diff --git a/.vscode/launch.json b/.vscode/launch.json
index 443afd0ee37346541306f796114a1cefc0a7414c..ff04f5a491a24b0f9234a3ad300adc3a9f193152 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -44,7 +44,7 @@
"cwd": "${workspaceFolder}",
"program": "${workspaceFolder}/.pyenv/bin/pytest",
"args": [
- "-sv", "tests/test_parsing.py::TestLocalBackend::test_two_sections"
+ "-sv", "tests/test_api.py::test_repo_calcs_user"
]
},
{
diff --git a/.vscode/temp.sql b/.vscode/temp.sql
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/docs/components.graffle/data.plist b/docs/components.graffle/data.plist
index c2ca48b1353cb7f2b210ed48d90c049eb9a82462..8573b8e2771c2ab3090f048854a0f2d7eeb1becc 100644
Binary files a/docs/components.graffle/data.plist and b/docs/components.graffle/data.plist differ
diff --git a/gui/src/api.js b/gui/src/api.js
index 94957c9026bda37921b0cb50d47dd0a7642dd61c..dca128fa9baaf805ac58f7abcc0b3c38959a9725 100644
--- a/gui/src/api.js
+++ b/gui/src/api.js
@@ -2,7 +2,7 @@ import { UploadRequest } from '@navjobs/upload'
import { apiBase, appStaticBase } from './config'
const auth_headers = {
- Authorization: 'Basic ' + btoa('me@gmail.com:nomad')
+ Authorization: 'Basic ' + btoa('sheldon.cooper@nomad-fairdi.tests.de:password')
}
const networkError = () => {
diff --git a/infrastructure/nomad/docker-compose.override.yml b/infrastructure/nomad/docker-compose.override.yml
index 32b59b9678cd18a6122d6bae0362d12bda15a2fa..ce472558e5cca863252b82bf15af68ffbaec3de3 100644
--- a/infrastructure/nomad/docker-compose.override.yml
+++ b/infrastructure/nomad/docker-compose.override.yml
@@ -15,6 +15,11 @@
version: '3.4'
services:
+ # postgres for NOMAD-coe repository API and GUI
+ postgres:
+ ports:
+ - 5432:5432
+
# broker for celery
rabbitmq:
ports:
diff --git a/infrastructure/nomad/docker-compose.yml b/infrastructure/nomad/docker-compose.yml
index 2f8972ae32420f0f6d196d8322ef1740cfe80ebb..e6e54ae19cf8c823734706d3f4e1a2b60906d730 100644
--- a/infrastructure/nomad/docker-compose.yml
+++ b/infrastructure/nomad/docker-compose.yml
@@ -21,6 +21,18 @@ x-common-variables: &nomad_backend_env
NOMAD_MONGO_HOST: mongo
services:
+ # postgres for NOMAD-coe repository API and GUI
+ postgres:
+ restart: always
+ image: postgres:9.4
+ container_name: nomad_postgres
+ environment:
+ POSTGRES_PASSWORD: 'nomad'
+ POSTGRES_USER: 'postgres'
+ POSTGRES_DB: 'nomad'
+ volumes:
+ - nomad_postgres:/var/lib/postgresql/data
+
# broker for celery
rabbitmq:
restart: always
@@ -110,6 +122,7 @@ services:
command: nginx -g 'daemon off;'
volumes:
+ nomad_postgres:
nomad_mongo:
nomad_elastic:
nomad_rabbitmq:
diff --git a/nomad/api.py b/nomad/api.py
deleted file mode 100644
index 2eae8570aaae04838161fe04a03c3e3e4b234967..0000000000000000000000000000000000000000
--- a/nomad/api.py
+++ /dev/null
@@ -1,874 +0,0 @@
-# Copyright 2018 Markus Scheidgen
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an"AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-from werkzeug.exceptions import HTTPException
-from flask import Flask, request, g, jsonify, send_file, Response
-from flask_restful import Resource, Api, abort
-from flask_cors import CORS
-from flask_httpauth import HTTPBasicAuth
-from elasticsearch.exceptions import NotFoundError
-from datetime import datetime
-import os.path
-import zipstream
-from zipfile import ZIP_DEFLATED
-from contextlib import contextmanager
-
-from nomad import config, infrastructure
-from nomad.files import UploadFile, ArchiveFile, ArchiveLogFile, RepositoryFile
-from nomad.utils import get_logger
-from nomad.processing import Upload, NotAllowedDuringProcessing
-from nomad.repo import RepoCalc
-from nomad.user import User
-
-base_path = config.services.api_base_path
-
-app = Flask(
- __name__,
- static_url_path='%s/docs' % base_path,
- static_folder=os.path.abspath(os.path.join(os.path.dirname(__file__), '../docs/.build/html')))
-CORS(app)
-
-app.config['SECRET_KEY'] = config.services.api_secret
-
-auth = HTTPBasicAuth()
-api = Api(app)
-
-
-@app.before_first_request
-def setup():
- infrastructure.setup()
-
-
-@auth.verify_password
-def verify_password(username_or_token, password):
- # first try to authenticate by token
- user = User.verify_auth_token(username_or_token)
- if not user:
- # try to authenticate with username/password
- user = User.objects(email=username_or_token).first()
- if not user:
- g.user = None
- return True # anonymous access
-
- if not user or not user.verify_password(password):
- return False
-
- g.user = user
- return True
-
-
-def login_really_required(func):
- @auth.login_required
- def wrapper(*args, **kwargs):
- if g.user is None:
- abort(401, message='Anonymous access is forbidden, authorization required')
- else:
- return func(*args, **kwargs)
- wrapper.__name__ = func.__name__
- wrapper.__doc__ = func.__doc__
- return wrapper
-
-
-@app.route('/api/token')
-@login_really_required
-def get_auth_token():
- token = g.user.generate_auth_token(600)
- return jsonify({'token': token.decode('ascii'), 'duration': 600})
-
-
-class UploadsRes(Resource):
- """ Uploads """
- @login_really_required
- def get(self):
- """
- Get a list of current users uploads.
-
- .. :quickref: upload; Get a list of current users uploads.
-
- **Example request**:
-
- .. sourcecode:: http
-
- GET /nomad/api/uploads HTTP/1.1
- Accept: application/json
-
- **Example response**:
-
- .. sourcecode:: http
-
- HTTP/1.1 200 OK
- Vary: Accept
- Content-Type: application/json
-
- [
- {
- "name": "examples_vasp_6.zip",
- "upload_id": "5b89469e0d80d40008077dbc",
- "presigned_url": "http://minio:9000/uploads/5b89469e0d80d40008077dbc?X-Amz-Algorithm=AWS4-...",
- "create_time": "2018-08-31T13:46:06.781000",
- "upload_time": "2018-08-31T13:46:07.531000",
- "is_stale": false,
- "completed": true,
- "status": "SUCCESS",
- "current_task": "cleanup",
- "tasks": ["uploading", "extracting", "parse_all", "cleanup"]
- "errors": [],
- "warnings": []
- }
- ]
-
- :resheader Content-Type: application/json
- :status 200: uploads successfully provided
- :returns: list of :class:`nomad.data.Upload`
- """
- return [upload.json_dict for upload in Upload.user_uploads(g.user)], 200
-
- @login_really_required
- def post(self):
- """
- Create a new upload. Creating an upload on its own wont do much, but provide
- a *presigned* upload URL. PUT a file to this URL to do the actual upload and
- initiate the processing.
-
- .. :quickref: upload; Create a new upload.
-
- **Example request**:
-
- .. sourcecode:: http
-
- POST /nomad/api/uploads HTTP/1.1
- Accept: application/json
- Content-Type: application/json
-
- {
- "name": "vasp_data.zip"
- }
-
- **Example response**:
-
- .. sourcecode:: http
-
- HTTP/1.1 200 OK
- Vary: Accept
- Content-Type: application/json
-
- {
- "name": "vasp_data.zip",
- "upload_id": "5b89469e0d80d40008077dbc",
- "presigned_url": "http://minio:9000/uploads/5b89469e0d80d40008077dbc?X-Amz-Algorithm=AWS4-...",
- "create_time": "2018-08-31T13:46:06.781000",
- "upload_time": "2018-08-31T13:46:07.531000",
- "is_stale": false,
- "completed": true,
- "status": "SUCCESS",
- "current_task": "cleanup",
- "tasks": ["uploading", "extracting", "parse_all", "cleanup"]
- "errors": [],
- "warnings": [],
- "calcs": [
- {
- "current_task": "archiving",
- "tasks": ["parsing", "normalizing", "archiving"]
- "status": "SUCCESS",
- "errors": [],
- "warnings": [],
- "parser": "parsers/vasp",
- "mainfile": "Si.xml"
- }
- ]
- }
-
- :jsonparam string name: An optional name for the upload.
- :jsonparem string local_path: An optional path the a file that is already on the server.
- In this case, uploading a file won't be possible, the local file is processed
- immediatly as if it was uploaded.
- :reqheader Content-Type: application/json
- :resheader Content-Type: application/json
- :status 200: upload successfully created
- :returns: a new instance of :class:`nomad.data.Upload`
- """
- json_data = request.get_json()
- if json_data is None:
- json_data = {}
-
- upload = Upload.create(
- user=g.user,
- name=json_data.get('name'),
- local_path=json_data.get('local_path'))
-
- if upload.local_path is not None:
- logger = get_logger(
- __name__, endpoint='uploads', action='post', upload_id=upload.upload_id)
- logger.info('file uploaded offline')
- upload.upload_time = datetime.now()
- upload.process()
- logger.info('initiated processing')
-
- return upload.json_dict, 200
-
-
-class UploadRes(Resource):
- """ Uploads """
- @login_really_required
- def get(self, upload_id):
- """
- Get an update on an existing upload. Will not only return the upload, but
- also its calculations paginated. Use the pagination params to determine
- the page.
-
- .. :quickref: upload; Get an update for an existing upload.
