Commit ccc879db authored by Markus Scheidgen's avatar Markus Scheidgen
Browse files

Addd bravado client. Added method names to swagger api. Refactored cli.

parent f2cde874
......@@ -28,6 +28,7 @@ ns = api.namespace('admin', description='Administrative operations')
@api.doc(params={'operation': 'The operation to perform.'})
class AdminOperationsResource(Resource):
# TODO in production this requires authorization
@api.response(200, 'Operation performed')
@api.response(404, 'Operation does not exist')
@api.response(400, 'Operation not available/disabled')
......@@ -37,6 +37,7 @@ ns = api.namespace(
@calc_route(ns, '/logs')
class ArchiveCalcLogResource(Resource):
@api.response(404, 'The upload or calculation does not exist')
@api.response(200, 'Archive data send')
......@@ -74,6 +75,7 @@ class ArchiveCalcLogResource(Resource):
class ArchiveCalcResource(Resource):
@api.response(404, 'The upload or calculation does not exist')
@api.response(200, 'Archive data send')
......@@ -127,6 +127,7 @@ ns = api.namespace(
class TokenResource(Resource):
@api.response(200, 'Token send', headers={'Content-Type': 'text/plain; charset=utf-8'})
def get(self):
......@@ -46,7 +46,7 @@ def calc_route(ns, prefix: str = ''):
ns.route('%s/<string:upload_hash>/<string:calc_hash>' % prefix)(
'upload_hash': 'The unique hash for the requested upload.',
'path': 'The path to a file or directory.'
'calc_hash': 'The unique hash for the requested calculation.'
return decorator
......@@ -55,6 +55,7 @@ raw_file_from_path_parser.add_argument(**raw_file_compress_argument)
@api.header('Content-Type', 'application/gz')
class RawFileFromPathResource(Resource):
@api.response(404, 'The upload or path does not exist')
@api.response(200, 'File(s) send', headers={'Content-Type': 'application/gz'})
@api.expect(raw_file_from_path_parser, validate=True)
......@@ -127,6 +128,7 @@ raw_files_request_parser.add_argument(
'upload_hash': 'The unique hash for the requested upload.'
class RawFilesResource(Resource):
@api.response(404, 'The upload or path does not exist')
@api.response(200, 'File(s) send', headers={'Content-Type': 'application/gz'})
@api.expect(raw_files_request_model, validate=True)
......@@ -139,6 +141,7 @@ class RawFilesResource(Resource):
return respond_to_get_raw_files(upload_hash, files, compress)
@api.response(404, 'The upload or path does not exist')
@api.response(200, 'File(s) send', headers={'Content-Type': 'application/gz'})
@api.expect(raw_files_request_parser, validate=True)
......@@ -34,6 +34,7 @@ ns = api.namespace('repo', description='Access repository metadata, edit user me
class RepoCalcResource(Resource):
@api.response(404, 'The upload or calculation does not exist')
@api.response(200, 'Metadata send')
def get(self, upload_hash, calc_hash):
Get calculation metadata in repository form.
......@@ -64,6 +65,7 @@ repo_request_parser.add_argument(
class RepoCalcsResource(Resource):
@api.response(400, 'Invalid requests, e.g. wrong owner type')
@api.expect(repo_request_parser, validate=True)
@api.marshal_with(repo_calcs_model, skip_none=True, code=200, description='Metadata send')
......@@ -20,6 +20,8 @@ files, and retrieve the processing status of uploads.
from flask import g, request
from flask_restplus import Resource, fields, abort
from datetime import datetime
from werkzeug.datastructures import FileStorage
import os.path
from nomad import config
from nomad.processing import Upload
......@@ -94,17 +96,20 @@ upload_operation_model = api.model('UploadOperation', {
upload_metadata_parser = api.parser()
upload_metadata_parser.add_argument('name', type=str, help='An optional name for the upload.', location='args')
upload_metadata_parser.add_argument('local_path', type=str, help='Use a local file on the server.', location='args')
upload_metadata_parser.add_argument('file', type=FileStorage, help='The file to upload.', location='files')
class UploadListResource(Resource):
@api.marshal_list_with(upload_model, skip_none=True, code=200, description='Uploads send')
def get(self):
""" Get the list of all uploads from the authenticated user. """
return [upload for upload in Upload.user_uploads(g.user)], 200
@api.marshal_list_with(upload_model, skip_none=True, code=200, description='Upload received')
@api.marshal_with(upload_model, skip_none=True, code=200, description='Upload received')
def put(self):
......@@ -124,6 +129,10 @@ class UploadListResource(Resource):
curl ".../nomad/api/uploads/" --upload-file local_file
local_path = request.args.get('local_path')
if local_path:
if not os.path.exists(local_path):
abort(404, message='The given local_path was not found.')
