- ConnectionResetError, # when rabbitMQ went down
- TimeoutError, # when rabbitMQ is not reachable
- ):
- pass
- ret['worker'] = len(workers)
- return ret
-
-
-def run_project_analysis_if_needed(project):
- if project.has_computation_going_on():
- return
- tasks = []
- post_worktable_tasks = []
-
- if not os.path.exists(project.get_worktable_path()):
- tasks.append(create_project_worktable.si(project.id))
-
- if project.get_metadata_file_path() and not os.path.exists(project.get_metadata_file_path()):
- tasks.append(create_project_metadata_file.si(project.id))
-
- if project.get_global_manhattan_plot_path() and not os.path.exists(project.get_global_manhattan_plot_path()):
- post_worktable_tasks.append(create_project_global_plot.si(project.id))
-
- if project.get_quadrant_plot_path() and not os.path.exists(project.get_quadrant_plot_path()):
- post_worktable_tasks.append(create_project_quadrant_plot.si(project.id))
-
- if project.get_qq_plot_path() and not os.path.exists(project.get_qq_plot_path()):
- post_worktable_tasks.append(create_project_qq_plot.si(project.id))
-
- if project.get_csv_path() and not os.path.exists(project.get_csv_path()):
- post_worktable_tasks.append(create_project_csv_file.si(project.id))
-
- if len(tasks) + len(post_worktable_tasks) == 0:
- return
- main_wf = chain(
- # first we check again that there is enough disk space
- ensure_space_in_project_dir_task.si(project.id),
- # we run the main task(s)
- *tasks,
- # we then compute the missing charts
- group(post_worktable_tasks),
- # it is mandatory to add a task that do nothing if group is used in order to have a success/failure status
- dummy_task.si(),
- )
- task = main_wf.delay()
- project.celery_id = task.id
- # Artificially create a result for the chain/chord so its state will survive reboot of rabbitmq.
- # Otherwise, the status would be PENDING which we consider, even if no task are pending.
- task.backend.store_result(task.id, None, "SENT")
- project.save()
-
-
-def create_project(
- phenotype_ids: List[str],
- chromosome: str = None,
- start: str = None,
- end: str = None,
- init_table_name: str = None,
-):
- init_table_path = os.path.join(config["DATA_DIR"], init_table_name)
- available_phenotypes=get_available_phenotypes(init_table_path)
- unavailable_requested_ids = set(phenotype_ids).difference(
- set(phenotype.id for phenotype in available_phenotypes)
- )
- if len(unavailable_requested_ids) > 0:
- raise HTTPException(status_code=404, detail=f"Phenotype IDs not found: {','.join(unavailable_requested_ids)}")
- phenotypes = [
- phenotype for phenotype in available_phenotypes if phenotype.id in phenotype_ids
- ]
- project = GlobalProject(phenotypes=phenotypes, init_table_path=init_table_path)
-
- project.create(fail_if_exists=False)
- ensure_space_in_project_dir(except_project_id=project.id)
-
- # if project.get_type_of_analysis() == Project.LOCAL_ANALYSIS:
- # # Local Analysis
- # global_plot_path = None
- # quadrant_plot_path = None
- # zoom_plot_path = project.get_zoom_plot_path()
- # delayed_gen_csv_file = False
- # else:
- # # genome wide Analysis
- # global_plot_path = project.get_global_manhattan_plot_path()
- # quadrant_plot_path = project.get_quadrant_plot_path()
- # zoom_plot_path = None
- # delayed_gen_csv_file = True
-
- return project
diff --git a/jass/test/__init__.py b/jass/test/__init__.py
index 7f6ab04bc94ab97ebf0e1746bbab91735d233504..482e6fa7b370156dec311a8b2b89e69f06f028d6 100644
--- a/jass/test/__init__.py
+++ b/jass/test/__init__.py
@@ -6,13 +6,13 @@ import unittest
# replace delay() and si() method with mocks
# to avoid freezing calls in unit tests
-from celery.app.task import Task
-from unittest.mock import MagicMock
-from fastapi.testclient import TestClient
+#from celery.app.task import Task
+#from unittest.mock import MagicMock
+#from fastapi.testclient import TestClient
-Task.delay = MagicMock()
-Task.si = MagicMock()
+#Task.delay = MagicMock()
+#Task.si = MagicMock()