-
- **Example request**:
-
- .. sourcecode:: http
-
- GET /nomad/api/uploads/5b89469e0d80d40008077dbc HTTP/1.1
- Accept: application/json
-
- **Example response**:
-
- .. sourcecode:: http
-
- HTTP/1.1 200 OK
- Vary: Accept
- Content-Type: application/json
-
- {
- "name": "vasp_data.zip",
- "upload_id": "5b89469e0d80d40008077dbc",
- "presigned_url": "http://minio:9000/uploads/5b89469e0d80d40008077dbc?X-Amz-Algorithm=AWS4-...",
- "create_time": "2018-08-31T13:46:06.781000",
- "upload_time": "2018-08-31T13:46:07.531000",
- "is_stale": false,
- "completed": true,
- "status": "SUCCESS",
- "current_task": "cleanup",
- "tasks": ["uploading", "extracting", "parse_all", "cleanup"]
- "errors": [],
- "warnings": [],
- "calcs": {
- "pagination": {
- "total": 1,
- "page": 1,
- "per_page": 25
- },
- "results": [
- {
- "current_task": "archiving",
- "tasks": ["parsing", "normalizing", "archiving"]
- "status": "SUCCESS",
- "errors": [],
- "warnings": [],
- "parser": "parsers/vasp",
- "mainfile": "Si.xml"
- }
- ]
- }
- }
-
- :param string upload_id: the id for the upload
- :qparam int page: the page starting with 1
- :qparam int per_page: desired calcs per page
- :qparam str order_by: the field to sort the calcs by, use [status,mainfile]
- :resheader Content-Type: application/json
- :status 200: upload successfully updated and retrieved
- :status 404: upload with id does not exist
- :returns: the :class:`nomad.data.Upload` instance
- """
- try:
- upload = Upload.get(upload_id)
- except KeyError:
- abort(404, message='Upload with id %s does not exist.' % upload_id)
-
- if upload.user_id != g.user.email:
- abort(404, message='Upload with id %s does not exist.' % upload_id)
-
- try:
- page = int(request.args.get('page', 1))
- per_page = int(request.args.get('per_page', 10))
- order_by = str(request.args.get('order_by', 'mainfile'))
- order = int(str(request.args.get('order', -1)))
- except Exception:
- abort(400, message='invalid pagination or ordering')
-
- try:
- assert page >= 1
- assert per_page > 0
- except AssertionError:
- abort(400, message='invalid pagination')
-
- if order_by not in ['mainfile', 'status', 'parser']:
- abort(400, message='invalid order_by field %s' % order_by)
-
- order_by = ('-%s' if order == -1 else '+%s') % order_by
-
- calcs = upload.all_calcs((page - 1) * per_page, page * per_page, order_by)
- failed_calcs = upload.failed_calcs
- result = upload.json_dict
- result['calcs'] = {
- 'pagination': dict(
- total=upload.total_calcs, page=page, per_page=per_page,
- successes=upload.processed_calcs - failed_calcs, failures=failed_calcs),
- 'results': [calc.json_dict for calc in calcs]
- }
-
- return result, 200
-
- @login_really_required
- def post(self, upload_id):
- """
- Move an upload out of the staging area. This changes the visibility of the upload.
- Clients can specify, if the calcs should be restricted.
-
- .. :quickref: upload; Move an upload out of the staging area.
-
- **Example request**:
-
- .. sourcecode:: http
-
- POST /nomad/api/uploads HTTP/1.1
- Accept: application/json
- Content-Type: application/json
-
- {
- "operation": "unstage"
- }
-
-
- :param string upload_id: the upload id
- :resheader Content-Type: application/json
- :status 200: upload unstaged successfully
- :status 404: upload could not be found
- :status 400: if the operation is not supported
- :returns: the upload record
- """
- try:
- upload = Upload.get(upload_id)
- except KeyError:
- abort(404, message='Upload with id %s does not exist.' % upload_id)
-
- if upload.user_id != g.user.email:
- abort(404, message='Upload with id %s does not exist.' % upload_id)
-
- json_data = request.get_json()
- if json_data is None:
- json_data = {}
-
- operation = json_data.get('operation')
- if operation == 'unstage':
- upload.unstage()
- return upload.json_dict, 200
-
- abort(400, message='Unsuported operation %s.' % operation)
-
- @login_really_required
- def delete(self, upload_id):
- """
- Deletes an existing upload. Only ``is_ready`` or ``is_stale`` uploads
- can be deleted. Deleting an upload in processing is not allowed.
-
- .. :quickref: upload; Delete an existing upload.
-
- **Example request**:
-
- .. sourcecode:: http
-
- DELETE /nomad/api/uploads/5b89469e0d80d40008077dbc HTTP/1.1
- Accept: application/json
-
- :param string upload_id: the id for the upload
- :resheader Content-Type: application/json
- :status 200: upload successfully deleted
- :status 400: upload cannot be deleted
- :status 404: upload with id does not exist
- :returns: the :class:`nomad.data.Upload` instance with the latest processing state
- """
- try:
- upload = Upload.get(upload_id)
- except KeyError:
- abort(404, message='Upload with id %s does not exist.' % upload_id)
-
- if upload.user_id != g.user.email:
- abort(404, message='Upload with id %s does not exist.' % upload_id)
-
- try:
- upload.delete()
- return upload.json_dict, 200
- except NotAllowedDuringProcessing:
- abort(400, message='You must not delete an upload during processing.')
-
-
-class UploadFileRes(Resource):
- """
- Upload a file to an existing upload. Can be used to upload files via bowser
- or other http clients like curl. This will start the processing of the upload.
-
- There are two basic ways to upload a file: multipart-formdata or simply streaming
- the file data. Both are supported. The later one does not allow to transfer a
- filename or other meta-data. If a filename is available, it will become the
- name of the upload.
-
- .. :quickref: upload; Upload a file to an existing upload.
-
- **Curl examples for both approaches**:
-
- .. sourcecode:: sh
-
- curl -X put "/nomad/api/uploads/5b89469e0d80d40008077dbc/file" -F file=@local_file
- curl "/nomad/api/uploads/5b89469e0d80d40008077dbc/file" --upload-file local_file
-
- :param string upload_id: the upload_id of the upload
- :resheader Content-Type: application/json
- :status 200: upload successfully received.
- :status 404: upload with given id does not exist
- :status 400: if the fileformat is not supported or the form data is different than expected.
- :returns: the upload (see GET /uploads/<upload_id>)
- """
- @login_really_required
- def put(self, upload_id):
- logger = get_logger(__name__, endpoint='upload', action='put', upload_id=upload_id)
-
- try:
- upload = Upload.get(upload_id)
- except KeyError:
- abort(404, message='Upload with id %s does not exist.' % upload_id)
-
- if upload.upload_time is not None:
- abort(400, message='A file was already uploaded to this uploade before.')
-
- uploadFile = UploadFile(upload_id)
-
- if request.mimetype == 'application/multipart-formdata':
- # multipart formdata, e.g. with curl -X put "url" -F file=@local_file
- # might have performance issues for large files: https://github.com/pallets/flask/issues/2086
- if 'file' in request.files:
- abort(400, message='Bad multipart-formdata, there is no file part.')
- file = request.files['file']
- if upload.name is '':
- upload.name = file.filename
-
- file.save(uploadFile.os_path)
- else:
- # simple streaming data in HTTP body, e.g. with curl "url" -T local_file
- try:
- with uploadFile.open('wb') as f:
- while not request.stream.is_exhausted:
- f.write(request.stream.read(1024))
-
- except Exception as e:
- logger.error('Error on streaming upload', exc_info=e)
- abort(400, message='Some IO went wrong, download probably aborted/disrupted.')
-
- if not uploadFile.is_valid:
- uploadFile.delete()
- abort(400, message='Bad file format, excpected %s.' % ", ".join(UploadFile.formats))
-
- logger.info('received uploaded file')
- upload.upload_time = datetime.now()
- upload.process()
- logger.info('initiated processing')
-
- return upload.json_dict, 200
-
-
-class RepoCalcRes(Resource):
- def get(self, upload_hash, calc_hash):
- """
- Get calculation data in repository form, which only entails the quanties shown
- in the repository. This is basically the elastic search index entry for the
- requested calculations. Calcs are references via *upload_hash*, *calc_hash*
- pairs.
-
- .. :quickref: repo; Get calculation data in repository form.
-
- **Example request**:
-
- .. sourcecode:: http
-
- GET /nomad/api/repo/W36aqCzAKxOCfIiMFsBJh3nHPb4a/7ddvtfRfZAvc3Crr7jOJ8UH0T34I HTTP/1.1
- Accept: application/json
-
- **Example response**:
-
- .. sourcecode:: http
-
- HTTP/1.1 200 OK
- Vary: Accept
- Content-Type: application/json
-
- {
- "calc_hash":"7ddvtfRfZAvc3Crr7jOJ8UH0T34I",
- "upload_time":"2018-08-30T08:41:51.771367",
- "upload_id":"5b87adb813a441000a70a968",
- "upload_hash":"W36aqCzAKxOCfIiMFsBJh3nHPb4a",
- "mainfile":"RopD3Mo8oMV_-E5bh8uW5PiiCRkH1/data/BrK_svSi/TFCC010.CAB/vasprun.xml.relax1",
- "program_name":"VASP",
- "program_version":"4.6.35 3Apr08 complex parallel LinuxIFC",
- "chemical_composition_bulk_reduced":"BrKSi2",
- "program_basis_set_type":"plane waves",
- "atom_species":[
- 35,
- 19,
- 14,
- 14
- ],
- "system_type":"Bulk",
- "crystal_system":"orthorhombic",
- "space_group_number":47,
- "configuration_raw_gid":"sq6wTJjRKb2VTajoDLVWDxHCgyN6i",
- "XC_functional_name":"GGA_X_PBE"
- }
-
- :param string upload_hash: the hash of the upload (from uploaded file contents)
- :param string calc_hash: the hash of the calculation (from mainfile)
- :resheader Content-Type: application/json
- :status 200: calc successfully retrieved
- :status 404: calc with given hashes does not exist
- :returns: the repository calculation entry
- """
- try:
- return RepoCalc.get(id='%s/%s' % (upload_hash, calc_hash)).json_dict, 200
- except NotFoundError:
- abort(404, message='There is no calculation for %s/%s' % (upload_hash, calc_hash))
- except Exception as e:
- abort(500, message=str(e))
-
-
-class RepoCalcsRes(Resource):
- @auth.login_required
- def get(self):
- """
- Get *'all'* calculations in repository from, paginated.
-
- .. :quickref: repo; Get *'all'* calculations in repository from, paginated.
-
- **Example request**:
-
- .. sourcecode:: http
-
- GET /nomad/api/repo?page=1&per_page=25 HTTP/1.1
- Accept: application/json
-
- **Example response**:
-
- .. sourcecode:: http
-
- HTTP/1.1 200 OK
- Vary: Accept
- Content-Type: application/json
-
- {
- "pagination":{
- "total":1,
- "page":1,
- "per_page":25
- },
- "results":[
- {
- "calc_hash":"7ddvtfRfZAvc3Crr7jOJ8UH0T34I",
- "upload_time":"2018-08-30T08:41:51.771367",
- "upload_id":"5b87adb813a441000a70a968",
- "upload_hash":"W36aqCzAKxOCfIiMFsBJh3nHPb4a",
- "mainfile":"RopD3Mo8oMV_-E5bh8uW5PiiCRkH1/data/BrK_svSi/TFCC010.CAB/vasprun.xml.relax1",
- "program_name":"VASP",
- "program_version":"4.6.35 3Apr08 complex parallel LinuxIFC",
- "chemical_composition_bulk_reduced":"BrKSi2",
- "program_basis_set_type":"plane waves",
- "atom_species":[
- 35,
- 19,
- 14,
- 14
- ],
- "system_type":"Bulk",
- "crystal_system":"orthorhombic",
- "space_group_number":47,
- "configuration_raw_gid":"sq6wTJjRKb2VTajoDLVWDxHCgyN6i",
- "XC_functional_name":"GGA_X_PBE"
- }
- ]
- }
-
- :qparam int page: the page starting with 1
- :qparam int per_page: desired calcs per page
- :qparam string owner: specifies which cals to return: all|user|staging, default is all
- :resheader Content-Type: application/json
- :status 200: calcs successfully retrieved
- :returns: a list of repository entries in ``results`` and pagination info
- """
- # TODO use argparse? bad request reponse an bad params, pagination as decorator
- page = int(request.args.get('page', 1))
- per_page = int(request.args.get('per_page', 10))
- owner = request.args.get('owner', 'all')
-
- try:
- assert page >= 1
- assert per_page > 0
- except AssertionError:
- abort(400, message='invalid pagination')
-
- if owner == 'all':
- search = RepoCalc.search().query('match_all')
- elif owner == 'user':
- if g.user is None:
- abort(401, message='Authentication required for owner value user.')
