From 6dad4b1cc57a54c86e001877afb95f6e4006c28b Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Sat, 22 Dec 2018 12:00:18 +0100
Subject: [PATCH] Refactored api arepo part to proper restplus.
---
nomad/api/__init__.py | 4 +-
nomad/api/repository.py | 193 ----------------------------------------
nomad/api/upload.py | 20 ++---
tests/test_api.py | 10 +--
4 files changed, 13 insertions(+), 214 deletions(-)
delete mode 100644 nomad/api/repository.py
diff --git a/nomad/api/__init__.py b/nomad/api/__init__.py
index e42758024b..7a20557905 100644
--- a/nomad/api/__init__.py
+++ b/nomad/api/__init__.py
@@ -24,12 +24,12 @@ There is a separate documentation for the API endpoints from a client perspectiv
.. automodule:: nomad.api.app
.. automodule:: nomad.api.auth
.. automodule:: nomad.api.upload
-.. automodule:: nomad.api.repository
+.. automodule:: nomad.api.repo
.. automodule:: nomad.api.archive
.. automodule:: nomad.api.admin
"""
from .app import app
-from . import auth, admin, upload, repository, archive, raw
+from . import auth, admin, upload, repo, archive, raw
@app.before_first_request
diff --git a/nomad/api/repository.py b/nomad/api/repository.py
deleted file mode 100644
index c6a9fae295..0000000000
--- a/nomad/api/repository.py
+++ /dev/null
@@ -1,193 +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.
-
-"""
-The repository API of the nomad@FAIRDI APIs. Currently allows to resolve repository
-meta-data.
-"""
-
-from elasticsearch.exceptions import NotFoundError
-from flask import g, request
-from flask_restplus import Resource, abort
-
-from nomad.repo import RepoCalc
-
-from .app import api, base_path
-from .auth import login_if_available
-
-
-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":"BrKSi2",
- "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):
- @login_if_available
- 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":"BrKSi2",
- "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=str(g.user.user_id))
- 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=str(g.user.user_id)).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]
- }
-
-
-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
index 9144a6bffe..39ba5fc27c 100644
--- a/nomad/api/upload.py
+++ b/nomad/api/upload.py
@@ -28,6 +28,7 @@ from nomad.files import UploadFile
from .app import api, base_path
from .auth import login_really_required
+from .common import pagination_request_parser, pagination_model
ns = api.namespace(
@@ -47,7 +48,7 @@ proc_model = api.model('Processing', {
'_async_status': fields.String(description='Only for debugging nomad')
})
-upload_model = api.inherit('Upload', proc_model, {
+upload_model = api.inherit('UploadProcessing', proc_model, {
'name': fields.String(
description='The name of the upload. This can be provided during upload '
'using the name query parameter.'),
@@ -65,7 +66,7 @@ upload_model = api.inherit('Upload', proc_model, {
'upload_time': fields.DateTime(dt_format='iso8601'),
})
-calc_model = api.inherit('Calculation', proc_model, {
+calc_model = api.inherit('UploadCalculationProcessing', proc_model, {
'archive_id': fields.String,
'mainfile': fields.String,
'upload_id': fields.String,
@@ -77,13 +78,10 @@ upload_with_calcs_model = api.inherit('UploadWithPaginatedCalculations', upload_
'total_calcs': fields.Integer,
'failed_calcs': fields.Integer,
'pending_calcs': fields.Integer,
- 'calcs': fields.Nested(model=api.model('PaginatedCalculations', {
- 'pagination': fields.Nested(model=api.model('Pagination', {
- 'total': fields.Integer,
+ 'calcs': fields.Nested(model=api.model('UploadPaginatedCalculations', {
+ 'pagination': fields.Nested(model=api.inherit('UploadCalculationPagination', pagination_model, {
'successes': fields.Integer,
'failures': fields.Integer,
- 'page': fields.Integer,
- 'per_page': fields.Integer,
})),
'results': fields.List(fields.Nested(model=calc_model))
}))
@@ -183,18 +181,12 @@ class ProxyUpload:
return self.upload.__getattribute__(name)
-pagination_parser = api.parser()
-pagination_parser.add_argument('page', type=int, help='The page, starting with 1.', location='args')
-pagination_parser.add_argument('per_page', type=int, help='Desired calcs per page.', location='args')
-pagination_parser.add_argument('order_by', type=str, help='The field to sort the calcs by, use [status,mainfile].', location='args')
-
-
@ns.route('/<string:upload_id>')
@api.doc(params={'upload_id': 'The unique id for the requested upload.'})
class Upload(Resource):
@api.response(404, 'Upload does not exist')
@api.marshal_with(upload_with_calcs_model, skip_none=True, code=200, description='Upload send')
- @api.expect(pagination_parser)
+ @api.expect(pagination_request_parser)
@login_really_required
def get(self, upload_id: str):
"""
diff --git a/tests/test_api.py b/tests/test_api.py
index 6af77eaca5..a9de7f6014 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -255,7 +255,7 @@ class TestRepo:
assert rv.status_code == 404
def test_calcs(self, client, example_elastic_calc, no_warn):
- rv = client.get('/repo')
+ rv = client.get('/repo/')
assert rv.status_code == 200
data = json.loads(rv.data)
results = data.get('results', None)
@@ -264,7 +264,7 @@ class TestRepo:
assert len(results) >= 1
def test_calcs_pagination(self, client, example_elastic_calc, no_warn):
- rv = client.get('/repo?page=1&per_page=1')
+ rv = client.get('/repo/?page=1&per_page=1')
assert rv.status_code == 200
data = json.loads(rv.data)
results = data.get('results', None)
@@ -273,7 +273,7 @@ class TestRepo:
assert len(results) == 1
def test_calcs_user(self, client, example_elastic_calc, test_user_auth, no_warn):
- rv = client.get('/repo?owner=user', headers=test_user_auth)
+ rv = client.get('/repo/?owner=user', headers=test_user_auth)
assert rv.status_code == 200
data = json.loads(rv.data)
results = data.get('results', None)
@@ -281,11 +281,11 @@ class TestRepo:
assert len(results) >= 1
def test_calcs_user_authrequired(self, client, example_elastic_calc, no_warn):
- rv = client.get('/repo?owner=user')
+ rv = client.get('/repo/?owner=user')
assert rv.status_code == 401
def test_calcs_user_invisible(self, client, example_elastic_calc, test_other_user_auth, no_warn):
- rv = client.get('/repo?owner=user', headers=test_other_user_auth)
+ rv = client.get('/repo/?owner=user', headers=test_other_user_auth)
assert rv.status_code == 200
data = json.loads(rv.data)
results = data.get('results', None)
--
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