from jass.models.inittable import create_inittable_file
@@ -24,35 +24,35 @@ class JassTestCase(unittest.TestCase):
os.path.dirname(os.path.abspath(__file__)), cls.test_folder, test_file_name
)
-class JassWebClientTestCase(JassTestCase):
- def setUp(self) -> None:
- from jass.config import config
- self.test_dir = tempfile.mkdtemp()
- config["DATA_DIR"] = self.test_dir
- shutil.copy(self.get_file_path_fn("initTable.hdf5"), self.test_dir)
- try:
- shutil.copy(self.get_file_path_fn("initTableTest1.hdf5"), self.test_dir)
- except FileNotFoundError:
- pass
-
- from jass.server import app
- self.testing_client = TestClient(app)
-
- def assert200(self, response, message):
- self.assertEqual(response.status_code, 200, message)
-
- # def create_app(self):
- # from jass.config import config
- #
- # self.test_dir = tempfile.mkdtemp()
- # config["DATA_DIR"] = self.test_dir
- # shutil.copy(self.get_file_path_fn("initTable.hdf5"), self.test_dir)
- #
- # self.jass_app = jass_app
- # application = self.jass_app.create_app()
- # application.config["TESTING"] = True
- # self.testing_client = application.test_client()
- # return application
-
- def tearDown(self):
- shutil.rmtree(self.test_dir)
+# class JassWebClientTestCase(JassTestCase):
+# def setUp(self) -> None:
+# from jass.config import config
+# self.test_dir = tempfile.mkdtemp()
+# config["DATA_DIR"] = self.test_dir
+# shutil.copy(self.get_file_path_fn("initTable.hdf5"), self.test_dir)
+# try:
+# shutil.copy(self.get_file_path_fn("initTableTest1.hdf5"), self.test_dir)
+# except FileNotFoundError:
+# pass
+#
+# from jass.server import app
+# self.testing_client = TestClient(app)
+#
+# def assert200(self, response, message):
+# self.assertEqual(response.status_code, 200, message)
+#
+# # def create_app(self):
+# # from jass.config import config
+# #
+# # self.test_dir = tempfile.mkdtemp()
+# # config["DATA_DIR"] = self.test_dir
+# # shutil.copy(self.get_file_path_fn("initTable.hdf5"), self.test_dir)
+# #
+# # self.jass_app = jass_app
+# # application = self.jass_app.create_app()
+# # application.config["TESTING"] = True
+# # self.testing_client = application.test_client()
+# # return application
+#
+# def tearDown(self):
+# shutil.rmtree(self.test_dir)
diff --git a/jass/test/data_real/combination_phenotypes.tsv b/jass/test/data_real/combination_phenotypes.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..756625ed3123c84c8a5a1cc65d941ecbcd56f65e
--- /dev/null
+++ b/jass/test/data_real/combination_phenotypes.tsv
@@ -0,0 +1,2 @@
+GRP1,z_MAGIC_FAST-GLUCOSE z_MAGIC_FAST-INSULIN z_MAGIC_GLUCOSE-TOLERANCE z_MAGIC_HBA1C
+GRP2,z_MAGIC_FAST-GLUCOSE z_MAGIC_FAST-INSULIN z_MAGIC_GLUCOSE-TOLERANCE
diff --git a/jass/test/test_init_table.py b/jass/test/test_init_table.py
index bb400510c1f734cb3e78c1f9846f695a62fe7e1f..5e7a055217a9419a577bad0c800ca58d4c3f502f 100644
--- a/jass/test/test_init_table.py
+++ b/jass/test/test_init_table.py
@@ -1,7 +1,7 @@
# coding: utf-8
from __future__ import absolute_import
-import os, shutil, tempfile
+import os, tempfile
from pandas.testing import assert_frame_equal
from pandas import read_hdf
diff --git a/jass/test/test_server.py b/jass/test/test_server.py
deleted file mode 100644
index 6234855e187645ceb519bf53df82f1f5b5dcbcc6..0000000000000000000000000000000000000000
--- a/jass/test/test_server.py
+++ /dev/null
@@ -1,91 +0,0 @@
-# coding: utf-8
-
-from __future__ import absolute_import
-import os, shutil, tempfile
-
-from six import BytesIO
-from flask import json, url_for
-
-from jass.config import config
-from . import JassWebClientTestCase
-
-
-class TestDefaultController(JassWebClientTestCase):
- """DefaultController integration test stubs"""
-
- test_folder = "data_real"
-
- def test_phenotypes_post(self):
- """
- Test case retrieving available phenotypes
- """
- response = self.testing_client.post("/api/phenotypes", json={})
- self.assert200(response, "Response body is : " + response.content.decode("utf-8"))