- search = RepoCalc.search().query('match_all')
- search = search.filter('term', user_id=g.user.email)
- elif owner == 'staging':
- if g.user is None:
- abort(401, message='Authentication required for owner value user.')
- search = RepoCalc.search().query('match_all')
- search = search.filter('term', user_id=g.user.email).filter('term', staging=True)
- else:
- abort(400, message='Invalid owner value. Valid values are all|user|staging, default is all')
-
- search = search[(page - 1) * per_page: page * per_page]
- return {
- 'pagination': {
- 'total': search.count(),
- 'page': page,
- 'per_page': per_page
- },
- 'results': [result.json_dict for result in search]
- }
-
-
-@app.route('%s/logs/<string:upload_hash>/<string:calc_hash>' % base_path, methods=['GET'])
-def get_calc_proc_log(upload_hash, calc_hash):
- """
- Get calculation processing log. Calcs are references via *upload_hash*, *calc_hash*
- pairs.
-
- .. :quickref: archive; Get calculation processing logs.
-
- **Example request**:
-
- .. sourcecode:: http
-
- GET /nomad/api/logs/W36aqCzAKxOCfIiMFsBJh3nHPb4a/7ddvtfRfZAvc3Crr7jOJ8UH0T34I HTTP/1.1
- Accept: application/json
-
- :param string upload_hash: the hash of the upload (from uploaded file contents)
- :param string calc_hash: the hash of the calculation (from mainfile)
- :resheader Content-Type: application/json
- :status 200: calc successfully retrieved
- :status 404: calc with given hashes does not exist
- :returns: the log data, a line by line sequence of structured logs
- """
- archive_id = '%s/%s' % (upload_hash, calc_hash)
-
- try:
- archive = ArchiveLogFile(archive_id)
- archive_path = archive.os_path
-
- rv = send_file(
- archive_path,
- mimetype='application/text',
- as_attachment=True,
- attachment_filename=os.path.basename(archive_path))
-
- return rv
- except KeyError:
- abort(404, message='Archive/calculation %s does not exist.' % archive_id)
- except FileNotFoundError:
- abort(404, message='Archive/calculation %s does not exist.' % archive_id)
- except Exception as e:
- logger = get_logger(
- __name__, endpoint='logs', action='get',
- upload_hash=upload_hash, calc_hash=calc_hash)
- logger.error('Exception on accessing calc proc log', exc_info=e)
- abort(500, message='Could not accessing the logs.')
-
-
-@app.route('%s/archive/<string:upload_hash>/<string:calc_hash>' % base_path, methods=['GET'])
-def get_calc(upload_hash, calc_hash):
- """
- Get calculation data in archive form. Calcs are references via *upload_hash*, *calc_hash*
- pairs.
-
- .. :quickref: archive; Get calculation data in archive form.
-
- **Example request**:
-
- .. sourcecode:: http
-
- GET /nomad/api/archive/W36aqCzAKxOCfIiMFsBJh3nHPb4a/7ddvtfRfZAvc3Crr7jOJ8UH0T34I HTTP/1.1
- Accept: application/json
-
- :param string upload_hash: the hash of the upload (from uploaded file contents)
- :param string calc_hash: the hash of the calculation (from mainfile)
- :resheader Content-Type: application/json
- :status 200: calc successfully retrieved
- :status 404: calc with given hashes does not exist
- :returns: the metainfo formated JSON data of the requested calculation
- """
- archive_id = '%s/%s' % (upload_hash, calc_hash)
-
- try:
- archive = ArchiveFile(archive_id)
- archive_path = archive.os_path
-
- rv = send_file(
- archive_path,
- mimetype='application/json',
- as_attachment=True,
- attachment_filename=os.path.basename(archive_path))
-
- if config.files.compress_archive:
- rv.headers['Content-Encoding'] = 'gzip'
-
- return rv
- except KeyError:
- abort(404, message='Archive %s does not exist.' % archive_id)
- except FileNotFoundError:
- abort(404, message='Archive %s does not exist.' % archive_id)
- except Exception as e:
- logger = get_logger(
- __name__, endpoint='archive', action='get',
- upload_hash=upload_hash, calc_hash=calc_hash)
- logger.error('Exception on accessing archive', exc_info=e)
- abort(500, message='Could not accessing the archive.')
-
-
-@app.route('%s/raw/<string:upload_hash>/<string:calc_hash>' % base_path, methods=['GET'])
-def get_raw(upload_hash, calc_hash):
- """
- Get calculation mainfile raw data. Calcs are references via *upload_hash*, *calc_hash*
- pairs. Returns the mainfile, unless an aux_file is specified. Aux files are stored
- in repository entries. See ``/repo`` endpoint.
-
- .. :quickref: repo; Get calculation raw data.
-
- **Example request**:
-
- .. sourcecode:: http
-
- GET /nomad/api/raw/W36aqCzAKxOCfIiMFsBJh3nHPb4a/7ddvtfRfZAvc3Crr7jOJ8UH0T34I HTTP/1.1
- Accept: application/gz
-
- :param string upload_hash: the hash of the upload (from uploaded file contents)
- :param string calc_hash: the hash of the calculation (from mainfile)
- :qparam str auxfile: an optional aux_file to download the respective aux file, default is mainfile
- :qparam all: set any value to get a .zip with main and aux files instead of an individual file
- :resheader Content-Type: application/json
- :status 200: calc raw data successfully retrieved
- :status 404: calc with given hashes does not exist or the given aux file does not exist
- :returns: the raw data in body
- """
- archive_id = '%s/%s' % (upload_hash, calc_hash)
- logger = get_logger(__name__, endpoint='raw', action='get', archive_id=archive_id)
-
- try:
- repo = RepoCalc.get(id=archive_id)
- except NotFoundError:
- abort(404, message='There is no calculation for %s/%s' % (upload_hash, calc_hash))
- except Exception as e:
- abort(500, message=str(e))
-
- repository_file = RepositoryFile(upload_hash)
-
- @contextmanager
- def raw_file(filename):
- try:
- the_file = repository_file.get_file(filename)
- with the_file.open() as f:
- yield f
- except KeyError:
- abort(404, message='The file %s does not exist.' % filename)
- except FileNotFoundError:
- abort(404, message='The file %s does not exist.' % filename)
-
- get_all = request.args.get('all', None) is not None
- if get_all:
- # retrieve the 'whole' calculation, meaning the mainfile and all aux files as
- # a .zip archive
- def generator():
- """ Stream a zip file with all files using zipstream. """
- def iterator():
- """ Replace the directory based iter of zipstream with an iter over all raw files. """
- def write(filename):
- """ Write a raw file to the zipstream. """
- def iter_content():
- """ Iterate the raw file contents. """
- with raw_file(filename) as file_object:
- while True:
- data = file_object.read(1024)
- if not data:
- break
- yield data
- return dict(arcname=filename, iterable=iter_content())
-
- yield write(repo.mainfile)
- try:
- for auxfile in repo.aux_files:
- yield write(os.path.join(os.path.dirname(repo.mainfile), auxfile))
- except Exception as e:
- logger.error('Exception while accessing auxfiles.', exc_info=e)
-
- zip_stream = zipstream.ZipFile(mode='w', compression=ZIP_DEFLATED)
- zip_stream.paths_to_write = iterator()
-
- for chunk in zip_stream:
- yield chunk
-
- response = Response(generator(), mimetype='application/zip')
- response.headers['Content-Disposition'] = 'attachment; filename={}'.format('%s.zip' % archive_id)
- return response
- else:
- # retrieve an individual raw file
- auxfile = request.args.get('auxfile', None)
- if auxfile:
- filename = os.path.join(os.path.dirname(repo.mainfile), auxfile)
- else:
- filename = repo.mainfile
-
- try:
- with raw_file(filename) as f:
- rv = send_file(
- f,
- mimetype='application/octet-stream',
- as_attachment=True,
- attachment_filename=os.path.basename(filename))
- return rv
- except HTTPException as e:
- raise e
- except Exception as e:
- logger = get_logger(
- __name__, endpoint='archive', action='get',
- upload_hash=upload_hash, calc_hash=calc_hash)
- logger.error('Exception on accessing archive', exc_info=e)
- abort(500, message='Could not accessing the archive.')
-
-
-@app.route('%s/admin/<string:operation>' % base_path, methods=['POST'])
-def call_admin_operation(operation):
- if operation == 'repair_uploads':
- Upload.repair_all()
- if operation == 'reset':
- infrastructure.reset()
- else:
- abort(400, message='Unknown operation %s' % operation)
-
- return 'done', 200
-
-
-api.add_resource(UploadsRes, '%s/uploads' % base_path)
-api.add_resource(UploadRes, '%s/uploads/<string:upload_id>' % base_path)
-api.add_resource(UploadFileRes, '%s/uploads/<string:upload_id>/file' % base_path)
-api.add_resource(RepoCalcsRes, '%s/repo' % base_path)
-api.add_resource(RepoCalcRes, '%s/repo/<string:upload_hash>/<string:calc_hash>' % base_path)
-
-
-if __name__ == '__main__':
- app.run(debug=True, port=8000)
diff --git a/nomad/api/__init__.py b/nomad/api/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..b837a030c8646b11519403f61e2bc041fd8a578c
--- /dev/null
+++ b/nomad/api/__init__.py
@@ -0,0 +1,20 @@
+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from .app import app
+from . import upload, repository, archive
+
+
+if __name__ == '__main__':
+ app.run(debug=True, port=8000)
diff --git a/nomad/api/app.py b/nomad/api/app.py
new file mode 100644
index 0000000000000000000000000000000000000000..ff96d31fd69aad5cb8b25fce2b172adad977d658
--- /dev/null
+++ b/nomad/api/app.py
@@ -0,0 +1,91 @@
+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from flask import Flask, g
+from flask_restful import Api, abort
+from flask_cors import CORS
+from flask_httpauth import HTTPBasicAuth
+import os.path
+
+from nomad import config, infrastructure
+from nomad.user import User
+from nomad.processing import Upload
+
+base_path = config.services.api_base_path
+
+app = Flask(
+ __name__,
+ static_url_path='%s/docs' % base_path,
+ static_folder=os.path.abspath(os.path.join(os.path.dirname(__file__), '../docs/.build/html')))
+CORS(app)
+
+app.config['SECRET_KEY'] = config.services.api_secret
+
+auth = HTTPBasicAuth()
+api = Api(app)
+
+
+@app.before_first_request
+def setup():
+ infrastructure.setup()
+
+
+@auth.verify_password
+def verify_password(username_or_token, password):
+ # first try to authenticate by token
+ g.user = User.verify_auth_token(username_or_token)
+ if not g.user:
+ # try to authenticate with username/password
+ try:
+ g.user = User.verify_user_password(username_or_token, password)
+ except Exception:
+ return False
+
+ if not g.user:
+ return True # anonymous access
+
+ return True
+
+
+def login_really_required(func):
+ @auth.login_required
+ def wrapper(*args, **kwargs):
+ if g.user is None:
+ abort(401, message='Anonymous access is forbidden, authorization required')
+ else:
+ return func(*args, **kwargs)
+ wrapper.__name__ = func.__name__
+ wrapper.__doc__ = func.__doc__
+ return wrapper
+
+
+@app.route('/api/token')
+@login_really_required
+def get_auth_token():
+ assert False, 'All authorization is none via NOMAD-coe repository GUI'
+ # TODO all authorization is done via NOMAD-coe repository GUI
+ # token = g.user.generate_auth_token(600)
+ # return jsonify({'token': token.decode('ascii'), 'duration': 600})
+
+
+@app.route('%s/admin/<string:operation>' % base_path, methods=['POST'])
+def call_admin_operation(operation):
+ if operation == 'repair_uploads':
+ Upload.repair_all()
+ if operation == 'reset':
+ infrastructure.reset()
+ else:
+ abort(400, message='Unknown operation %s' % operation)
+
+ return 'done', 200
diff --git a/nomad/api/archive.py b/nomad/api/archive.py
new file mode 100644
index 0000000000000000000000000000000000000000..4cf9347ee712de67e59fa8fd473e1288b154516b
--- /dev/null
+++ b/nomad/api/archive.py
@@ -0,0 +1,123 @@
+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import os.path
+
+from flask import send_file
+from flask_restful import abort
+
+from nomad import config
+from nomad.files import ArchiveFile, ArchiveLogFile
+from nomad.utils import get_logger
+
+from .app import app, base_path
+
+
+@app.route('%s/logs/<string:upload_hash>/<string:calc_hash>' % base_path, methods=['GET'])
+def get_calc_proc_log(upload_hash, calc_hash):
+ """
+ Get calculation processing log. Calcs are references via *upload_hash*, *calc_hash*
+ pairs.