# create upload
upload = Upload.create(
......@@ -183,6 +192,7 @@ class ProxyUpload:
@api.doc(params={'upload_id': 'The unique id for the requested upload.'})
class UploadResource(Resource):
@api.response(404, 'Upload does not exist')
@api.marshal_with(upload_with_calcs_model, skip_none=True, code=200, description='Upload send')
......@@ -232,6 +242,7 @@ class UploadResource(Resource):
return result, 200
@api.response(404, 'Upload does not exist')
@api.response(400, 'Not allowed during processing or when not in staging')
@api.marshal_with(upload_model, skip_none=True, code=200, description='Upload deleted')
......@@ -260,6 +271,7 @@ class UploadResource(Resource):
except NotAllowedDuringProcessing:
abort(400, message='You must not delete an upload during processing.')
@api.response(404, 'Upload does not exist or is not allowed')
@api.response(400, 'Operation is not supported')
@api.marshal_with(upload_model, skip_none=True, code=200, description='Upload unstaged successfully')
......@@ -307,6 +319,7 @@ upload_command_model = api.model('UploadCommand', {
class UploadCommandResource(Resource):
@api.marshal_with(upload_command_model, code=200, description='Upload command send')
def get(self):
......@@ -316,7 +329,7 @@ class UploadCommandResource(Resource):,
upload_command = 'curl -H "X-Token: "%s" "%s" --upload-file <local_file>' % (
upload_command = 'curl -H "X-Token: %s" "%s" --upload-file <local_file>' % (
g.user.get_auth_token().decode('utf-8'), upload_url)
return dict(upload_url=upload_url, upload_command=upload_command), 200
......@@ -13,20 +13,19 @@
# limitations under the License.
Simple client library for the nomad api that allows to bulk upload files via shell command.
Swagger/bravado based python client library for the API and various usefull shell commands.
import os.path
import os
import sys
import subprocess
import shlex
import time
import requests
from requests.auth import HTTPBasicAuth
import click
from typing import Union, Callable, cast
import logging
from bravado.requests_client import RequestsClient
from bravado.client import SwaggerClient
from nomad import config, utils
from nomad.files import UploadFile
......@@ -34,11 +33,35 @@ from nomad.parsing import parsers, parser_dict, LocalBackend
from nomad.normalizing import normalizers
api_base = 'http://localhost/nomad/api'
api_base = 'http://%s:%d/%s' % (,,
user = ''
pw = 'password'
def _cli_client():
return create_client()
def create_client(
host: str =,
port: int =,
base_path: str =,
user: str = user, password: str = None):
""" A factory method to create the client. """
if user is not None:
http_client = RequestsClient()
http_client.set_basic_auth(host, user, pw)
http_client = None
client = SwaggerClient.from_url(
'http://%s:%d%s/swagger.json' % (host, port, base_path),
return client
def handle_common_errors(func):
def wrapper(*args, **kwargs):
......@@ -51,7 +74,6 @@ def handle_common_errors(func):
return wrapper
def upload_file(file_path: str, name: str = None, offline: bool = False, unstage: bool = False):
Upload a file to nomad.
......@@ -62,70 +84,38 @@ def upload_file(file_path: str, name: str = None, offline: bool = False, unstage
offline: allows to process data without upload, requires client to be run on the server
unstage: automatically unstage after successful processing
auth = HTTPBasicAuth(user, pw)
if name is None:
name = os.path.basename(file_path)
post_data = dict(name=name)
client = _cli_client()
if offline:
upload = client.uploads.upload(
local_path=os.path.abspath(file_path), name=name).reponse().result
click.echo('process offline: %s' % file_path)
upload ='%s/uploads' % api_base, json=post_data, auth=auth).json()
if not offline:
upload_cmd = upload['upload_command']
upload_cmd = upload_cmd.replace('local_file', file_path)
click.echo('uploaded: %s' % file_path)
while True:
upload = requests.get('%s/uploads/%s' % (api_base, upload['upload_id']), auth=auth).json()
status = upload['status']
calcs_pagination = upload['calcs'].get('pagination')
if calcs_pagination is None:
with open(file_path, 'rb') as f:
upload = client.uploads.upload(file=f, name=name).response().result
click.echo('process online: %s' % file_path)
while upload.status not in ['SUCCESS', 'FAILURE']:
upload = client.uploads.get_upload(upload_id=upload.upload_id).response().result
calcs = upload.calcs.pagination
if calcs is None:
total, successes, failures = 0, 0, 0
total, successes, failures = (
calcs_pagination[key] for key in ('total', 'successes', 'failures'))
total, successes, failures = (, calcs.successes, calcs.failures)
ret = '\n' if status in ('SUCCESS', 'FAILURE') else '\r'
ret = '\n' if upload.status in ('SUCCESS', 'FAILURE') else '\r'
'status: %s; task: %s; parsing: %d/%d/%d %s' %
(status, upload['current_task'], successes, failures, total, ret), end='')
if status in ('SUCCESS', 'FAILURE'):
(upload.status, upload.current_task, successes, failures, total, ret), end='')
if status == 'FAILURE':
if upload.status == 'FAILURE':
click.echo('There have been errors:')
for error in upload['errors']:
for error in upload.errors:
click.echo(' %s' % error)
elif unstage:
post_data = dict(operation='unstage')'%s/uploads/%s' % (api_base, upload['upload_id']), json=post_data, auth=auth).json()
def walk_through_files(path, extension='.zip'):
Returns all abs path of all files in a sub tree of the given path that match
the given extension.