-
- response = self.testing_client.post(
- "/api/phenotypes",
- json={"initTableName": "initTable.hdf5"},
- )
- self.assert200(response, "Response body is : " + response.content.decode("utf-8"))
- json_response_main = json.loads(response.content.decode("utf-8"))
- phenotypes_main = set(p["id"] for p in json_response_main)
-
- response = self.testing_client.post(
- "/api/phenotypes",
- json={"initTableName": "initTableTest1.hdf5"},
- )
- self.assert200(response, "Response body is : " + response.content.decode("utf-8"))
- json_response_t1 = json.loads(response.content.decode("utf-8"))
- phenotypes_t1 = set(p["id"] for p in json_response_t1)
-
- self.assertNotEqual(json_response_t1, json_response_main)
- self.assertNotEqual(phenotypes_main, phenotypes_t1)
- self.assertEqual(phenotypes_main.intersection(phenotypes_t1), set())
-
- response = self.testing_client.post(
- "/api/phenotypes",
- json={"initTableName": "initTableMissing.hdf5"},
- )
- self.assertEqual(response.status_code, 404, response.content.decode("utf-8"))
-
- def test_create_project(self):
- """
- Test case for creating a project
- """
- response = self.testing_client.post(
- "/api/projects",
- json={"phenotypeID": ["z_MAGIC_FAST-GLUCOSE"]},
- )
- self.assert200(response, "Response body is : " + response.content.decode("utf-8"))
-
- def test_initmeta(self):
- response = self.testing_client.post("/api/initmeta", json={})
- self.assert200(response, "Response body is : " + response.content.decode("utf-8"))
- respMain = json.loads(response.content.decode("utf-8"))
-
- response = self.testing_client.post("/api/initmeta", json={"initTableName": "initTableTest1.hdf5"})
- self.assert200(response, "Response body is : " + response.content.decode("utf-8"))
- respT1 = json.loads(response.content.decode("utf-8"))
-
- self.assertNotEqual(respT1, respMain)
- for key in {
- 'nb_phenotypes',
- 'nb_snps',
- 'name',
- 'desc',
- 'ancestry',
- 'assembly',
- }:
- self.assertIn(key , respMain)
-
- def test_get_tables(self):
- response = self.testing_client.get("/api/tables")
- self.assert200(response, "Response body is : " + response.content.decode("utf-8"))
- resp = json.loads(response.content.decode("utf-8"))
- self.assertSetEqual({"initTable.hdf5", "initTableTest1.hdf5"}, set(resp))
-
-
-if __name__ == "__main__":
- import unittest
-
- unittest.main()
diff --git a/jass/test/test_worktable.py b/jass/test/test_worktable.py
index 8509e2056c7d773d114c6d26a5f54bab1f86b523..0c086355e3cf0d73a39fdbc85aae5ef69c68afec 100644
--- a/jass/test/test_worktable.py
+++ b/jass/test/test_worktable.py
@@ -7,7 +7,7 @@ from pandas import read_hdf
from pandas.testing import assert_frame_equal
from jass.models.worktable import create_worktable_file
-from jass.util import coerce_pickle_protocol
+
from . import JassTestCase
diff --git a/jass/util.py b/jass/util.py
index 7de53dc08a41cc053246087ac981b7a7e0a9e51b..b271e02254d2aa9a34f6974dd0b6458e4c6dc52b 100644
--- a/jass/util.py
+++ b/jass/util.py
@@ -6,8 +6,8 @@ import pickle
import numpy as np
import six
-from starlette.responses import Response
-from starlette.staticfiles import StaticFiles
+#from starlette.responses import Response
+#from starlette.staticfiles import StaticFiles
from typing import Tuple
try:
@@ -173,34 +173,34 @@ def coerce_pickle_protocol(level):
return PickleProtocol(level)
-class SinglePageApplication(StaticFiles):
- """
- https://stackoverflow.com/a/68843198/2144569
- """
-
- def __init__(self, directory: os.PathLike, index='index.html') -> None:
- self.index = index
-
- # set html=True to resolve the index even when no
- # the base path is passed in
- super().__init__(directory=directory, packages=None, html=True, check_dir=True)
-
- def lookup_path(self, path: str) -> Tuple[str, os.stat_result]:
- """Returns the index file when no match is found.
-
- Args:
- path (str): Resource path.
-
- Returns:
- [tuple[str, os.stat_result]]: Always returns a full path and stat result.
