Updated to v1.0

.devcontainer/Dockerfile

@@ -23,7 +23,7 @@ ENV LC_ALL C.UTF-8
 RUN echo "deb http://http.debian.net/debian buster main" > /etc/apt/sources.list.d/debian-unstable.list
 
 
-RUN pip install numpy requests matplotlib pronto jupyter flask matplotlib pytest mypy sphinx
+RUN pip install numpy scipy requests matplotlib pronto jupyter flask matplotlib pytest mypy sphinx pandas plotly kaleido
 #RUN pip install -e .  # devcontainer.json: "postCreateCommand": "pip install -e .",
 
 ARG USERNAME=vscode

.devcontainer/devcontainer.json

@@ -3,7 +3,8 @@
 	"dockerFile": "Dockerfile",
 	"context": "..",
 	"extensions": [
-		"ms-python.python", "littlefoxteam.vscode-python-test-adapter", "njpwerner.autodocstring"
+		"ms-python.python", "ms-python.vscode-pylance", "littlefoxteam.vscode-python-test-adapter", "ms-vscode.test-adapter-converter", 
+		"njpwerner.autodocstring", "ms-toolsai.jupyter"
 	],
 	"settings": {
 		"python.pythonPath": "/usr/local/bin/python"

.github/workflows/container_build.yml

@@ -1,17 +1,45 @@
-name: container-build
+name: container-build-and-push
 on:
     pull_request:
       types: ['opened', 'edited', 'reopened', 'synchronize']  
+
 jobs:
-  build:
+  docker:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@master
-    - name: Publish to Registry
-      uses: elgohr/Publish-Docker-Github-Action@master
-      with:
-        name: mwalzer/mzqc-pylib
-        username: ${{ secrets.quay_user_mzqc_action }}
-        password: ${{ secrets.quay_pw_mzqc_action }}
-        registry: quay.io
-        dockerfile: containers/Dockerfile
+      -
+        name: Checkout
+        uses: actions/checkout@v2
+      -
+        name: Set tags
+        run: echo mwalzerpymzqc:${GITHUB_REF##*/}
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+#      -
+#        name: Login to DockerHub
+#        uses: docker/login-action@v1 
+#        with:
+#          username: ${{ secrets.DOCKERHUB_USERNAME }}
+#          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Login to quay.io
+        uses: docker/login-action@v1 
+        with:
+          registry: quay.io
+          username: ${{ secrets.quay_user_mzqc_action }}
+          password: ${{ secrets.quay_pw_mzqc_action }}
+      -
+        name: Build and push
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: containers/Dockerfile
+          platforms: linux/amd64
+          push: true
+          tags: |
+            quay.io/mwalzer/pymzqc:latest_pullrequest_build
+            quay.io/mwalzer/pymzqc:${{ github.head_ref }}_${{ github.sha }}

.github/workflows/release_container.yml

@@ -1,18 +1,41 @@
 name: release-container
 on:
     release:
-      types: ['published', 'prereleased']  
+      types: ['published']  
 jobs:
-  build:
+  docker:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@master
-    - name: Publish to Registry
-      uses: elgohr/Publish-Docker-Github-Action@master
-      with:
-        name: mwalzer/mzqc-pylib
-        username: ${{ secrets.quay_user_mzqc_action }}
-        password: ${{ secrets.quay_pw_mzqc_action }}
-        registry: quay.io
-        tag_names: true
-        dockerfile: containers/Dockerfile
+      -
+        name: Checkout
+        uses: actions/checkout@v2
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+#      -
+#        name: Login to DockerHub
+#        uses: docker/login-action@v1 
+#        with:
+#          username: ${{ secrets.DOCKERHUB_USERNAME }}
+#          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Login to quay.io
+        uses: docker/login-action@v1 
+        with:
+          registry: quay.io
+          username: ${{ secrets.quay_user_mzqc_action }}
+          password: ${{ secrets.quay_pw_mzqc_action }}
+      -
+        name: Build and push
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: containers/Dockerfile
+          platforms: linux/amd64
+          push: true
+          tags: |
+            quay.io/mwalzer/pymzqc:latest
+            quay.io/mwalzer/pymzqc:${{ github.event.release.tag_name }}

.gitignore

@@ -1,14 +1,13 @@
 
 mzqc/__pycache__/
-
 tests/__pycache__/
 
 .mypy_cache/
-
 .pytest_cache/
 
 mzqc_pylib.egg-info/
+pymzqc.egg-info/
 
+_build/
 doc/build/**
-
 doc/source/codegen/**

.vscode/settings.json

@@ -7,5 +7,14 @@
     ],
     "python.testing.unittestEnabled": false,
     "python.testing.nosetestsEnabled": false,
-    "python.testing.pytestEnabled": true
+    "python.testing.pytestEnabled": true,
+    "jupyter.jupyterServerType": "local",
+    "python.pythonPath": "/usr/local/bin/python",
+    "python.testing.unittestArgs": [
+        "-v",
+        "-s",
+        "./tests",
+        "-p",
+        "*test*.py"
+    ]
 }

