def _login(self, email: str, password: str, token: str = None):
self.session.cookies.clear()
self.session = Util.mount_standard_session(self.session)
headers = {}
body = {
'email': email,
'password': password,
}
if token:
body['token'] = token
response = self.session.post(
url='{}/api/auth'.format(self.url),
json=body,
headers=headers,
)
Util.raise_detailed_error(response)
self.user = response.json()
# Persist so can quickly run again without needing to enter 2FA token.
self.save_session_to_disk()
def list(self):
response = self.session.get(self.url + '?filter=',
headers={
'content-type': 'application/json'
})
Util.raise_detailed_error(response)
return response
def get(self, job_id=None):
if job_id is None:
job_id = self.job_id
url = '{}/{}'.format(self.url, job_id)
response = self.session.get(url, headers={'content-type': 'application/json'})
Util.raise_detailed_error(response)
return response.json()
def download_original_file(self, entity_id: int,
destination_filename: str) -> str:
"""
Download the originally uploaded file corresponding to a PipeBio document.
Two requests are made:
1. Request a signed url for this document (GET /api/v2/entities/:id/original)
2. Download the data from that signed url (GET <result-from-step-1>)
"""
# First request a signed url from PipeBio.
signed_url_response = self.session.get(
'{}/api/v2/entities/{}/original'.format(self.url, entity_id), )
# Did the signed-url request work ok?
Util.raise_detailed_error(signed_url_response)
# Parse the results to get the signed url.
download_url = signed_url_response.json()['url']
# Download the original file.
download_response = requests.get(download_url)
# Did the download request work ok?
Util.raise_detailed_error(download_response)
# Write the result to disk in chunks.
with open(destination_filename, 'wb') as f:
for chunk in download_response.iter_content(chunk_size=8192):
f.write(chunk)
return destination_filename
def create_file(self,
project_id: str,
parent_id: int,
name: str,
entity_type: EntityTypes = EntityTypes.SEQUENCE_DOCUMENT,
visible=False) -> dict:
print('create_file for parent_id:' + str(parent_id) + ' name:' +
str(name))
payload = {
'name': name,
'type': entity_type.value,
'visible': visible,
'shareableId': project_id,
}
if parent_id is not None:
payload['parentId'] = int(str(parent_id))
response = self.session.post(
'{}/api/v2/entities'.format(self.url),
headers={'Content-type': 'Application/json'},
data=json.dumps(payload),
)
print('create_file response:' + str(response.status_code))
Util.raise_detailed_error(response)
return response.json()
def create(self, entity_id: int, type: AttachmentType, data: Union[dict, List]):
print('Creating attachment: entity_id={},kind={}'.format(entity_id, type.value))
url = '{}/{}/attachments'.format(self.url, entity_id)
json = {"data": data, "type": type.value}
response = self.session.post(url, json=json)
Util.raise_detailed_error(response)
print('Creating attachment: response', response.status_code)
return response.json()
def get(self, entity_id):
response = self.session.get(
'{}/api/v2/entities/{}'.format(self.url, entity_id),
headers={'Content-type': 'Application/json'},
)
print('get response:' + str(response.status_code))
Util.raise_detailed_error(response)
return response.json()
def _save_web_tmp_db(self, sql, tpl):
try:
with DBConnect.get_connection() as con:
with con.cursor() as cur:
cur.execute(sql, tpl)
except:
Util.put('_save_web_tmp_db エラー',
traceback.format_exc() + '\r\n\r\n' + sql)
def list(self) -> List[dict]:
url = '{}/api/v2/shareables'.format(self.url)
response = self.session.get(url)
print('ShareablesService:list - response:' + str(response.status_code))
Util.raise_detailed_error(response)
return response.json()['data']
def mark_file_visible(self, entity_summary: UploadSummary):
print('marking visible:', entity_summary)
response = self.session.patch(
'{}/api/v2/entities/{}'.format(self.url, entity_summary.id),
headers={'Content-type': 'Application/json'},
data=json.dumps(entity_summary.to_json()),
)
print('mark_file_visible response:' + str(response.status_code))
print('mark_file_visible text :' + str(response.text))
Util.raise_detailed_error(response)
return response.json()
def start_import_job(self):
"""
Enable the cloud-function to trigger a job run via the kubernetes job processing engine.