path (str): the directory
extension (str): the extension, incl. '.', e.g. '.zip' (default)
for (dirpath, _, filenames) in os.walk(path):
for filename in filenames:
if filename.endswith(extension):
yield os.path.abspath(os.path.join(dirpath, filename))
client.uploads.exec(upload_id=upload.upload_id, operation='unstage').reponse()
class CalcProcReproduction:
......@@ -158,9 +148,10 @@ class CalcProcReproduction:
if not os.path.exists(local_path) or override:
# download raw if not already downloaded or if override is set
# download with request, since bravado does not support streaming
# TODO currently only downloads mainfile'Downloading calc.')
req = requests.get('%s/raw/%s?files=%s' % (api_base, self.upload_hash, self.mainfile), stream=True)
req = requests.get('%s/raw/%s/%s' % (api_base, self.upload_hash, os.path.dirname(self.mainfile)), stream=True)
with open(local_path, 'wb') as f:
for chunk in req.iter_content(chunk_size=1024):
......@@ -243,10 +234,12 @@ class CalcProcReproduction:
@click.option('-h', '--host', default='localhost', help='The host nomad runs on, default is "localhost".')
@click.option('-p', '--port', default=80, help='the port nomad runs with, default is 80.')
@click.option('-h', '--host',, help='The host nomad runs on, default is "%s".' %
@click.option('-p', '--port',, help='the port nomad runs with, default is %d.' %
@click.option('-u', '--user', default=None, help='the user name to login, default no login.')
@click.option('-w', '--password', default=None, help='the password use to login.')
@click.option('-v', '--verbose', help='sets log level to debug', is_flag=True)
def cli(host: str, port: int, verbose: bool):
def cli(host: str, port: int, verbose: bool, user: str, password: str):
if verbose:
config.console_log_level = logging.DEBUG
......@@ -255,6 +248,14 @@ def cli(host: str, port: int, verbose: bool):
global api_base
api_base = 'http://%s:%d/nomad/api' % (host, port)
global _cli_client
def _cli_client(): # pylint: disable=W0612
if user is not None:
return create_client(host=host, port=port, user=user, password=password)
return create_client(host=host, port=port)
help='Upload files to nomad. The given path can be a single file or a directory. '
......@@ -281,9 +282,12 @@ def upload(path, name: str, offline: bool, unstage: bool):
upload_file(path, name, offline, unstage)
elif os.path.isdir(path):
for file_path in walk_through_files(path):
name = os.path.basename(file_path)
upload_file(file_path, name, offline, unstage)
for (dirpath, _, filenames) in os.walk(path):
for filename in filenames:
if filename.endswith('.zip'):
file_path = os.path.abspath(os.path.join(dirpath, filename))
name = os.path.basename(file_path)
upload_file(file_path, name, offline, unstage)
click.echo('Unknown path type %s.' % path)
......@@ -291,11 +295,7 @@ def upload(path, name: str, offline: bool, unstage: bool):
@cli.command(help='Attempts to reset the nomad.')
def reset():
response ='%s/admin/reset' % api_base, auth=HTTPBasicAuth(user, pw))
if response.status_code != 200:
click.echo('API return %s' % str(response.status_code))
@cli.command(help='Run processing locally.')
......@@ -25,4 +25,5 @@ psycopg2-binary
\ No newline at end of file
\ No newline at end of file
Supports Markdown
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