+
+ .. :quickref: archive; Get calculation processing logs.
+
+ **Example request**:
+
+ .. sourcecode:: http
+
+ GET /nomad/api/logs/W36aqCzAKxOCfIiMFsBJh3nHPb4a/7ddvtfRfZAvc3Crr7jOJ8UH0T34I HTTP/1.1
+ Accept: application/json
+
+ :param string upload_hash: the hash of the upload (from uploaded file contents)
+ :param string calc_hash: the hash of the calculation (from mainfile)
+ :resheader Content-Type: application/json
+ :status 200: calc successfully retrieved
+ :status 404: calc with given hashes does not exist
+ :returns: the log data, a line by line sequence of structured logs
+ """
+ archive_id = '%s/%s' % (upload_hash, calc_hash)
+
+ try:
+ archive = ArchiveLogFile(archive_id)
+ if not archive.exists():
+ raise FileNotFoundError()
+
+ archive_path = archive.os_path
+
+ rv = send_file(
+ archive_path,
+ mimetype='application/text',
+ as_attachment=True,
+ attachment_filename=os.path.basename(archive_path))
+
+ return rv
+ except FileNotFoundError:
+ abort(404, message='Archive/calculation %s does not exist.' % archive_id)
+ except Exception as e:
+ logger = get_logger(
+ __name__, endpoint='logs', action='get',
+ upload_hash=upload_hash, calc_hash=calc_hash)
+ logger.error('Exception on accessing calc proc log', exc_info=e)
+ abort(500, message='Could not accessing the logs.')
+
+
+@app.route('%s/archive/<string:upload_hash>/<string:calc_hash>' % base_path, methods=['GET'])
+def get_calc(upload_hash, calc_hash):
+ """
+ Get calculation data in archive form. Calcs are references via *upload_hash*, *calc_hash*
+ pairs.
+
+ .. :quickref: archive; Get calculation data in archive form.
+
+ **Example request**:
+
+ .. sourcecode:: http
+
+ GET /nomad/api/archive/W36aqCzAKxOCfIiMFsBJh3nHPb4a/7ddvtfRfZAvc3Crr7jOJ8UH0T34I HTTP/1.1
+ Accept: application/json
+
+ :param string upload_hash: the hash of the upload (from uploaded file contents)
+ :param string calc_hash: the hash of the calculation (from mainfile)
+ :resheader Content-Type: application/json
+ :status 200: calc successfully retrieved
+ :status 404: calc with given hashes does not exist
+ :returns: the metainfo formated JSON data of the requested calculation
+ """
+ archive_id = '%s/%s' % (upload_hash, calc_hash)
+
+ try:
+ archive = ArchiveFile(archive_id)
+ if not archive.exists():
+ raise FileNotFoundError()
+
+ archive_path = archive.os_path
+
+ rv = send_file(
+ archive_path,
+ mimetype='application/json',
+ as_attachment=True,
+ attachment_filename=os.path.basename(archive_path))
+
+ if config.files.compress_archive:
+ rv.headers['Content-Encoding'] = 'gzip'
+
+ return rv
+ except FileNotFoundError:
+ abort(404, message='Archive %s does not exist.' % archive_id)
+ except Exception as e:
+ logger = get_logger(
+ __name__, endpoint='archive', action='get',
+ upload_hash=upload_hash, calc_hash=calc_hash)
+ logger.error('Exception on accessing archive', exc_info=e)
+ abort(500, message='Could not accessing the archive.')
diff --git a/nomad/api/repository.py b/nomad/api/repository.py
new file mode 100644
index 0000000000000000000000000000000000000000..c5f887668c66b46a8793573fa342253fd37c0e90
--- /dev/null
+++ b/nomad/api/repository.py
@@ -0,0 +1,305 @@
+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import os.path
+from contextlib import contextmanager
+from zipfile import ZIP_DEFLATED
+
+import zipstream
+from elasticsearch.exceptions import NotFoundError
+from flask import Response, g, request, send_file
+from flask_restful import Resource, abort
+from werkzeug.exceptions import HTTPException
+
+from nomad.files import RepositoryFile
+from nomad.repo import RepoCalc
+from nomad.utils import get_logger
+
+from .app import api, app, auth, base_path
+
+
+class RepoCalcRes(Resource):
+ def get(self, upload_hash, calc_hash):
+ """
+ Get calculation data in repository form, which only entails the quanties shown
+ in the repository. This is basically the elastic search index entry for the
+ requested calculations. Calcs are references via *upload_hash*, *calc_hash*
+ pairs.
+
+ .. :quickref: repo; Get calculation data in repository form.
+
+ **Example request**:
+
+ .. sourcecode:: http
+
+ GET /nomad/api/repo/W36aqCzAKxOCfIiMFsBJh3nHPb4a/7ddvtfRfZAvc3Crr7jOJ8UH0T34I HTTP/1.1
+ Accept: application/json
+
+ **Example response**:
+
+ .. sourcecode:: http
+
+ HTTP/1.1 200 OK
+ Vary: Accept
+ Content-Type: application/json
+
+ {
+ "calc_hash":"7ddvtfRfZAvc3Crr7jOJ8UH0T34I",
+ "upload_time":"2018-08-30T08:41:51.771367",
+ "upload_id":"5b87adb813a441000a70a968",
+ "upload_hash":"W36aqCzAKxOCfIiMFsBJh3nHPb4a",
+ "mainfile":"RopD3Mo8oMV_-E5bh8uW5PiiCRkH1/data/BrK_svSi/TFCC010.CAB/vasprun.xml.relax1",
+ "program_name":"VASP",
+ "program_version":"4.6.35 3Apr08 complex parallel LinuxIFC",
+ "chemical_composition_bulk_reduced":"BrKSi2",
+ "program_basis_set_type":"plane waves",
+ "atom_species":[
+ 35,
+ 19,
+ 14,
+ 14
+ ],
+ "system_type":"Bulk",
+ "crystal_system":"orthorhombic",
+ "space_group_number":47,
+ "configuration_raw_gid":"sq6wTJjRKb2VTajoDLVWDxHCgyN6i",
+ "XC_functional_name":"GGA_X_PBE"
+ }
+
+ :param string upload_hash: the hash of the upload (from uploaded file contents)
+ :param string calc_hash: the hash of the calculation (from mainfile)
+ :resheader Content-Type: application/json
+ :status 200: calc successfully retrieved
+ :status 404: calc with given hashes does not exist
+ :returns: the repository calculation entry
+ """
+ try:
+ return RepoCalc.get(id='%s/%s' % (upload_hash, calc_hash)).json_dict, 200
+ except NotFoundError:
+ abort(404, message='There is no calculation for %s/%s' % (upload_hash, calc_hash))
+ except Exception as e:
+ abort(500, message=str(e))
+
+
+class RepoCalcsRes(Resource):
+ @auth.login_required
+ def get(self):
+ """
+ Get *'all'* calculations in repository from, paginated.
+
+ .. :quickref: repo; Get *'all'* calculations in repository from, paginated.
+
+ **Example request**:
+
+ .. sourcecode:: http
+
+ GET /nomad/api/repo?page=1&per_page=25 HTTP/1.1
+ Accept: application/json
+
+ **Example response**:
+
+ .. sourcecode:: http
+
+ HTTP/1.1 200 OK
+ Vary: Accept
+ Content-Type: application/json
+
+ {
+ "pagination":{
+ "total":1,
+ "page":1,
+ "per_page":25
+ },
+ "results":[
+ {
+ "calc_hash":"7ddvtfRfZAvc3Crr7jOJ8UH0T34I",
+ "upload_time":"2018-08-30T08:41:51.771367",
+ "upload_id":"5b87adb813a441000a70a968",
+ "upload_hash":"W36aqCzAKxOCfIiMFsBJh3nHPb4a",
+ "mainfile":"RopD3Mo8oMV_-E5bh8uW5PiiCRkH1/data/BrK_svSi/TFCC010.CAB/vasprun.xml.relax1",
+ "program_name":"VASP",
+ "program_version":"4.6.35 3Apr08 complex parallel LinuxIFC",
+ "chemical_composition_bulk_reduced":"BrKSi2",
+ "program_basis_set_type":"plane waves",
+ "atom_species":[
+ 35,
+ 19,
+ 14,
+ 14
+ ],
+ "system_type":"Bulk",
+ "crystal_system":"orthorhombic",
+ "space_group_number":47,
+ "configuration_raw_gid":"sq6wTJjRKb2VTajoDLVWDxHCgyN6i",
+ "XC_functional_name":"GGA_X_PBE"
+ }
+ ]
+ }
+
+ :qparam int page: the page starting with 1
+ :qparam int per_page: desired calcs per page
+ :qparam string owner: specifies which cals to return: all|user|staging, default is all
+ :resheader Content-Type: application/json
+ :status 200: calcs successfully retrieved
+ :returns: a list of repository entries in ``results`` and pagination info
+ """
+ # TODO use argparse? bad request reponse an bad params, pagination as decorator
+ page = int(request.args.get('page', 1))
+ per_page = int(request.args.get('per_page', 10))
+ owner = request.args.get('owner', 'all')
+
+ try:
+ assert page >= 1
+ assert per_page > 0
+ except AssertionError:
+ abort(400, message='invalid pagination')
+
+ if owner == 'all':
+ search = RepoCalc.search().query('match_all')
+ elif owner == 'user':
+ if g.user is None:
+ abort(401, message='Authentication required for owner value user.')
+ search = RepoCalc.search().query('match_all')
+ search = search.filter('term', user_id=g.user.email)
+ elif owner == 'staging':
+ if g.user is None:
+ abort(401, message='Authentication required for owner value user.')