:return:
"""
response = self.session.patch(
'{}/{}/import'.format(self.url, self.job_id),
headers={'content-type': 'application/json'}
)
Util.raise_detailed_error(response)
return response
def create(self, name: str) -> dict:
url = '{}/api/v2/shareables'.format(self.url)
response = self.session.post(
url,
data=json.dumps({'name': name}),
)
print('ShareablesService:list - response:' + str(response.status_code))
Util.raise_detailed_error(response)
return response.json()
def upsert(self, entity_id: int, type: AttachmentType, data: Union[dict, List], version: int = 1,
ignore_version=True):
"""
Create or update if exists.
"""
print('Upserting attachment: entity_id={},type={},version={},ignore_version={}'.format(entity_id, type.value,
version,
ignore_version))
url = '{}/{}/attachments'.format(self.url, entity_id)
json = {"data": data, "version": version, "type": type.value, "ignoreVersion": ignore_version}
response = self.session.put(url, json=json)
Util.raise_detailed_error(response)
print('Creating attachment: response', response.status_code)
def lambda_handler(event, context):
reload(sys)
sys.setdefaultencoding("utf-8")
Util.put('lambda_handler', str(event))
# イベントで振る舞いを変える
for event_record in event['Records']:
if 's3' in event_record: # S3イベントの場合
key = Util.url_decode(event_record['s3']['object']['key'])
Util.put('key', key)
import s3_main
s3_main.data_import(key)
else: # cronイベントの場合
pass
def upload_data_to_signed_url(self, absolute_file_location: str, signed_url: str, signed_headers):
# 1. Start the signed-upload.
# NOTE: Url and headers cannot be modified or the upload will fail.
create_upload_response = self.session.post(signed_url, headers=signed_headers)
Util.raise_detailed_error(create_upload_response)
response_headers = create_upload_response.headers
location = response_headers['Location']
# 2. Upload bytes.
with open(absolute_file_location, 'rb') as file:
upload_response = self.session.put(location, data=file)
Util.raise_detailed_error(upload_response)
print('Upload response: ', upload_response.status_code)
print('Upload response:', upload_response.text)
def example_02a_download_result_as_tsv(document_id: int):
"""
Download the raw file as a TSV.
"""
client = PipebioClient()
# Either login with hardcoded variables or use environment variables:
# e.g.
# client.login(<my-email>, <my-password>, <my-token>)
# or:
# PIPE_EMAIL=<my-email> PIPE_PASSWORD=<my-password> PIPE_TOKEN=<my-token> python login.py
client.login()
# Display who we are logged in as.
user = client.authentication.user
print('\nLogged in as {}. \n'.format(user['firstName'], user['lastName']))
# Set the download name and folder.
destination_filename = "download.tsv"
destination_location = Util.get_executed_file_location()
absolute_location = os.path.join(destination_location, '..',
f'Downloads/{destination_filename}')
client.sequences.download(document_id, destination=absolute_location)
return absolute_location
def list_entities(self, shareable_id: str):
url = '{}/api/v2/shareables/{}/entities'.format(self.url, shareable_id)
response = self.session.get(url)
print('ShareablesService:list_entities - response:' +
str(response.status_code))
Util.raise_detailed_error(response)
file = StringIO(response.text)
reader = csv.DictReader(file, dialect='excel-tab')
rows = []
for row in reader:
rows.append(row)
return rows
def create_signed_upload(self, file_name: str, parent_id: int, project_id: str, organization_id: str) -> dict:
data = {
'name': file_name,
'type': EntityTypes.SEQUENCE_DOCUMENT.value,
'targetFolderId': parent_id,
'shareableId': project_id,
'ownerId': organization_id,
}
# if details is not None:
# # Details should be an
# data['details'] = []
# for detail in details:
# data['details'].append(detail.to_json())
response = self.session.post('{}/api/v2/signed-url'.format(self.base_url), json=data)
Util.raise_detailed_error(response)
return response.json()
def create(self,
owner_id: str,
shareable_id: str,
job_type: JobType,
name: str,
input_entity_ids: List[int],
params=None) -> str:
"""
:param owner_id: - organization id owning this job
:param shareable_id: - project in which the docuemnts are
:param job_type:
:param name: - helpful user facing name
:param input_entity_ids: - document ids
:param params: - specific to this job_type
:return:
"""
if params is None:
params = {}
response = self.session.post(self.url,
headers={
'content-type': 'application/json'
},
data=json.dumps({
'name': name,
'params': params,
'shareableId': shareable_id,
'ownerId': owner_id,
'inputEntities': input_entity_ids,
'type': job_type.value
}))
Util.raise_detailed_error(response)
data = response.json()
job_id = data['id']
self.job_id = job_id
return job_id
def save(cls, org_file_name, arr_csv_container, str_collaborator):
u"csv_containerの配列をもらって、ファイルに保存、S3にUP、そのパスを返す"
tmp_csv_file_name = org_file_name.replace('_org.', '.')