- """
- full_path, stat_result = super().lookup_path(path)
-
- # if a file cannot be found
- if stat_result is None:
- return super().lookup_path(self.index)
-
- return full_path, stat_result
+# class SinglePageApplication(StaticFiles):
+# """
+# https://stackoverflow.com/a/68843198/2144569
+# """
+#
+# def __init__(self, directory: os.PathLike, index='index.html') -> None:
+# self.index = index
+#
+# # set html=True to resolve the index even when no
+# # the base path is passed in
+# super().__init__(directory=directory, packages=None, html=True, check_dir=True)
+#
+# def lookup_path(self, path: str) -> Tuple[str, os.stat_result]:
+# """Returns the index file when no match is found.
+#
+# Args:
+# path (str): Resource path.
+#
+# Returns:
+# [tuple[str, os.stat_result]]: Always returns a full path and stat result.
+# """
+# full_path, stat_result = super().lookup_path(path)
+#
+# # if a file cannot be found
+# if stat_result is None:
+# return super().lookup_path(self.index)
+#
+# return full_path, stat_result
def np_encoder(object):
if isinstance(object, np.generic):
@@ -208,15 +208,15 @@ def np_encoder(object):
return object
-class JSONNumpyResponse(Response):
- media_type = "application/json"
-
- def render(self, content: typing.Any) -> bytes:
- return json.dumps(
- content,
- ensure_ascii=False,
- allow_nan=False,
- indent=None,
- separators=(",", ":"),
- default=np_encoder,
- ).encode("utf-8")
\ No newline at end of file
+# class JSONNumpyResponse(Response):
+# media_type = "application/json"
+#
+# def render(self, content: typing.Any) -> bytes:
+# return json.dumps(
+# content,
+# ensure_ascii=False,
+# allow_nan=False,
+# indent=None,
+# separators=(",", ":"),
+# default=np_encoder,
+# ).encode("utf-8")
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 0a12f559a15f20fde1fa2fd95e6b309d88e83728..01260fb9e36df62daf45045d3aab48aa65f72059 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,3 @@
-flask-smorest
-flask-cors
-aiohttp
-python_dateutil
setuptools
numpy<2.0.0
pandas
@@ -10,12 +6,9 @@ scipy
matplotlib>=3.7.4
seaborn
celery
-importlib-metadata==4.13.0
pydantic<2.0
fastapi
-httpx
uvicorn[standard]
typing_extensions; python_version < '3.8'
requests
-h5py
wheel
diff --git a/scripts/__init__.py b/scripts/__init__.py
index f467725b00ccfe19f921fb8a6fa41d12cfafa082..1f1936152ef05f96cc5a43fe50a4c93359902bd4 100644
--- a/scripts/__init__.py
+++ b/scripts/__init__.py
@@ -14,4 +14,4 @@ Submodules
util
"""
-from jass.tasks import celery
+#from jass.tasks import celery
diff --git a/test_docker_compose.sh b/test_docker_compose.sh
deleted file mode 100755
index 376ffc083583148758339a94760a284ed7741dfe..0000000000000000000000000000000000000000
--- a/test_docker_compose.sh
+++ /dev/null
@@ -1,144 +0,0 @@
-#!/usr/bin/env bash
-
-if [ "$(docker compose ps | grep jass | grep -v Exit | wc -l)" == "0" ]; then
- docker compose -f docker-compose.yaml -f docker-compose.test.yaml up -d --build || exit 99
- echo "Waiting some time for interface to be up"
- sleep 5
-else
- rm -rf projects/project_407db5eb73e8b3a0dd9fd8a3c018db6d
-fi
-
-
-echo "Testing /"
-curl -I http://0.0.0.0:3001/ \
- 1> log/01-index.log \
- 2> log/01-index.err
-
-if [ "$(cat log/01-index.log | grep "200 OK" | wc -l)" == "0" ]; then exit 01; fi
-
-
-echo "Testing /phenotypes"
-curl -I http://0.0.0.0:3001/phenotypes/ \
- 1> log/02-phenotypes.log \
- 2> log/02-phenotypes.err
-
-if [ "$(cat log/02-*.log | grep "200 OK" | wc -l)" == "0" ]; then exit 02; fi
-
-
-echo "Test fetching phenotypes through API"