+ search = RepoCalc.search().query('match_all')
+ search = search.filter('term', user_id=g.user.email).filter('term', staging=True)
+ else:
+ abort(400, message='Invalid owner value. Valid values are all|user|staging, default is all')
+
+ search = search[(page - 1) * per_page: page * per_page]
+ return {
+ 'pagination': {
+ 'total': search.count(),
+ 'page': page,
+ 'per_page': per_page
+ },
+ 'results': [result.json_dict for result in search]
+ }
+
+
+@app.route('%s/raw/<string:upload_hash>/<string:calc_hash>' % base_path, methods=['GET'])
+def get_raw(upload_hash, calc_hash):
+ """
+ Get calculation mainfile raw data. Calcs are references via *upload_hash*, *calc_hash*
+ pairs. Returns the mainfile, unless an aux_file is specified. Aux files are stored
+ in repository entries. See ``/repo`` endpoint.
+
+ .. :quickref: repo; Get calculation raw data.
+
+ **Example request**:
+
+ .. sourcecode:: http
+
+ GET /nomad/api/raw/W36aqCzAKxOCfIiMFsBJh3nHPb4a/7ddvtfRfZAvc3Crr7jOJ8UH0T34I HTTP/1.1
+ Accept: application/gz
+
+ :param string upload_hash: the hash of the upload (from uploaded file contents)
+ :param string calc_hash: the hash of the calculation (from mainfile)
+ :qparam str auxfile: an optional aux_file to download the respective aux file, default is mainfile
+ :qparam all: set any value to get a .zip with main and aux files instead of an individual file
+ :resheader Content-Type: application/json
+ :status 200: calc raw data successfully retrieved
+ :status 404: calc with given hashes does not exist or the given aux file does not exist
+ :returns: the raw data in body
+ """
+ archive_id = '%s/%s' % (upload_hash, calc_hash)
+ logger = get_logger(__name__, endpoint='raw', action='get', archive_id=archive_id)
+
+ try:
+ repo = RepoCalc.get(id=archive_id)
+ except NotFoundError:
+ abort(404, message='There is no calculation for %s/%s' % (upload_hash, calc_hash))
+ except Exception as e:
+ abort(500, message=str(e))
+
+ repository_file = RepositoryFile(upload_hash)
+
+ @contextmanager
+ def raw_file(filename):
+ try:
+ the_file = repository_file.get_file(filename)
+ with the_file.open() as f:
+ yield f
+ except KeyError:
+ abort(404, message='The file %s does not exist.' % filename)
+ except FileNotFoundError:
+ abort(404, message='The file %s does not exist.' % filename)
+
+ get_all = request.args.get('all', None) is not None
+ if get_all:
+ # retrieve the 'whole' calculation, meaning the mainfile and all aux files as
+ # a .zip archive
+ def generator():
+ """ Stream a zip file with all files using zipstream. """
+ def iterator():
+ """ Replace the directory based iter of zipstream with an iter over all raw files. """
+ def write(filename):
+ """ Write a raw file to the zipstream. """
+ def iter_content():
+ """ Iterate the raw file contents. """
+ with raw_file(filename) as file_object:
+ while True:
+ data = file_object.read(1024)
+ if not data:
+ break
+ yield data
+ return dict(arcname=filename, iterable=iter_content())
+
+ yield write(repo.mainfile)
+ try:
+ for auxfile in repo.aux_files:
+ yield write(os.path.join(os.path.dirname(repo.mainfile), auxfile))
+ except Exception as e:
+ logger.error('Exception while accessing auxfiles.', exc_info=e)
+
+ zip_stream = zipstream.ZipFile(mode='w', compression=ZIP_DEFLATED)
+ zip_stream.paths_to_write = iterator()
+
+ for chunk in zip_stream:
+ yield chunk
+
+ response = Response(generator(), mimetype='application/zip')
+ response.headers['Content-Disposition'] = 'attachment; filename={}'.format('%s.zip' % archive_id)
+ return response
+ else:
+ # retrieve an individual raw file
+ auxfile = request.args.get('auxfile', None)
+ if auxfile:
+ filename = os.path.join(os.path.dirname(repo.mainfile), auxfile)
+ else:
+ filename = repo.mainfile
+
+ try:
+ with raw_file(filename) as f:
+ rv = send_file(
+ f,
+ mimetype='application/octet-stream',
+ as_attachment=True,
+ attachment_filename=os.path.basename(filename))
+ return rv
+ except HTTPException as e:
+ raise e
+ except Exception as e:
+ logger = get_logger(
+ __name__, endpoint='archive', action='get',
+ upload_hash=upload_hash, calc_hash=calc_hash)
+ logger.error('Exception on accessing archive', exc_info=e)
+ abort(500, message='Could not accessing the archive.')
+
+
+api.add_resource(RepoCalcsRes, '%s/repo' % base_path)
+api.add_resource(RepoCalcRes, '%s/repo/<string:upload_hash>/<string:calc_hash>' % base_path)
diff --git a/nomad/api/upload.py b/nomad/api/upload.py
new file mode 100644
index 0000000000000000000000000000000000000000..eb5541862bb1323b347f7f191fc9e326e8166f39
--- /dev/null
+++ b/nomad/api/upload.py
@@ -0,0 +1,424 @@
+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from datetime import datetime
+
+from flask import g, request
+from flask_restful import Resource, abort
+
+from nomad.files import UploadFile
+from nomad.processing import NotAllowedDuringProcessing, Upload
+from nomad.utils import get_logger
+
+from .app import api, base_path, login_really_required
+
+
+class UploadsRes(Resource):
+ """ Uploads """
+ @login_really_required
+ def get(self):
+ """
+ Get a list of current users uploads.
+
+ .. :quickref: upload; Get a list of current users uploads.
+
+ **Example request**:
+
+ .. sourcecode:: http
+
+ GET /nomad/api/uploads HTTP/1.1
+ Accept: application/json
+
+ **Example response**:
+
+ .. sourcecode:: http
+
+ HTTP/1.1 200 OK
+ Vary: Accept
+ Content-Type: application/json
+
+ [
+ {
+ "name": "examples_vasp_6.zip",
+ "upload_id": "5b89469e0d80d40008077dbc",
+ "presigned_url": "http://minio:9000/uploads/5b89469e0d80d40008077dbc?X-Amz-Algorithm=AWS4-...",
+ "create_time": "2018-08-31T13:46:06.781000",
+ "upload_time": "2018-08-31T13:46:07.531000",
+ "is_stale": false,
+ "completed": true,
+ "status": "SUCCESS",
+ "current_task": "cleanup",
+ "tasks": ["uploading", "extracting", "parse_all", "cleanup"]
+ "errors": [],
+ "warnings": []
+ }
+ ]
+
+ :resheader Content-Type: application/json
+ :status 200: uploads successfully provided
+ :returns: list of :class:`nomad.data.Upload`
+ """
+ return [upload.json_dict for upload in Upload.user_uploads(g.user)], 200
+
+ @login_really_required
+ def post(self):
+ """
+ Create a new upload. Creating an upload on its own wont do much, but provide
+ a *presigned* upload URL. PUT a file to this URL to do the actual upload and
+ initiate the processing.
+
+ .. :quickref: upload; Create a new upload.
+
+ **Example request**:
+
+ .. sourcecode:: http
+
+ POST /nomad/api/uploads HTTP/1.1
+ Accept: application/json
+ Content-Type: application/json
+
+ {
+ "name": "vasp_data.zip"
+ }
+
+ **Example response**:
+
+ .. sourcecode:: http
+
+ HTTP/1.1 200 OK
+ Vary: Accept
+ Content-Type: application/json
+
+ {
+ "name": "vasp_data.zip",
+ "upload_id": "5b89469e0d80d40008077dbc",
+ "presigned_url": "http://minio:9000/uploads/5b89469e0d80d40008077dbc?X-Amz-Algorithm=AWS4-...",
+ "create_time": "2018-08-31T13:46:06.781000",
+ "upload_time": "2018-08-31T13:46:07.531000",
+ "is_stale": false,
+ "completed": true,
+ "status": "SUCCESS",
+ "current_task": "cleanup",
+ "tasks": ["uploading", "extracting", "parse_all", "cleanup"]
+ "errors": [],
+ "warnings": [],
+ "calcs": [
+ {
+ "current_task": "archiving",
+ "tasks": ["parsing", "normalizing", "archiving"]
+ "status": "SUCCESS",
+ "errors": [],
+ "warnings": [],
+ "parser": "parsers/vasp",
+ "mainfile": "Si.xml"
+ }
+ ]
+ }
+
+ :jsonparam string name: An optional name for the upload.
+ :jsonparem string local_path: An optional path the a file that is already on the server.
+ In this case, uploading a file won't be possible, the local file is processed
+ immediatly as if it was uploaded.
+ :reqheader Content-Type: application/json
+ :resheader Content-Type: application/json
+ :status 200: upload successfully created
+ :returns: a new instance of :class:`nomad.data.Upload`
+ """
+ json_data = request.get_json()
+ if json_data is None:
+ json_data = {}
+
+ upload = Upload.create(
+ user=g.user,
+ name=json_data.get('name'),
+ local_path=json_data.get('local_path'))
+
+ if upload.local_path is not None:
+ logger = get_logger(
+ __name__, endpoint='uploads', action='post', upload_id=upload.upload_id)
+ logger.info('file uploaded offline')
+ upload.upload_time = datetime.now()
+ upload.process()
+ logger.info('initiated processing')
+
+ return upload.json_dict, 200
+
+
+class UploadRes(Resource):
+ """ Uploads """
+ @login_really_required
+ def get(self, upload_id):
+ """
+ Get an update on an existing upload. Will not only return the upload, but
+ also its calculations paginated. Use the pagination params to determine
+ the page.
+
+ .. :quickref: upload; Get an update for an existing upload.
+
+ **Example request**:
+
+ .. sourcecode:: http
+
+ GET /nomad/api/uploads/5b89469e0d80d40008077dbc HTTP/1.1
+ Accept: application/json
+
+ **Example response**:
+
+ .. sourcecode:: http
+
+ HTTP/1.1 200 OK
+ Vary: Accept
+ Content-Type: application/json
+
+ {
+ "name": "vasp_data.zip",
+ "upload_id": "5b89469e0d80d40008077dbc",
+ "presigned_url": "http://minio:9000/uploads/5b89469e0d80d40008077dbc?X-Amz-Algorithm=AWS4-...",
+ "create_time": "2018-08-31T13:46:06.781000",
+ "upload_time": "2018-08-31T13:46:07.531000",
+ "is_stale": false,
+ "completed": true,
+ "status": "SUCCESS",
+ "current_task": "cleanup",
+ "tasks": ["uploading", "extracting", "parse_all", "cleanup"]
+ "errors": [],
+ "warnings": [],
+ "calcs": {
+ "pagination": {
+ "total": 1,
+ "page": 1,
+ "per_page": 25
+ },
+ "results": [
+ {
+ "current_task": "archiving",
+ "tasks": ["parsing", "normalizing", "archiving"]
+ "status": "SUCCESS",
+ "errors": [],
+ "warnings": [],
+ "parser": "parsers/vasp",
+ "mainfile": "Si.xml"
+ }
+ ]
+ }
+ }
+
+ :param string upload_id: the id for the upload
+ :qparam int page: the page starting with 1
+ :qparam int per_page: desired calcs per page
+ :qparam str order_by: the field to sort the calcs by, use [status,mainfile]
+ :resheader Content-Type: application/json
+ :status 200: upload successfully updated and retrieved
+ :status 404: upload with id does not exist
+ :returns: the :class:`nomad.data.Upload` instance
+ """
+ try:
+ upload = Upload.get(upload_id)
+ except KeyError:
+ abort(404, message='Upload with id %s does not exist.' % upload_id)
+
+ if upload.user_id != g.user.email:
+ abort(404, message='Upload with id %s does not exist.' % upload_id)
+
+ try:
+ page = int(request.args.get('page', 1))
+ per_page = int(request.args.get('per_page', 10))
+ order_by = str(request.args.get('order_by', 'mainfile'))
+ order = int(str(request.args.get('order', -1)))
+ except Exception:
+ abort(400, message='invalid pagination or ordering')
+
+ try:
+ assert page >= 1
+ assert per_page > 0
+ except AssertionError:
+ abort(400, message='invalid pagination')
+
+ if order_by not in ['mainfile', 'status', 'parser']:
+ abort(400, message='invalid order_by field %s' % order_by)
+
+ order_by = ('-%s' if order == -1 else '+%s') % order_by
+
+ calcs = upload.all_calcs((page - 1) * per_page, page * per_page, order_by)
+ failed_calcs = upload.failed_calcs
+ result = upload.json_dict
+ result['calcs'] = {
+ 'pagination': dict(
+ total=upload.total_calcs, page=page, per_page=per_page,
+ successes=upload.processed_calcs - failed_calcs, failures=failed_calcs),
+ 'results': [calc.json_dict for calc in calcs]
+ }
+
+ return result, 200
+
+ @login_really_required
+ def post(self, upload_id):
+ """
+ Move an upload out of the staging area. This changes the visibility of the upload.
