def setUp(self):
self.app = self.create_app()
self.client = app.test_client()
self.ctx = self.app.test_request_context()
self.ctx.push()
Config.initialize('project/config_mock.ini')
self.pagenames = [
'/', 'qrespcurator', 'startfromscratch', 'getTreeInfo',
'addToWorkflow', 'mint', 'preview/files_paper',
'previewchartworkflow?paperid=files_paper&chartid=c0',
'qrespexplorer',
'search?servers=https%3A%2F%2Fpaperstack.uchicago.edu',
'searchWord?searchWord=&paperTitle=&tags=&doi=&collectionList=[]&authorsList=[]&publicationList=[]',
'paperdetails/5941869f1bd40fd44db0024a',
'chartworkflow?paperid=5941869f1bd40fd44db0024a&chartid=c0',
'insertDOI?paperId=5941869f1bd40fd44db0024a&doi=25678',
'oauth2callback'
]
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
with open(os.path.join(__location__, 'data.json')) as f:
paperdata = json.load(f)
paperdata = ConvertField.convertToString(
["files", "properties", "URLs", "patches"], [
CURATOR_FIELD.CHARTS, CURATOR_FIELD.TOOLS,
CURATOR_FIELD.DATASETS, CURATOR_FIELD.SCRIPTS,
CURATOR_FIELD.HEADS
], paperdata)
paperform = PaperForm(**paperdata)
detailsform = DetailsForm(**paperform.info.insertedBy.data)
serverform = ServerForm(
**{'hostUrl': 'https://notebook.rcc.uchicago.edu/files'})
chartform = {
'id': 'c0',
'caption': 'chart 1',
'number': '1',
'files':
'charts/figure1/figure1.csv, charts/figure1/figure1.ipynb, charts/figure1/figure1.jpg',
'imageFile': 'charts/figure1/figure1.jpg',
'notebookFile': 'charts/figure1/figure1.ipynb',
'properties': 'potential energy, band gap'
}
toolform = {
'id': 't0',
'kind': 'software',
'packageName': 'West',
'URLs': '',
'version': '3.0.0',
'programName': 'wstat.x',
'patches': 'tools/modded_qbox.diff',
'description': 'Modified west code',
'facilityName': '',
'measurement': ''
}
datasetform = {
'id': 'd0',
'files': 'datasets/datasetA.dat, datasets/datasetB.dat',
'readme': 'DAT files',
'URLs': ''
}
scriptform = {
'id': 'd0',
'files': 'datasets/datasetA.dat, datasets/datasetB.dat',
'readme': 'DAT files',
'URLs': ''
}
referenceform = {
'kind': 'journal',
'DOI': '10.1021/jacs.6b00225',
'title':
'Photoelectron Spectra of Aqueous Solutions from First Principles',
'page': '6912-6915',
'publishedAbstract':
'We present a combined computational and experimental study of the photoelectron spectrum of a simple aqueous solution of NaCl. Measurements were conducted on microjets, and first-principles calculations were performed using hybrid functionals and many-body perturbation theory at the G0W0 level, starting with wave functions computed in ab initio molecular dynamics simulations. We show excellent agreement between theory and experiments for the positions of both the solute and solvent excitation energies on an absolute energy scale and for peak intensities. The best comparison was obtained using wave functions obtained with dielectric-dependent self-consistent and range-separated hybrid functionals. Our computational protocol opens the way to accurate, predictive calculations of the electronic properties of electrolytes, of interest to a variety of energy problems.',
'volume': '138',
'year': 2016,
'URLs': 'http://dx.doi.org/10.1021/jacs.6b00225',
'school': ''
}
documentationform = DocumentationForm(**paperform.documentation.data)
adminform = {
'hostname': 'mongomock://localhost',
'port': 27017,
'username': None,
'password': None,
'dbname': 'mongoenginetest',
'collection': 'paper'
}
self.postPageForms = {
'uploadFile': paperform,
'details': detailsform,
'server': serverform,
'charts': chartform,
'charts/delete': chartform,
'tools': toolform,
'tools/delete': toolform,
'datasets': datasetform,
'datasets/delete': datasetform,
'scripts': scriptform,
'scripts/delete': scriptform,
'reference': referenceform,
'fetchReferenceDOI': {
'doi': '10.1021/nl903868w'
},
'documentation': documentationform,
'addToWorkflow': {},
'saveNodesAndEdges': [['t0', 'd0'], [{
'id': 't0'
}, {
'id': 'd0'
}]],
'publish': {},
'download': {},
'verifyPasscode': {
'passcode': '123456'
},
'admin': adminform,
'getDescriptor': {
"metadata": paperform.data
}
}
import connexion
import os
from flask_session import Session
from flask_sitemap import Sitemap
from project.config import Config
from flask_mongoengine import MongoEngine
from flask_cors import CORS
Config.initialize()
# Create the application instance
connexionapp = connexion.FlaskApp(__name__)
# Read the swagger.yml file to configure the endpoints
swagger_file = (os.path.join(os.getcwd(), 'project/swagger.yml'))
connexionapp.add_api(swagger_file)
app = connexionapp.app
# Create protection and session variables
app.secret_key = Config.get_setting('SECRETS', 'FLASK_SECRET_KEY')
SESSION_TYPE = 'filesystem'
app.config.from_object(__name__)
app.config['env'] = 'DEV'
os.environ['OAUTHLIB_INSECURE_TRANSPORT'] = '1'
Session(app)
ext = Sitemap(app)
CORS(app)
#initialize db
if Config.get_setting(app.config['env'], 'MONGODB_HOST'):
db = MongoEngine()