-curl --location --request POST http://0.0.0.0:8080/api/phenotypes/ \
---header 'Content-Type: application/json' \
---data-raw '{"initTableName":"initTableTest1.hdf5"}' \
- -o log/11-post-phenotypes.json \
- 1> log/11-post-phenotypes.log \
- 2> log/11-post-phenotypes.err
-
-if [ "$(cat log/11-*.json | grep "Internal Server Error" | wc -l)" == "1" ]; then exit 11; fi
-
-
-echo "Test fetching phenotypes through API"
-curl --location --request POST http://0.0.0.0:8080/api/phenotypes/ \
---header 'Content-Type: application/json' \
---data-raw '{"initTableName":"initTable.hdf5"}' \
- -o log/12-post-phenotypes.json \
- 1> log/12-post-phenotypes.log \
- 2> log/12-post-phenotypes.err
-
-if [ "$(cat log/12-*.json | grep "Internal Server Error" | wc -l)" == "1" ]; then exit 12; fi
-
-if [ "$(cat log/11-*.json)" == "$(cat log/12-*.json)" ]; then echo "should not be equal"; exit 12; fi
-
-
-echo "Testing project creation"
-curl --location --request POST 'http://0.0.0.0:8080/api/projects' \
---header 'Accept: text/html' \
---header 'Content-Type: application/json' \
---data-raw '{"phenotypeID": ["z_MAGIC_FAST-GLUCOSE", "z_MAGIC_FAST-INSULIN"]}' \
- -o log/03-post-project.json \
- 1> log/03-post-project.log \
- 2> log/03-post-project.err
-
-PROJECT_ID=$(jq .id log/03-post-project.json | sed 's/\"//g')
-if [ ! -d "projects/project_$PROJECT_ID" ]; then
- exit 03
-fi
-
-
-echo "Trigger running"
-curl --location http://0.0.0.0:8080/api/projects/$PROJECT_ID/ \
- -o log/04-project.json \
- 1> log/04-project.log \
- 2> log/04-project.err
-
-if [ ! -f projects/project_$PROJECT_ID/meta.json ]; then exit 04; fi
-
-
-echo "Waiting some time project to be completed"
-
-while [ $(grep CREATING projects/project_$PROJECT_ID/meta.json | wc -l) == "1" ]; do
- echo "... still running"
- sleep 1
-done
-echo "... done"
-
-if [ $(grep ERROR projects/project_$PROJECT_ID/meta.json | wc -l) == "1" ]; then exit 14; fi
-
-echo "Testing manhattan plot"
-curl --location http://0.0.0.0:8080/api/projects/$PROJECT_ID/globalmanhattan \
- -o log/05-globalmanhattan.png \
- 1> log/05-globalmanhattan.log \
- 2> log/05-globalmanhattan.err
-
-if [ ! -s log/05-*.png ]; then exit 05; fi
-
-
-echo "Testing quadrant plot"
-curl --location http://0.0.0.0:8080/api/projects/$PROJECT_ID/quadrant \
- -o log/06-quadrant.png \
- 1> log/06-quadrant.log \
- 2> log/06-quadrant.err
-
-if [ ! -s log/06-*.png ]; then exit 06; fi
-
-
-echo "Testing genome_full"
-curl --location http://0.0.0.0:8080/api/projects/$PROJECT_ID/genome_full \
- -o log/07-genome_full.csv \
- 1> log/07-genome_full.log \
- 2> log/07-genome_full.err
-
-if [ ! -s log/07-*.csv ]; then exit 07; fi
-
-echo "Waiting for worktable"
-I=0
-while [[ "$(jq .status.worktable projects/project_$PROJECT_ID/meta.json)" != "\"READY\"" ]]; do
- I=$(expr $I + 1)
- if [ $I -gt 120 ]; then
- echo "Waited too long, exiting"
- exit 77
- fi
- echo "... waiting for worktable"
- sleep 1
-done
-echo "... done"
-
-echo "Testing heatmap"
-curl --location http://0.0.0.0:8080/api/projects/$PROJECT_ID/heatmap/chr9/Region699 \
- -o log/08-heatmap.csv \
- 1> log/08-heatmap.log \
- 2> log/08-heatmap.err
-
-if [ "$(cat log/08-*.csv | wc -l)" -le "2" ]; then exit 08; fi
-
-
-echo "Testing manhattan"
-curl --location http://0.0.0.0:8080/api/projects/$PROJECT_ID/manhattan/chr9/Region699 \
- -o log/09-manhattan.csv \
- 1> log/09-manhattan.log \
- 2> log/09-manhattan.err
-
-if [ "$(cat log/09-*.csv | wc -l)" -le "2" ]; then exit 09; fi
-
-echo "SUCCESS !!!"
-
-exit 0
\ No newline at end of file