+ Clients can specify, if the calcs should be restricted.
+
+ .. :quickref: upload; Move an upload out of the staging area.
+
+ **Example request**:
+
+ .. sourcecode:: http
+
+ POST /nomad/api/uploads HTTP/1.1
+ Accept: application/json
+ Content-Type: application/json
+
+ {
+ "operation": "unstage"
+ }
+
+
+ :param string upload_id: the upload id
+ :resheader Content-Type: application/json
+ :status 200: upload unstaged successfully
+ :status 404: upload could not be found
+ :status 400: if the operation is not supported
+ :returns: the upload record
+ """
+ try:
+ upload = Upload.get(upload_id)
+ except KeyError:
+ abort(404, message='Upload with id %s does not exist.' % upload_id)
+
+ if upload.user_id != g.user.email:
+ abort(404, message='Upload with id %s does not exist.' % upload_id)
+
+ json_data = request.get_json()
+ if json_data is None:
+ json_data = {}
+
+ operation = json_data.get('operation')
+ if operation == 'unstage':
+ upload.unstage()
+ return upload.json_dict, 200
+
+ abort(400, message='Unsuported operation %s.' % operation)
+
+ @login_really_required
+ def delete(self, upload_id):
+ """
+ Deletes an existing upload. Only ``is_ready`` or ``is_stale`` uploads
+ can be deleted. Deleting an upload in processing is not allowed.
+
+ .. :quickref: upload; Delete an existing upload.
+
+ **Example request**:
+
+ .. sourcecode:: http
+
+ DELETE /nomad/api/uploads/5b89469e0d80d40008077dbc HTTP/1.1
+ Accept: application/json
+
+ :param string upload_id: the id for the upload
+ :resheader Content-Type: application/json
+ :status 200: upload successfully deleted
+ :status 400: upload cannot be deleted
+ :status 404: upload with id does not exist
+ :returns: the :class:`nomad.data.Upload` instance with the latest processing state
+ """
+ try:
+ upload = Upload.get(upload_id)
+ except KeyError:
+ abort(404, message='Upload with id %s does not exist.' % upload_id)
+
+ if upload.user_id != g.user.email:
+ abort(404, message='Upload with id %s does not exist.' % upload_id)
+
+ try:
+ upload.delete()
+ return upload.json_dict, 200
+ except NotAllowedDuringProcessing:
+ abort(400, message='You must not delete an upload during processing.')
+
+
+class UploadFileRes(Resource):
+ """
+ Upload a file to an existing upload. Can be used to upload files via bowser
+ or other http clients like curl. This will start the processing of the upload.
+
+ There are two basic ways to upload a file: multipart-formdata or simply streaming
+ the file data. Both are supported. The later one does not allow to transfer a
+ filename or other meta-data. If a filename is available, it will become the
+ name of the upload.
+
+ .. :quickref: upload; Upload a file to an existing upload.
+
+ **Curl examples for both approaches**:
+
+ .. sourcecode:: sh
+
+ curl -X put "/nomad/api/uploads/5b89469e0d80d40008077dbc/file" -F file=@local_file
+ curl "/nomad/api/uploads/5b89469e0d80d40008077dbc/file" --upload-file local_file
+
+ :param string upload_id: the upload_id of the upload
+ :resheader Content-Type: application/json
+ :status 200: upload successfully received.
+ :status 404: upload with given id does not exist
+ :status 400: if the fileformat is not supported or the form data is different than expected.
+ :returns: the upload (see GET /uploads/<upload_id>)
+ """
+ @login_really_required
+ def put(self, upload_id):
+ logger = get_logger(__name__, endpoint='upload', action='put', upload_id=upload_id)
+
+ try:
+ upload = Upload.get(upload_id)
+ except KeyError:
+ abort(404, message='Upload with id %s does not exist.' % upload_id)
+
+ if upload.upload_time is not None:
+ abort(400, message='A file was already uploaded to this uploade before.')
+
+ uploadFile = UploadFile(upload_id)
+
+ if request.mimetype == 'application/multipart-formdata':
+ # multipart formdata, e.g. with curl -X put "url" -F file=@local_file
+ # might have performance issues for large files: https://github.com/pallets/flask/issues/2086
+ if 'file' in request.files:
+ abort(400, message='Bad multipart-formdata, there is no file part.')
+ file = request.files['file']
+ if upload.name is '':
+ upload.name = file.filename
+
+ file.save(uploadFile.os_path)
+ else:
+ # simple streaming data in HTTP body, e.g. with curl "url" -T local_file
+ try:
+ with uploadFile.open('wb') as f:
+ while not request.stream.is_exhausted:
+ f.write(request.stream.read(1024))
+
+ except Exception as e:
+ logger.error('Error on streaming upload', exc_info=e)
+ abort(400, message='Some IO went wrong, download probably aborted/disrupted.')
+
+ if not uploadFile.is_valid:
+ uploadFile.delete()
+ abort(400, message='Bad file format, excpected %s.' % ", ".join(UploadFile.formats))
+
+ logger.info('received uploaded file')
+ upload.upload_time = datetime.now()
+ upload.process()
+ logger.info('initiated processing')
+
+ return upload.json_dict, 200
+
+
+api.add_resource(UploadsRes, '%s/uploads' % base_path)
+api.add_resource(UploadRes, '%s/uploads/<string:upload_id>' % base_path)
+api.add_resource(UploadFileRes, '%s/uploads/<string:upload_id>/file' % base_path)
diff --git a/nomad/client.py b/nomad/client.py
index a602884b0eddf8105d5800ba5ae0987a25bc6383..8893bf8a5a3d6613836b41cfb2b6a390544a82e1 100644
--- a/nomad/client.py
+++ b/nomad/client.py
@@ -35,8 +35,8 @@ from nomad.normalizing import normalizers
api_base = 'http://localhost/nomad/api'
-user = 'other@gmail.com'
-pw = 'nomad'
+user = 'leonard.hofstadter@nomad-fairdi.tests.de'
+pw = 'password'
def handle_common_errors(func):
@@ -325,11 +325,13 @@ def api():
@cli.command(help='Runs tests and linting. Useful before commit code.')
-def qa():
+@click.option('--skip-tests', help='Do not test, just do code checks.', is_flag=True)
+def qa(skip_tests: bool):
os.chdir(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
ret_code = 0
- click.echo('Run tests ...')
- ret_code += os.system('python -m pytest tests')
+ if not skip_tests:
+ click.echo('Run tests ...')
+ ret_code += os.system('python -m pytest tests')
click.echo('Run code style checks ...')
ret_code += os.system('python -m pycodestyle --ignore=E501,E701 nomad tests')
click.echo('Run linter ...')
diff --git a/nomad/dependencies.py b/nomad/dependencies.py
index f6d7ce65d5007a1857d9a3245fec46a050a8ce81..f910cfceb092a1dbdc18a8fafc85ae7064e36024 100644
--- a/nomad/dependencies.py
+++ b/nomad/dependencies.py
@@ -158,11 +158,12 @@ class PythonGit():
dependencies = [
- PythonGit(
- name='repository-api',
- git_url='https://gitlab.mpcdf.mpg.de/NoMaD/NomadRepositoryParser.git',
- git_branch='v2.1'
- ),
+ # repository api is not really usuable, because it is written in python 2.x
+ # PythonGit(
+ # name='repository-api',
+ # git_url='https://gitlab.mpcdf.mpg.de/NoMaD/NomadRepositoryParser.git',
+ # git_branch='v2.1'
+ # ),
PythonGit(
name='nomad-meta-info',
git_url='https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info.git',
diff --git a/nomad/infrastructure.py b/nomad/infrastructure.py
index 7faca085a8e686076e4be586d666d95651e4be5e..8f60712d342c2da155a11c991b0dea620885a4c6 100644
--- a/nomad/infrastructure.py
+++ b/nomad/infrastructure.py
@@ -33,15 +33,17 @@ mongo_client = None
""" The pymongo mongodb client. """
+repository_db = None
+""" The repository postgres db sqlalchemy client. """
+
+
def setup():
""" Creates connections to mongodb and elastic search. """
global elastic_client
setup_logging()
setup_mongo()
setup_elastic()
-
- from nomad import user
- user.ensure_test_users()
+ setup_repository_db()
def setup_logging():
@@ -79,11 +81,20 @@ def setup_elastic():
logger.info('init elastic index')
+def setup_repository_db():
+ """ Creates a sqlalchemy session for the NOMAD-coe repository postgres db. """
+ from sqlalchemy import create_engine
+ from sqlalchemy.orm import sessionmaker
+
+ global repository_db
+
+ engine = create_engine('postgresql://postgres:nomad@localhost:5432/nomad', echo=False)
+ repository_db = sessionmaker(bind=engine)()
+
+
def reset():
- """ Resets the databases mongo/user and elastic/calcs. Be careful. """
+ """ Resets the databases mongo and elastic/calcs. Be careful. """
mongo_client.drop_database(config.mongo.users_db)
- from nomad import user
- user.ensure_test_users()
elastic_client.indices.delete(index=config.elastic.calc_index)
from nomad.repo import RepoCalc
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index 02a78b6c8b1c7a5614ee03f5149537ce83292485..25ab0d609931e62bbb5bf728cc81316fb57c0fa5 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -422,7 +422,7 @@ class Upload(Chord):
kwargs.update(user_id=user.email)
self = super().create(**kwargs)
- basic_auth_token = base64.b64encode(b'%s:' % user.generate_auth_token()).decode('utf-8')
+ basic_auth_token = base64.b64encode(b'%s:' % user.get_auth_token()).decode('utf-8')
self.upload_url = cls._external_objects_url('/uploads/%s/file' % self.upload_id)
self.upload_command = 'curl -H "Authorization: Basic %s" "%s" --upload-file local_file' % (
diff --git a/nomad/user.py b/nomad/user.py
index 16351bbb25417ba6de540b50a9d5fd6146021f43..a006be6a242d411e9036119a0eb08eabcb485126 100644
--- a/nomad/user.py
+++ b/nomad/user.py
@@ -16,79 +16,102 @@
Module with some prototypes/placeholder for future user management in nomad@FAIR.
