Python GirderClient.get方法代码示例

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import get [as 别名]
class NewtIntegrationTest(BaseIntegrationTest):
    def __init__(self, name, girder_url, girder_user, girder_password, machine, job_timeout=60 * 5):
        super(NewtIntegrationTest, self).__init__(name, girder_url, girder_user, girder_password, job_timeout)
        self._cluster_id = None
        self._machine = machine

    def setUp(self):

        # First authenticate with NEWT
        self._session = Session()
        r = self._session.post(
            "https://newt.nersc.gov/newt/auth", {"username": self._girder_user, "password": self._girder_password}
        )

        self.assertEqual(r.status_code, 200)
        print r.json()
        self._newt_session_id = r.json()["newt_sessionid"]

        # Now authenticate with Girder using the session id
        url = "%s/api/v1/newt/authenticate/%s" % (self._girder_url, self._newt_session_id)
        r = self._session.put(url)
        self.assertEqual(r.status_code, 200)

        url = "%s/api/v1/newt/authenticate/%s" % (self._girder_url, self._newt_session_id)
        r = self._session.put(url)
        self.assertEqual(r.status_code, 200)

        url = "%s/api/v1" % self._girder_url
        self._client = GirderClient(apiUrl=url)
        self._client.token = self._session.cookies["girderToken"]

        user = self._client.get("user/me")
        self._user_id = user["_id"]
        r = self._client.listFolder(self._user_id, "user", name="Private")
        r = list(r)
        self.assertEqual(len(r), 1)
        self._private_folder_id = r[0]["_id"]

    def tearDown(self):
        super(NewtIntegrationTest, self).tearDown()
        if self._cluster_id:
            try:
                url = "clusters/%s" % self._cluster_id
                self._client.delete(url)
            except Exception:
                traceback.print_exc()

    def create_cluster(self):
        body = {"config": {"host": self._machine}, "name": "NewtIntegrationTest", "type": "newt"}

        r = self._client.post("clusters", data=json.dumps(body))
        self._cluster_id = r["_id"]

        # Now test the connection
        r = self._client.put("clusters/%s/start" % self._cluster_id)
        sleeps = 0
        while True:
            time.sleep(1)
            r = self._client.get("clusters/%s/status" % self._cluster_id)

            if r["status"] == "running":
                break
            elif r["status"] == "error":
                r = self._client.get("clusters/%s/log" % self._cluster_id)
                self.fail(str(r))

            if sleeps > 9:
                self.fail("Cluster never moved into running state")
            sleeps += 1

    def assert_output(self):
        r = self._client.listItem(self._output_folder_id)
        self.assertEqual(len(r), 4)

        stdout_item = None
        for i in r:
            if i["name"].startswith("CumulusIntegrationTestJob-%s.o" % self._job_id):
                stdout_item = i
                break

        self.assertIsNotNone(stdout_item)
        r = self._client.get("item/%s/files" % i["_id"])
        self.assertEqual(len(r), 1)

        url = "%s/api/v1/file/%s/download" % (self._girder_url, r[0]["_id"])
        r = self._session.get(url)
        self.assertEqual(r.content, self._data)

    def test(self):
        try:
            self.create_cluster()
            self.create_script()
            self.create_input()
            self.create_output_folder()
            self.create_job()
            self.submit_job(timeout=self._job_timeout)
            self.assert_output()
        except HttpError as error:
            self.fail(error.responseText)

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import get [as 别名]
def import_calc(config):
    try:
        target_port = None
        if config.port:
            target_port = config.port
        target_scheme = None
        if config.scheme:
            target_scheme = config.scheme
        target_apiroot = None
        if config.apiroot:
            target_apiroot = config.apiroot

        client = GirderClient(host=config.host, port=target_port,
                              scheme=target_scheme, apiRoot=target_apiroot)
        client.authenticate(apiKey=config.apiKey)

        me = client.get('/user/me')
        if not me:
            print('Error: Girder token invalid, please verify')
            return

        folderParams = {
            'parentId': me['_id'],
            'parentType': 'user',
            'name': 'Private'
        }

        # Get the private folder id first
        folder = next(client.listResource('folder', folderParams))
        folder = next(client.listFolder(me['_id'], 'user', 'Private'))

        for file_name in config.datafile:
            print ('\nUploading ' + file_name)
            file_id = {}
            with open(file_name, 'r') as fp:
                fileNameBase = os.path.basename(file_name)
                size = os.path.getsize(file_name)
                file_id = client.uploadFile(folder['_id'], fp, fileNameBase,
                                            size, 'folder')

            body = {
                'fileId': file_id['_id']
            }

            if config.public:
                body['public'] = True


            mol = client.sendRestRequest('POST', 'molecules', data=json.dumps(body))

            if mol and '_id' in mol:
                config.moleculeId = mol['_id']
                print('Molecule ID: ' + mol['_id'])
            else:
                print(mol)

    except HttpError as error:
        print(error.responseText, file=sys.stderr)

