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Commit 6dad4b1c authored by Markus Scheidgen's avatar Markus Scheidgen
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Refactored api arepo part to proper restplus.

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nomad/api/__init__.py
+ 2
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View file @ 6dad4b1c
......@@ -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
......
nomad/api/repository.py deleted 100644 → 0
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# 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)
nomad/api/upload.py
+ 6
− 14
View file @ 6dad4b1c
......@@ -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):
"""
......
tests/test_api.py
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......@@ -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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