"""
-from mongoengine import Document, EmailField, StringField, ReferenceField, ListField
-from passlib.apps import custom_app_context as pwd_context
-from itsdangerous import TimedJSONWebSignatureSerializer as Serializer, BadSignature, SignatureExpired
+from passlib.hash import bcrypt
+from sqlalchemy import Column, Integer, String
+from sqlalchemy.ext.declarative import declarative_base
-from nomad import config
+from nomad import infrastructure
-class User(Document):
- """ Represents users in the database. """
- email = EmailField(primary_key=True)
- name = StringField()
- password_hash = StringField()
+Base = declarative_base()
- def hash_password(self, password):
- self.password_hash = pwd_context.encrypt(password)
- def verify_password(self, password):
- return pwd_context.verify(password, self.password_hash)
+class Session(Base): # type: ignore
+ __tablename__ = 'sessions'
- def generate_auth_token(self, expiration=600):
- s = Serializer(config.services.api_secret, expires_in=expiration)
- return s.dumps({'id': self.id})
+ token = Column(String, primary_key=True)
+ user_id = Column(String)
+
+
+class LoginException(Exception):
+ pass
+
+
+class User(Base): # type: ignore
+ """
+ SQLAlchemy model class that represents NOMAD-coe repository postgresdb *users*.
+ Provides functions for authenticating via password or session token.
+
+ It is not intended to create or update users. This should be done via the
+ NOMAD-coe repository GUI.
+ """
+ __tablename__ = 'users'
+
+ user_id = Column(Integer, primary_key=True)
+ email = Column(String)
+ firstname = Column(String)
+ lastname = Column(String)
+ password = Column(String)
+
+ def __repr__(self):
+ return '<User(email="%s")>' % self.email
+
+ def _hash_password(self, password):
+ assert False, 'Login functions are done by the NOMAD-coe repository GUI'
+ # password_hash = bcrypt.encrypt(password, ident='2y')
+ # self.password = password_hash
+
+ def _verify_password(self, password):
+ return bcrypt.verify(password, self.password)
+
+ def _generate_auth_token(self, expiration=600):
+ assert False, 'Login functions are done by the NOMAD-coe repository GUI'
+
+ def get_auth_token(self):
+ repository_db = infrastructure.repository_db
+ session = repository_db.query(Session).filter_by(user_id=self.user_id).first()
+ if not session:
+ raise LoginException('No session, user probably not logged in at NOMAD-coe repository GUI')
+
+ return session.token.encode('utf-8')
+
+ @staticmethod
+ def verify_user_password(email, password):
+ repository_db = infrastructure.repository_db
+ user = repository_db.query(User).filter_by(email=email).first()
+ if not user:
+ return None
+
+ if user._verify_password(password):
+ return user
+ else:
+ raise LoginException('Wrong password')
@staticmethod
def verify_auth_token(token):
- s = Serializer(config.services.api_secret)
- try:
- data = s.loads(token)
- except SignatureExpired:
- return None # valid token, but expired
- except BadSignature:
- return None # invalid token
-
- return User.objects(email=data['id']).first()
-
-
-class DataSet(Document):
- name = StringField()
- description = StringField()
- doi = StringField()
-
- user = ReferenceField(User)
- calcs = ListField(StringField)
-
- meta = {
- 'indexes': [
- 'user',
- 'doi',
- 'calcs'
- ]
- }
-
-
-# provid a test user for testing
-me = None
-other = None
-
-
-def ensure_test_users():
- global me
- me = User.objects(email='me@gmail.com').first()
- if me is None:
- me = User(
- email='me@gmail.com',
- name='Me Meyer')
- me.hash_password('nomad')
- me.save()
-
- global other
- me = User.objects(email='other@gmail.com').first()
- if me is None:
- me = User(
- email='other@gmail.com',
- name='Other User')
- me.hash_password('nomad')
- me.save()
+ repository_db = infrastructure.repository_db
+ session = repository_db.query(Session).filter_by(token=token).first()
+ if session is None:
+ return None
+
+ user = repository_db.query(User).filter_by(user_id=session.user_id).first()
+ assert user, 'User in sessions must exist.'
+ return user
+
+
+def ensure_test_user(email):
+ """
+ Allows tests to make sure that the default test users exist in the database.
+ Returns:
+ The user as :class:`User` instance.
+ """
+ existing = infrastructure.repository_db.query(User).filter_by(
+ email=email).first()
+ assert existing, 'Test user %s does not exist.' % email
+
+ session = infrastructure.repository_db.query(Session).filter_by(
+ user_id=existing.user_id).first()
+ assert session, 'Test user %s has no session.' % email
+ assert session.token == email, 'Test user %s session has unexpected token.' % email
+
+ return existing
diff --git a/repository/repo_postgres_schema b/repository/repo_postgres_schema
new file mode 100644
index 0000000000000000000000000000000000000000..c473a1789122fbf991afb83874afd0671a18737a
--- /dev/null
+++ b/repository/repo_postgres_schema
@@ -0,0 +1 @@
+- "login_token" or "sessions", whats the difference, what should be used for authenticating uploader.
\ No newline at end of file
diff --git a/repository/repository_es_example.js b/repository/repository_es_example.js
new file mode 100644
index 0000000000000000000000000000000000000000..8a17b9e54bba52d14fab470c70f9240b44770478
--- /dev/null
+++ b/repository/repository_es_example.js
@@ -0,0 +1,2375 @@
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+ "nmd://RB1HuRB75DziRkYLw2loQ5HBBerDR/data/AgSnV_sv/TBCC006.CAB/DOSCAR.relax1.bz2",
+ "nmd://RB1HuRB75DziRkYLw2loQ5HBBerDR/data/AgSnV_sv/TBCC006.CAB/EIGENVAL.relax1.bz2",
+ "nmd://RB1HuRB75DziRkYLw2loQ5HBBerDR/data/AgSnV_sv/TBCC006.CAB/INCAR.relax1.bz2",
+ "nmd://RB1HuRB75DziRkYLw2loQ5HBBerDR/data/AgSnV_sv/TBCC006.CAB/KPOINTS.relax1.bz2",
+ "nmd://RB1HuRB75DziRkYLw2loQ5HBBerDR/data/AgSnV_sv/TBCC006.CAB/OUTCAR.relax1.bz2",
+ "nmd://RB1HuRB75DziRkYLw2loQ5HBBerDR/data/AgSnV_sv/TBCC006.CAB/POSCAR.relax1.bz2"
+ ],
+ "main_file_uri": "nmd://RB1HuRB75DziRkYLw2loQ5HBBerDR/data/AgSnV_sv/TBCC006.CAB/vasprun.xml.relax1",
+ "section_repository_userdata": {
+ "section_citation": [
+ {
+ "citation_repo_id": 52,
+ "citation_value": "http://aflowlib.org"
+ },
+ {
+ "citation_repo_id": 53,
+ "citation_value": "http://www.sciencedirect.com/science/article/pii/S0927025614003322"
+ },
+ {
+ "citation_repo_id": 54,
+ "citation_value": "http://www.sciencedirect.com/science/article/pii/S0927025612000687"
+ }
+ ],
+ "repository_access_now": "Open",
+ "section_author_info": [
+ {
+ "author_repo_id": 134,
+ "author_first_name": "Frisco",
+ "author_last_name": "Rose",
+ "author_name": "Frisco Rose"
+ },
+ {
+ "author_repo_id": 135,
+ "author_first_name": "Richard",
+ "author_last_name": "Taylor",
+ "author_name": "Richard Taylor"
+ },
+ {
+ "author_repo_id": 136,
+ "author_first_name": "Ohad",
+ "author_last_name": "Levy",
+ "author_name": "Ohad Levy"
+ },
+ {
+ "author_repo_id": 137,
+ "author_first_name": "Cormac",
+ "author_last_name": "Toher",
+ "author_name": "Cormac Toher"
+ },
+ {
+ "author_repo_id": 138,
+ "author_first_name": "Marco Buongiorno",
+ "author_last_name": "Nardelli",
+ "author_name": "Marco Buongiorno Nardelli"
+ },
+ {
+ "author_repo_id": 145,
+ "author_first_name": "Wahyu",
+ "author_last_name": "Setyawan",
+ "author_name": "Wahyu Setyawan"
+ },
+ {
+ "author_repo_id": 146,
+ "author_first_name": "Shidong",
+ "author_last_name": "Wang",
+ "author_name": "Shidong Wang"
+ },
+ {
+ "author_repo_id": 147,
+ "author_first_name": "Junkai",
+ "author_last_name": "Xue",
+ "author_name": "Junkai Xue"
+ },
+ {
+ "author_repo_id": 148,
+ "author_first_name": "Kesong",
+ "author_last_name": "Yang",
+ "author_name": "Kesong Yang"
+ },
+ {
+ "author_repo_id": 149,
+ "author_first_name": "Lance",
+ "author_last_name": "Nelson",
+ "author_name": "Lance Nelson"
+ },
+ {
+ "author_repo_id": 150,
+ "author_first_name": "Gus",
+ "author_last_name": "Hart",
+ "author_name": "Gus Hart"
+ },
+ {
+ "author_repo_id": 151,
+ "author_first_name": "Stefano",
+ "author_last_name": "Sanvito",
+ "author_name": "Stefano Sanvito"
+ },
+ {
+ "author_repo_id": 152,
+ "author_first_name": "Natalio",
+ "author_last_name": "Mingo",
+ "author_name": "Natalio Mingo"
+ },
+ {
+ "author_repo_id": 125,
+ "author_first_name": "Stefano",
+ "author_last_name": "Curtarolo",
+ "author_name": "Stefano Curtarolo"
+ }
+ ]
+ },
+ "repository_calc_id": 3506036,
+ "upload_id": 967,
+ "section_repository_parserdata": {
+ "repository_code_version": [
+ "VASP 4.6.35"
+ ],
+ "repository_atomic_elements": [
+ "Ag",
+ "Sn",
+ "V"
+ ],
+ "repository_spacegroup_nr": [
+ 99
+ ],
+ "repository_system_type": [
+ "Bulk"
+ ],
+ "repository_basis_set_type": [
+ "plane waves"
+ ],
+ "repository_crystal_system": [
+ "tetragonal"
+ ],
+ "repository_checksum": "LFXP7M7US6WD7WEE2YEERH5CJQRSFKGPO7RBAXAA67KWWCI",
+ "repository_parser_id": "RepoBaseParser",
+ "repository_chemical_formula": [
+ "SnAgV2"
+ ],
+ "repository_atomic_elements_count": 3,
+ "repository_xc_treatment": [
+ "GGA"
+ ],
+ "repository_program_name": [
+ "VASP"
+ ]
+ },
+ "section_uploader_info": {
+ "uploader_username": "stefano",
+ "uploader_last_name": "Curtarolo",
+ "uploader_repo_id": 125,
+ "uploader_first_name": "Stefano"
+ },
+ "upload_date": 1425207600000,
+ "repository_calc_pid": "3avrk",
+ "repository_archive_gid": [
+ "RB1HuRB75DziRkYLw2loQ5HBBerDR"
+ ]
+ },
+ "query_auxiliary_data": {
+ "value_counts": {
+ "section_repository_info": {
+ "repository_grouping_checksum": 1,
+ "repository_filepaths": 10,
+ "secondary_file_uris": 9,
+ "main_file_uri": 1,
+ "section_repository_userdata": {
+ "section_citation": {
+ "citation_repo_id": 3,