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import get [as 别名]
parser = argparse.ArgumentParser()
parser.add_argument("path", type=str,
                    help="path to Arbor web apps")
parser.add_argument("-g", "--girder-host", type=str, default='localhost',
                    help="host to Girder instance")
parser.add_argument("-p", "--girder-port", type=int, default=9000,
                    help="port to Girder instance")

args = parser.parse_args()


# Get the ID for our Analyses folder.
c = GirderClient(host=args.girder_host, port=args.girder_port)
c.authenticate('girder', 'girder')
folderSearch = c.get('resource/search', parameters={
    'q': 'Analyses',
    'types': '["folder"]'
})
folderId = folderSearch['folder'][0]['_id']

# Disable authorization requirements for running romanesco tasks
c.put('system/setting', parameters={
    'key': 'flow.require_auth',
    'value': 'false'
})

# Check if these analyses already exist.  If so, we won't re-upload them.
uploadACR = False
uploadPGS = False

searchACR = c.get('resource/search', {
    'q': 'aceArbor',

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import get [as 别名]
class BaseIntegrationTest(unittest.TestCase):
    def __init__(self, name, girder_url, girder_user, girder_password, job_timeout=60, cleanup=True):
        super(BaseIntegrationTest, self).__init__(name)
        self._job_id = None
        self._script_id = None
        self._output_folder_id = None
        self._input_folder_id = None
        self._girder_url = girder_url
        self._girder_user = girder_user
        self._girder_password = girder_password
        self._job_timeout = job_timeout
        self._data = 'Need more input!'
        self._cleanup = cleanup

    def setUp(self):
        url = '%s/api/v1' % self._girder_url
        self._client = GirderClient(apiUrl=url)
        self._client.authenticate(self._girder_user,
                                  self._girder_password)

        user = self._client.get('user/me')
        self._user_id = user['_id']
        r = list(self._client.listFolder(self._user_id, 'user', name='Private'))
        self.assertEqual(len(r), 1)
        self._private_folder_id = r[0]['_id']

    def tearDown(self):

        if not self._cleanup:
            return

        if self._job_id:
            try:
                url = 'jobs/%s' % self._job_id
                self._client.delete(url)
            except Exception as e:
                traceback.print_exc()

        if self._script_id:
            try:
                url = 'scripts/%s' % self._script_id
                self._client.delete(url)
            except Exception:
                traceback.print_exc()

        if self._output_folder_id:
            try:
                url = 'folder/%s' % self._output_folder_id
                self._client.delete(url)
            except Exception:
                traceback.print_exc()

        if self._input_folder_id:
            try:
                url = 'folder/%s' % self._input_folder_id
                self._client.delete(url)
            except Exception:
                traceback.print_exc()

    def create_script(self, commands=[
                'sleep 10', 'cat CumulusIntegrationTestInput'
            ]):
        body = {
            'commands': commands,
            'name': 'CumulusIntegrationTestLob'
        }

        r = self._client.post('scripts', data=json.dumps(body))
        self._script_id = r['_id']

    def create_input(self, folder_name='CumulusInput'):

        r = self._client.createFolder(self._private_folder_id, folder_name)
        self._input_folder_id = r['_id']
        size = len(self._data)

        item = self._client.uploadFile(self._input_folder_id,
                    StringIO(self._data), 'CumulusIntegrationTestInput', size,
                    parentType='folder')

        self._item_id = item['itemId']

    def create_output_folder(self, folder_name='CumulusOutput'):
        r = self._client.createFolder(self._private_folder_id, folder_name)
        self._output_folder_id = r['_id']

    def create_job(self, job_name='CumulusIntegrationTestJob', tail=None):
        body = {
            'name': job_name,
            'scriptId': self._script_id,
            'output': [{
              'folderId': self._output_folder_id,
              'path': '.'
            }],
            'input': [
              {
                'folderId': self._input_folder_id,
                'path': '.'
              }
            ]
#.........这里部分代码省略.........

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import get [as 别名]
for root, dirs, files in os.walk(arbor_collections_path):
  for file in files:
    if not file.endswith(".json"):
      continue

    # Get the name of this file and the directory that it's in.
    # We use the directory name as the collection name in Girder.
    fullpath = os.path.join(root, file)
    analysis_filename = os.path.basename(fullpath)
    analysis_name = os.path.splitext(analysis_filename)[0]
    analysis_dir = os.path.dirname(fullpath)
    collection_name = os.path.basename(analysis_dir)

    # Create this collection if it doesn't already exist.
    collection_search = c.get('resource/search', parameters={
        'q': collection_name,
        'types': '["collection"]'
    })
    if len(collection_search["collection"]) == 0:
        collection = c.post('collection', parameters={
            'name': collection_name,
            'description': collection_name,
            'public': 'true'
        })
        c.post('folder', parameters={
            'parentType': 'collection',
            'parentId': collection['_id'],
            'name': 'Data',
            'description': 'Data Folder',
            'public': 'true'
        })
        c.post('folder', parameters={