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2019, Mathias Walzer
+Copyright (c) 2019-22, Mathias Walzer
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -8,7 +8,7 @@ modification, are permitted provided that the following conditions are met:
     * Redistributions in binary form must reproduce the above copyright
       notice, this list of conditions and the following disclaimer in the
       documentation and/or other materials provided with the distribution.
-    * Neither the name of EBI nor bigbio nor the
+    * Neither the name of EBI nor PSI nor MS-Quality-Hub nor the
       names of its contributors may be used to endorse or promote products
       derived from this software without specific prior written permission.
 

README.md

@@ -1,7 +1,8 @@
 # MZQC python library
-![](https://github.com/bigbio/mzqc-pylib/workflows/unit-tests/badge.svg)
-![](https://github.com/bigbio/mzqc-pylib/workflows/release-container/badge.svg)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/bigbio/mzqc-pylib/v0.1.1?filepath=jupyter%2FMZQC_in_5_minutes.ipynb)
+[![unit-tests](https://github.com/MS-Quality-hub/pymzqc/actions/workflows/unit_tests.yml/badge.svg)](https://github.com/MS-Quality-hub/pymzqc/actions/workflows/unit_tests.yml)
+[![Docker Repository on Quay](https://quay.io/repository/mwalzer/pymzqc/status "Docker Repository on Quay")](https://quay.io/repository/mwalzer/pymzqc)
+![](https://readthedocs.org/projects/pymzqc/badge/?version=v1.0.0&style=flat)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/MS-Quality-hub/pymzqc/v1.0.0?filepath=jupyter%2FMZQC_in_5_minutes.ipynb)
 
 A python library to use mzQC files. Specifically, have a usable object representation of mzQC that can
 * serialise
@@ -10,14 +11,14 @@ A python library to use mzQC files. Specifically, have a usable object represent
 * semantic checks
 
 ## Install
-Please install mzqc-pylib via [PyPI](https://pypi.org/). If you want the latest development install
+Please install pymzqc via [PyPI](https://pypi.org/). If you want the latest development install
 ```
-pip install -U git+https://github.com/bigbio/mzqc-pylib.git#egg=mzqc-pylib
+pip install -U git+https://github.com/MS-Quality-hub/pymzqc.git#egg=pymzqc
 ```
-However, we recommend using the [containers](https://quay.io/repository/mwalzer/mzqc-pylib) to check out the latest updates.
+However, we recommend using the [containers](https://quay.io/repository/mwalzer/pymzqc) to check out the latest updates.
 
 ## Documentation
-To get a nice and simple overview of how the mzQC-pylib works, visit [here](https://mzqc-pylib.readthedocs.io).
+To get a nice and simple overview of how pymzqc works, visit [here](https://pymzqc.readthedocs.io).
 The code documentation style convention is of the type "Sphinx/numpy".
 If you however have successfully installed the library and want to **jump right in and use the library**, we suggest the [interactive guide](#5min-interactive-guide).
 
@@ -33,4 +34,4 @@ Contributions are welcome! (Fork and open PR)
 This library implements python modules for (de-)serialisation and validity checks of the [PSI fileformat mzQC](http://www.psidev.info/groups/quality-control). To see the raw fileformat, including json schema and specification documentation, see https://github.com/HUPO-PSI/mzQC/. **The library follows the formats versioning**(which is 'v(Major).(Minor).(Patch)').
 
 ## 5min interactive guide
-Have a go with our [interactive python notebook](https://mybinder.org/v2/gh/bigbio/mzqc-pylib/v0.1.1?filepath=jupyter%2FMZQC_in_5_minutes.ipynb) to explore what is possible. ([static version](https://github.com/bigbio/mzqc-pylib/blob/master/jupyter/MZQC_in_5_minutes.ipynb))
+Have a go with our [interactive python notebook](https://mybinder.org/v2/gh/MS-Quality-hub/pymzqc/v1.0.0?filepath=jupyter%2FMZQC_in_5_minutes.ipynb) to explore what is possible. ([static version](https://github.com/MS-Quality-hub/pymzqc/blob/master/jupyter/MZQC_in_5_minutes.ipynb))