tmp_csv_zip_file_name = tmp_csv_file_name.replace('.csv', '.zip')
tmp_csv_file_path = '/tmp/' + tmp_csv_file_name
tmp_csv_zip_file_path = tmp_csv_file_path.replace('.csv', '.zip')
with open(tmp_csv_file_path, 'ab') as f: # aでファイルが無ければ作る
# 改行やカンマ、コーテーションなどのCSVフォーマットを崩す文字列がある場合だけ、ダブルコーテーションでくくられる
csv_writer = csv.writer(f, quoting=csv.QUOTE_MINIMAL)
# ヘッダーを書く
header_row_data = []
header_row_data.append('店舗名')
header_row_data.append('店舗電話番号')
csv_writer.writerow(header_row_data)
for i, csv_container in enumerate(arr_csv_container): # indexつきで処理
try:
row_data = []
row_data.append(csv_container.name)
row_data.append(csv_container.telephone)
csv_writer.writerow(row_data)
except:
Util.put('CsvController.save', traceback.format_exc())
with zipfile.ZipFile(tmp_csv_zip_file_path, 'w',
zipfile.ZIP_DEFLATED) as zipFile:
zipFile.write(tmp_csv_file_path, tmp_csv_file_name)
s3 = boto3.resource('s3')
bucket = s3.Bucket(Settings.get_s3_bucket())
# 変換結果をバックアップの意味でUP
with open(tmp_csv_zip_file_path, 'rb') as csv_up_data:
bucket.put_object(Key=str_collaborator + '/' +
tmp_csv_zip_file_name,
Body=csv_up_data)
return tmp_csv_file_name
def get_fields(self, entity_id: int, ignore_id=False) -> List[Column]:
"""
Returns the fields for a document or 404 if there are no fields (e.g. it's a folder).
:return:
"""
response = self.session.get(
'{}/api/v2/entities/{}/fields'.format(self.url, entity_id), )
Util.raise_detailed_error(response)
columns = []
for field in response.json():
if ignore_id and field == 'id':
continue
else:
# Not all columns have field so we need to check it's set.
description = field[
'description'] if 'description' in field else None
columns.append(
Column(field['name'], TableColumnType[field['type']],
description))
return columns
def data_import(csv_path):
reload(sys)
sys.setdefaultencoding("utf-8")
Util.put('変換開始', csv_path)
with open(csv_path) as f:
reader = csv.reader(f)
next(reader) # ヘッダーを読み飛ばす場合
arr_csv_cnt = []
# 一行ずつ処理
for row in reader: # indexつきで処理
# CSVフォーマットのクラスへ保持する
csv_cnt = CsvContainer()
csv_cnt.name = row[0]
csv_cnt.telephone = row[1]
# …ホントは続く
arr_csv_cnt.append(csv_cnt)
return arr_csv_cnt
def data_import(key):
u'S3トリガのメイン関数'
try:
reload(sys)
sys.setdefaultencoding("utf-8")
Util.put('s3_main.data_import 開始', key)
# S3からDL 別名で保存
s3 = boto3.resource('s3')
bucket = s3.Bucket(Settings.get_s3_bucket())
code = 'netmarketing' # とりあえず決め打ち 本来は判別する
org_csv_file_name = '{cd}_{dt}_{hs}_org.csv'.format(
cd=code,
dt=datetime.now().strftime('%Y%m%d_%H%M%S'),
hs=hashlib.sha224(key).hexdigest()[0:10] # 複数ファイル更新時にも被らないように
)
org_csv_file_path = '/tmp/' + org_csv_file_name
bucket.download_file(key, org_csv_file_path)
# CSVを各提供元の仕様に則って変換、CSVデータの配列を返す
arr_csv_container = []
import collaborator.netmarketing as collabo # 本来は提携先によって取得処理を違わせる
arr_csv_container = collabo.data_import(org_csv_file_path)
# S3にCSVファイルとしてUP、ファイル名を返す
csv_file = CsvController.save(org_csv_file_name, arr_csv_container,
code)
# データをサービス用DBに保存
CsvController.insert_web_tmp_db(arr_csv_container, csv_file)
# S3のファイルをバックアップしてから削除
org_zip_file_name = org_csv_file_name.replace('.csv', '.zip')
org_zip_file_path = org_csv_file_path.replace('.csv', '.zip')
with zipfile.ZipFile(org_zip_file_path, 'w',
zipfile.ZIP_DEFLATED) as zipFile:
zipFile.write(org_csv_file_path, org_csv_file_name)
with open(org_zip_file_path, 'rb') as org_up_data:
bucket.put_object(Key=code + '/' + org_zip_file_name,
Body=org_up_data)
s3.Object(Settings.get_s3_bucket(), key).delete()
Util.put('s3_main.data_import 終了', '[name] : ' + code)
except:
# エラー書き込み
import traceback
Util.put('s3_main.data_import エラー', traceback.format_exc())
def example_02c_download_result_to_biological_format(document_id):
"""
Download the format in Genbank, Fasta, Fastq, Ab1 etc.
"""
client = PipebioClient()
# Either login with hardcoded variables or use environment variables:
# e.g.
# client.login(<my-email>, <my-password>, <my-token>)
# or:
# PIPE_EMAIL=<my-email> PIPE_PASSWORD=<my-password> PIPE_TOKEN=<my-token> python login.py
client.login()
# Display who we are logged in as.
user = client.authentication.user
print('\nLogged in as {}. \n'.format(user['firstName'], user['lastName']))
# Specify a target folder on this computer to download the file to.
destination_folder = Util.get_executed_file_location()
return client.export(document_id, ExportFormat.GENBANK.value,
destination_folder)
def example_02d_download_original_file(document_id: int,
destination_filename: str = None
) -> str:
"""
Download the original, un-parsed file.
"""
client = PipebioClient()
# Either login with hardcoded variables or use environment variables.
# PIPE_EMAIL=<my-email> PIPE_PASSWORD=<my-password> PIPE_TOKEN=<my-token> python login.py
client.login()
# Display who we are logged in as.
user = client.authentication.user
print('\nLogged in as {}. \n'.format(user['firstName'], user['lastName']))
# Set the download name and folder.
destination_filename = "download.tsv" if destination_filename is None else destination_filename
destination_location = Util.get_executed_file_location()
absolute_location = os.path.join(destination_location,
f'../Downloads/{destination_filename}')
return client.entities.download_original_file(document_id,
absolute_location)
def get(self, entity_id: str, type: AttachmentType, version: int = 1):
url = '{}/{}/attachments/{}'.format(self.url, entity_id, type.value, json={'version': version})
response = self.session.get(url)
Util.raise_detailed_error(response)
return response.json()
def __init__(self, url, session: requests.sessions, job_id=None):
self.base_url = url
self.url = url + '/api/v2/jobs'
self.session = Util.mount_standard_session(session)
self.job_id = job_id
self.status = 'RUNNING'
def __init__(self, url: str, session: requests.sessions):
self._url = url
self.url = '{0}/api/v2'.format(url)
self.session = Util.mount_standard_session(session)
self.entities = Entities(url, session)