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import get [as 别名]
        'gridWidth': lon_select_index,
        'gridHeight': lat_select_index,
        'x0': float(data.variables[lon_name][0]),
        'y0': float(data.variables[lat_name][0]),
        'dx': float(data.variables[lon_name][1] - data.variables[lon_name][0]),
        'dy': float(data.variables[lat_name][1] - data.variables[lat_name][0]),
        'values': variable[timestep][:lat_select_index, :lon_select_index].reshape(variable[timestep][:lat_select_index, :lon_select_index].size).tolist()
    }

    return contour_data

client = GirderClient(host, port)
client.token = token

# Get the user
user = client.get('user/me')
# Get the dataset folder
parameters = {
    'userId': user['_id']
}
dataset_folder = client.get('minerva_dataset/folder', parameters=parameters)['folder']
dataset_folder_id = dataset_folder['_id']
parameters = {
    'id': fileId,
    'type': 'file'
}

# Get the file resource so we can get the name
input_file = client.get('resource/%s' % str(fileId), parameters=parameters)
input_file_name = input_file['name']
output_file_name = input_file_name.replace('.nc', '.json')

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import get [as 别名]
except:
    c.sendRestRequest(
        "POST",
        "user",
        {
            "login": "girder",
            "password": "girder",
            "email": "[email protected]",
            "firstName": "Girder",
            "lastName": "Admin",
        },
    )
    c.authenticate("girder", "girder")

# Create a tangelo hub collection if there isn't one
coll_search = c.get("resource/search", parameters={"q": "Default", "types": '["collection"]'})
if len(coll_search["collection"]) == 0:
    collection = c.post(
        "collection", parameters={"name": "Default", "description": "Default workspace", "public": "true"}
    )
    c.post(
        "folder",
        parameters={
            "parentType": "collection",
            "parentId": collection["_id"],
            "name": "Data",
            "description": "Data Folder",
            "public": "true",
        },
    )
    c.post(

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import get [as 别名]
class NewtIntegrationTest(BaseIntegrationTest):

    def __init__(self, name, girder_url, girder_user, girder_password, machine,
                 job_timeout=60*5):
        super(NewtIntegrationTest, self).__init__(name, girder_url, girder_user,
                                                  girder_password, job_timeout)
        self._cluster_id = None
        self._machine = machine

    def setUp(self):

        # First authenticate with NEWT
        self._session = Session()
        r = self._session.post('https://newt.nersc.gov/newt/auth',
                               {
                                    'username': self._girder_user,
                                    'password': self._girder_password})

        self.assertEqual(r.status_code, 200)
        print r.json()
        self._newt_session_id = r.json()['newt_sessionid']

        # Now authenticate with Girder using the session id
        url = '%s/api/v1/newt/authenticate/%s' % (self._girder_url, self._newt_session_id)
        r = self._session.put(url)
        self.assertEqual(r.status_code, 200)

        url = '%s/api/v1/newt/authenticate/%s' % (self._girder_url, self._newt_session_id)
        r = self._session.put(url)
        self.assertEqual(r.status_code, 200)

        url = '%s/api/v1' % self._girder_url
        self._client = GirderClient(apiUrl=url)
        self._client.token = self._session.cookies['girderToken']

        user = self._client.get('user/me')
        self._user_id = user['_id']
        r = self._client.listFolder(self._user_id, 'user', name='Private')
        self.assertEqual(len(r), 1)
        self._private_folder_id = r[0]['_id']

    def tearDown(self):
        super(NewtIntegrationTest, self).tearDown()
        if self._cluster_id:
            try:
                url = 'clusters/%s' % self._cluster_id
                self._client.delete(url)
            except Exception:
                traceback.print_exc()

    def create_cluster(self):
        body = {
            'config': {
                'host': self._machine
            },
            'name': 'NewtIntegrationTest',
            'type': 'newt'
        }

        r = self._client.post('clusters', data=json.dumps(body))
        self._cluster_id = r['_id']

        # Now test the connection
        r = self._client.put('clusters/%s/start' % self._cluster_id)
        sleeps = 0
        while True:
            time.sleep(1)
            r = self._client.get('clusters/%s/status' % self._cluster_id)

            if r['status'] == 'running':
                break
            elif r['status'] == 'error':
                r = self._client.get('clusters/%s/log' % self._cluster_id)
                self.fail(str(r))

            if sleeps > 9:
                self.fail('Cluster never moved into running state')
            sleeps += 1

    def assert_output(self):
        r = self._client.listItem(self._output_folder_id)
        self.assertEqual(len(r), 4)

        stdout_item = None
        for i in r:
            if i['name'].startswith('CumulusIntegrationTestJob-%s.o' % self._job_id):
                stdout_item = i
                break

        self.assertIsNotNone(stdout_item)
        r = self._client.get('item/%s/files' % i['_id'])
        self.assertEqual(len(r), 1)

        url =   '%s/api/v1/file/%s/download' % (self._girder_url, r[0]['_id'])
        r = self._session.get(url)
        self.assertEqual(r.content, self._data)


    def test(self):
        try:
#.........这里部分代码省略.........