+ "citation_value": 3
+ },
+ "repository_open_date": 0,
+ "repository_access_now": 1,
+ "repository_comment": 0,
+ "section_author_info": {
+ "author_name": 14,
+ "author_last_name": 14,
+ "author_first_name": 13,
+ "author_repo_id": 14
+ }
+ },
+ "repository_calc_id": 1,
+ "upload_id": 1,
+ "section_repository_parserdata": {
+ "repository_code_version": 1,
+ "repository_atomic_elements": 3,
+ "repository_spacegroup_nr": 1,
+ "repository_system_type": 1,
+ "repository_basis_set_type": 1,
+ "repository_crystal_system": 1,
+ "repository_checksum": 1,
+ "repository_parser_id": 1,
+ "repository_chemical_formula": 1,
+ "repository_atomic_elements_count": 1,
+ "repository_xc_treatment": 1,
+ "repository_program_name": 1
+ },
+ "section_uploader_info": {
+ "uploader_username": 1,
+ "uploader_last_name": 1,
+ "uploader_name": 0,
+ "uploader_repo_id": 1,
+ "uploader_first_name": 1
+ },
+ "upload_date": 1,
+ "repository_calc_pid": 1,
+ "repository_archive_gid": 1
+ }
+ }
+ }
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/repository/utils.http b/repository/utils.http
new file mode 100644
index 0000000000000000000000000000000000000000..afa0e7a6b892185f961a6baf27477642721e353a
--- /dev/null
+++ b/repository/utils.http
@@ -0,0 +1,19 @@
+DELETE http://localhost:9200/index2018-11-15 HTTP/1.1;
+
+###
+DELETE http://localhost:9200/topics2018-11-15 HTTP/1.1;
+
+###
+GET http://localhost:9200/_cat/indices HTTP/1.1;
+
+###
+GET http://localhost:9200/index2018-11-15/_search HTTP/1.1;
+
+
+###
+POST http://localhost:8111/repo/repo-update/index/calculation HTTP/1.1;
+content-type: application/json
+
+{
+ "calc_ids": [10]
+}
diff --git a/requirements.txt b/requirements.txt
index f2e266a72df3a2b35492d90142015bc8323c6ae8..a143a738754b588fedcaaafc92c4d69d3f1302ce 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -24,3 +24,6 @@ sphinxcontrib.httpdomain
sphinx_rtd_theme
zipstream
bagit
+psycopg2
+sqlalchemy
+bcrypt
diff --git a/tests/conftest.py b/tests/conftest.py
index 3f711d14697d6b16fbe623a2811493ca9fbd02c4..06aa62d576dbac567d6519d8387c27768c790a10 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -81,7 +81,6 @@ def mockmongo(monkeypatch):
disconnect()
connection = connect('test_db', host='mongomock://localhost')
monkeypatch.setattr('nomad.infrastructure.setup_mongo', lambda **kwargs: None)
- user.ensure_test_users()
yield
@@ -94,6 +93,22 @@ def elastic():
assert infrastructure.elastic_client is not None
+@pytest.fixture(scope='session')
+def repository_db():
+ infrastructure.setup_repository_db()
+ assert infrastructure.repository_db is not None
+
+
+@pytest.fixture(scope='session')
+def test_user(repository_db):
+ return user.ensure_test_user(email='sheldon.cooper@nomad-fairdi.tests.de')
+
+
+@pytest.fixture(scope='session')
+def other_test_user(repository_db):
+ return user.ensure_test_user(email='leonard.hofstadter@nomad-fairdi.tests.de')
+
+
@pytest.fixture(scope='function')
def mocksearch(monkeypatch):
uploads_by_hash = {}
diff --git a/tests/processing/test_data.py b/tests/processing/test_data.py
index fd69a6728a34d10070300509e40e57009f570eed..14033040c459b7059206d1513ed81b72855b9393 100644
--- a/tests/processing/test_data.py
+++ b/tests/processing/test_data.py
@@ -64,8 +64,8 @@ def uploaded_id_with_warning(request, clear_files) -> Generator[str, None, None]
yield example_upload_id
-def run_processing(uploaded_id: str) -> Upload:
- upload = Upload.create(upload_id=uploaded_id, user=user.me)
+def run_processing(uploaded_id: str, test_user) -> Upload:
+ upload = Upload.create(upload_id=uploaded_id, user=test_user)
upload.upload_time = datetime.now()
assert upload.status == 'RUNNING'
@@ -110,33 +110,33 @@ def assert_processing(upload: Upload, mocksearch=None):
@pytest.mark.timeout(30)
-def test_processing(uploaded_id, worker, mocksearch, no_warn):
- upload = run_processing(uploaded_id)
+def test_processing(uploaded_id, worker, mocksearch, test_user, no_warn):
+ upload = run_processing(uploaded_id, test_user)
assert_processing(upload, mocksearch)
@pytest.mark.timeout(30)
-def test_processing_with_warning(uploaded_id_with_warning, worker, mocksearch):
- upload = run_processing(uploaded_id_with_warning)
+def test_processing_with_warning(uploaded_id_with_warning, worker, test_user, mocksearch):
+ upload = run_processing(uploaded_id_with_warning, test_user)
assert_processing(upload, mocksearch)
@pytest.mark.parametrize('uploaded_id', [example_files[1]], indirect=True)
-def test_processing_doublets(uploaded_id, worker, with_error):
+def test_processing_doublets(uploaded_id, worker, test_user, with_error):
- upload = run_processing(uploaded_id)
+ upload = run_processing(uploaded_id, test_user)
assert upload.status == 'SUCCESS'
assert RepoCalc.upload_exists(upload.upload_hash) # pylint: disable=E1101
- upload = run_processing(uploaded_id)
+ upload = run_processing(uploaded_id, test_user)
assert upload.status == 'FAILURE'
assert len(upload.errors) > 0
assert 'already' in upload.errors[0]
@pytest.mark.timeout(30)
-def test_process_non_existing(worker, with_error):
- upload = run_processing('__does_not_exist')
+def test_process_non_existing(worker, test_user, with_error):
+ upload = run_processing('__does_not_exist', test_user)
assert upload.completed
assert upload.current_task == 'extracting'
@@ -146,7 +146,7 @@ def test_process_non_existing(worker, with_error):
@pytest.mark.parametrize('task', ['extracting', 'parse_all', 'cleanup', 'parsing'])
@pytest.mark.timeout(30)
-def test_task_failure(monkeypatch, uploaded_id, worker, task, with_error):
+def test_task_failure(monkeypatch, uploaded_id, worker, task, test_user, with_error):
# mock the task method to through exceptions
if hasattr(Upload, task):
cls = Upload
@@ -163,7 +163,7 @@ def test_task_failure(monkeypatch, uploaded_id, worker, task, with_error):
monkeypatch.setattr('nomad.processing.data.%s.%s' % (cls.__name__, task), mock)
# run the test
- upload = run_processing(uploaded_id)
+ upload = run_processing(uploaded_id, test_user)
assert upload.completed
diff --git a/tests/test_api.py b/tests/test_api.py
index 6e6624fbe13cf0643b87e9d7290eb6815fae28c5..e68e43ed5226601c388e6bf668951bfe3f6fed48 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -32,7 +32,7 @@ from tests.test_repo import example_elastic_calc # noqa pylint: disable=unused-
@pytest.fixture(scope='function')
-def client(mockmongo):
+def client(mockmongo, repository_db):
disconnect()
connect('users_test', host=config.mongo.host, port=config.mongo.port, is_mock=True)
@@ -43,18 +43,23 @@ def client(mockmongo):
Upload._get_collection().drop()
-@pytest.fixture(scope='session')
-def test_user_auth():
+def create_auth_headers(user):
+ basic_auth_str = '%s:password' % user.email
+ basic_auth_bytes = basic_auth_str.encode('utf-8')
+ basic_auth_base64 = base64.b64encode(basic_auth_bytes).decode('utf-8')
return {
- 'Authorization': 'Basic %s' % base64.b64encode(b'me@gmail.com:nomad').decode('utf-8')
+ 'Authorization': 'Basic %s' % basic_auth_base64
}
@pytest.fixture(scope='session')
-def test_other_user_auth():
- return {
- 'Authorization': 'Basic %s' % base64.b64encode(b'other@gmail.com:nomad').decode('utf-8')
- }
+def test_user_auth(test_user):
+ return create_auth_headers(test_user)
+
+
+@pytest.fixture(scope='session')
+def test_other_user_auth(other_test_user):
+ return create_auth_headers(other_test_user)
def assert_uploads(upload_json_str, count=0, **kwargs):
diff --git a/tests/test_repo.py b/tests/test_repo.py
index d789890029fbea38ff7ab7c4e32356e67a52cdbd..ef572bf29a59028de3fa546f9abc4082c71e5768 100644
--- a/tests/test_repo.py
+++ b/tests/test_repo.py
@@ -27,7 +27,7 @@ from tests.test_parsing import parsed_template_example # pylint: disable=unused
@pytest.fixture(scope='function')
-def example_elastic_calc(normalized_template_example: LocalBackend, elastic) \
+def example_elastic_calc(normalized_template_example: LocalBackend, elastic, test_user) \
-> Generator[RepoCalc, None, None]:
upload_file = UploadFile('test_upload_id', local_path=example_file)
@@ -49,7 +49,7 @@ def example_elastic_calc(normalized_template_example: LocalBackend, elastic) \
additional=dict(
mainfile=mainfile,
upload_time=datetime.now(),
- staging=True, restricted=False, user_id='me@gmail.com',
+ staging=True, restricted=False, user_id=test_user.email,
aux_files=auxfiles),
refresh='true')
@@ -82,7 +82,7 @@ def test_create_elastic_calc(example_elastic_calc: RepoCalc, no_warn):
def test_create_existing_elastic_calc(
- example_elastic_calc: RepoCalc, normalized_template_example):
+ example_elastic_calc: RepoCalc, normalized_template_example, test_user):
try:
RepoCalc.create_from_backend(
normalized_template_example,
@@ -92,7 +92,7 @@ def test_create_existing_elastic_calc(
additional=dict(
mainfile='/test/mainfile',
upload_time=datetime.now(),
- staging=True, restricted=False, user_id='me'),
+ staging=True, restricted=False, user_id=test_user.email),
refresh='true')
assert False
except AlreadyExists:
diff --git a/tests/test_user.py b/tests/test_user.py
new file mode 100644
index 0000000000000000000000000000000000000000..84b0b200bf6051bd5811adb65b79546ab015f909
--- /dev/null
+++ b/tests/test_user.py
@@ -0,0 +1,16 @@
+from nomad.user import User
+
+
+def assert_user(user, reference):
+ assert user is not None
+ assert user.user_id == reference.user_id
+
+
+def test_token_authorize(test_user):
+ user = User.verify_auth_token(test_user.email)
+ assert_user(user, test_user)
+
+
+def test_password_authorize(test_user):
+ user = User.verify_user_password(test_user.email, 'password')
+ assert_user(user, test_user)