Python GirderClient.post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 post [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 post [as 别名]
    def _update_girder(taskflow, body):
        taskflow = to_taskflow(taskflow)
        taskflow_id = taskflow['id']
        girder_token = taskflow['girder_token']
        girder_api_url = taskflow['girder_api_url']

        client = GirderClient(apiUrl=girder_api_url)
        client.token = girder_token

        client = _create_girder_client(girder_api_url, girder_token)

        # If this is a retry then we have already create a task get it from
        # the current tasks headers.
        if body['retries'] > 0:
            taskflow_task_id = \
                current_task.request.headers[TASKFLOW_TASK_ID_HEADER]

            # Celery always fires the postrun handler with a state of SUCCESS
            # for retries. So we need to save the retries here so we can
            # determine in the postrun handler if the task is really complete.
            current_task.request.headers[TASKFLOW_RETRY_HEADER] \
                = body['retries']
        else:
                # This is a new task so create a taskflow task instance
            body = {
                'celeryTaskId': body['id'],
                'name': body['task']
            }
            url = 'taskflows/%s/tasks' % taskflow_id
            r = client.post(url, data=json.dumps(body))
            taskflow_task_id = r['_id']
        return taskflow, taskflow_task_id

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import post [as 别名]
ensure_user(client,
            login=user,
            password=password,
            email='[email protected]',
            firstName='Girder',
            lastName='Admin')

client.authenticate(user, password)

s3_assetstore_name = 's3'

if find_assetstore(s3_assetstore_name) is None:
    client.post('assetstore',
                parameters=dict(name=s3_assetstore_name,
                                type=str(AssetstoreType.S3),
                                bucket=args.s3,
                                accessKeyId=args.aws_key_id,
                                secret=args.aws_secret_key))

client.put(
    'system/plugins',
    parameters=dict(plugins=json.dumps(['jobs', 'worker', 'osumo']))
)
client.put('system/restart')

sleep(30)

client.put('system/setting',
           parameters=dict(list=json.dumps([
               dict(key='worker.broker', value=args.broker),
               dict(key='worker.backend', value=args.broker),

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import post [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 post [as 别名]
client = GirderClient(host=args.host, port=args.port)
register_and_authenticate(client,
                          login=args.user,
                          password=args.password,
                          email='{}@localhost.com'.format(args.user),
                          firstName='Girder',
                          lastName='Admin')

local_assetstore_name = 'local'

if find_assetstore(local_assetstore_name) is None:
    client.post('assetstore',
                parameters=dict(name=local_assetstore_name,
                                type=str(AssetstoreType.FILESYSTEM),
                                root=os.path.join(args.data_root,
                                                  'assetstores',
                                                  'local'),
                                readOnly="false"))

client.put('system/plugins',
           parameters=dict(plugins=json.dumps(['celery_jobs',
                                               'climos_test',
                                               'user_quota',
                                               'hdfs_assetstore',
                                               'jobs',
                                               'romanesco',
                                               'sparktest'])))

client.put('system/restart')

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import post [as 别名]
    # 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={
            'parentType': 'collection',
            'parentId': collection['_id'],
            'name': 'Analyses',
            'description': 'Analysis folder',
            'public': 'true'

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import post [as 别名]
try:
    # Now download the dataset
    (fd, filepath) = tempfile.mkstemp()
    os.close(fd)
    client.downloadFile(fileId, filepath)

    # Create temp file and convert to GeoJs contour JSON format
    output_dir = tempfile.mkdtemp()
    output_filepath = os.path.join(output_dir, output_file_name)
    with open(output_filepath, 'w') as fp:
        fp.write(json_util.dumps(convert(filepath, variable, timestep)))

    # Create an item for this file
    output_item = client.createItem(dataset_folder_id, output_file_name, output_file_name)

    # Now upload the result
    client.uploadFileToItem(output_item['_id'], output_filepath)

    output_item_id = output_item['_id']

    # Finally promote item to dataset
    client.post('minerva_dataset/%s/dataset' % output_item_id)

finally:
    if filepath and os.path.exists(filepath):
        os.remove(filepath)
    if output_dir and os.path.exists(output_dir):
        shutil.rmtree(output_dir)

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import post [as 别名]
        "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(
        "folder",
        parameters={
            "parentType": "collection",

# 需要导入模块: from girder_client import GirderClient [as 别名]
# 或者: from girder_client.GirderClient import post [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.........