acessories/heroku/Procfile

@@ -0,0 +1 @@
+web: gunicorn  mzqc_heroku_validator:app

acessories/heroku/mzqc_heroku_validator.py

@@ -0,0 +1,64 @@
+#sudo apt update
+#sudo apt install python3 python3-pip python3-flask 
+#pip install Flask
+#pip install git+https://github.com/MS-Quality-hub/pymzqc.git@v1.0.0
+#pip install flask-restful
+#pip install gunicorn
+
+import json
+from flask import Flask
+from flask import Flask, jsonify, request
+from flask_restful import Resource, Api
+from flask_cors import CORS
+
+from mzqc.MZQCFile import MzQcFile as mzqc_file
+from mzqc.MZQCFile import JsonSerialisable as mzqc_io
+from mzqc.SemanticCheck import SemanticCheck
+from mzqc.SyntaxCheck import SyntaxCheck
+
+app = Flask(__name__)
+api = Api(app)
+CORS(app)
+
+class Status(Resource):
+    def get(self):
+        try:
+            return {'status': 'API is running'}
+        except:
+            return {'status': 'API fetch was unsuccessful'}
+
+class Validator(Resource):
+    def post(self):
+        default_unknown = jsonify({"general": "No mzQC structure detectable."})
+        inpu = request.form.get('validator_input', None)
+        try:
+            target = mzqc_io.FromJson(inpu)
+        except Exception as e:
+            return default_unknown
+
+        if type(target['mzQC']) != mzqc_file:
+            return default_unknown
+        else:
+            safe = target['mzQC']
+            removed_items = list(filter(lambda x: not x.uri.startswith('http'), safe.controlledVocabularies))
+            safe.controlledVocabularies = list(filter(lambda x: x.uri.startswith('http'), safe.controlledVocabularies))
+            print(safe)
+            sem_val_res = SemanticCheck().validate(safe)
+            print(sem_val_res)
+            proto_response = {k: [str(i) for i in v] for k,v in sem_val_res.items()}
+            proto_response.update({"unrecognised CVs": [str(it) for it in removed_items]})
+            print(proto_response)
+            valt = mzqc_io.ToJson(target)
+            syn_val_res = SyntaxCheck().validate(valt)
+            proto_response.update(syn_val_res)
+            # convert val_res ErrorTypes to strings
+            # add note on removed CVs
+            return jsonify(proto_response)
+        return default_unknown
+
+
+api.add_resource(Status, '/','/status/')
+api.add_resource(Validator, '/validator/')
+
+if __name__ == '__main__':
+    app.run()

acessories/heroku/requirements.txt

@@ -0,0 +1,80 @@
+git+git://github.com/MS-Quality-hub/pymzqc.git@v1.0.0
+aniso8601==9.0.1
+argon2-cffi==20.1.0
+async-generator==1.10
+attrs==21.2.0
+backcall==0.2.0
+bleach==3.3.1
+certifi==2021.5.30
+cffi==1.14.6
+chardet==4.0.0
+charset-normalizer==2.0.3
+click==8.0.1
+cycler==0.10.0
+debugpy==1.3.0
+decorator==4.4.2
+defusedxml==0.7.1
+entrypoints==0.3
+fastobo==0.10.1
+Flask==2.0.1
+Flask-Cors==3.0.10
+Flask-RESTful==0.3.9
+gunicorn==20.1.0
+idna==3.2
+ipykernel==6.0.3
+ipython==7.25.0
+ipython-genutils==0.2.0
+ipywidgets==7.6.3
+itsdangerous==2.0.1
+jedi==0.18.0
+Jinja2==3.0.1
+jsonschema==3.2.0
+jupyter==1.0.0
+jupyter-client==6.1.12
+jupyter-console==6.4.0
+jupyter-core==4.7.1
+jupyterlab-pygments==0.1.2
+jupyterlab-widgets==1.0.0
+kiwisolver==1.3.1
+MarkupSafe==2.0.1
+matplotlib==3.4.2
+matplotlib-inline==0.1.2
+mistune==0.8.4
+nbclient==0.5.3
+nbconvert==6.1.0
+nbformat==5.1.3
+nest-asyncio==1.5.1
+networkx==2.5.1
+notebook==6.4.0
+numpy==1.21.1
+packaging==21.0
+pandocfilters==1.4.3
+parso==0.8.2
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==8.3.1
+prometheus-client==0.11.0
+prompt-toolkit==3.0.19
+pronto==2.4.2
+ptyprocess==0.7.0
+pycparser==2.20
+Pygments==2.9.0
+pyparsing==2.4.7
+pyrsistent==0.18.0
+python-dateutil==2.8.2
+pytz==2021.1
+pyzmq==22.1.0
+qtconsole==5.1.1
+QtPy==1.9.0
+requests==2.26.0
+Send2Trash==1.7.1
+six==1.16.0
+terminado==0.10.1
+testpath==0.5.0
+tornado==6.1
+traitlets==5.0.5
+urllib3==1.26.6
+wcwidth==0.2.5
+webencodings==0.5.1
+Werkzeug==2.0.1
+widgetsnbextension==3.5.1

acessories/heroku/runtime.txt

@@ -0,0 +1 @@
+python-3.8.11

acessories/heroku/wsgi.py

@@ -0,0 +1,4 @@
+from mzqc_heroku_validator import app
+
+if __name__ == '__main__':
+    app.run()