def post(self):
parser = RequestParsers.study_type_report_parser()
studytype = None
args = parser.parse_args(req=request)
studytype = args['studytype']
slim = args['slim']
verbose = args['verbose']
drive = args['drive']
if studytype:
studytype = studytype.strip()
else:
abort(400)
# User authentication
user_token = None
if "user_token" in request.headers:
user_token = request.headers["user_token"]
else:
abort(401)
wsc = WsClient()
is_curator, __, __, __, study_location, __, __, __ = wsc.get_permissions('MTBLS1', user_token)
if is_curator is False:
abort(413)
reporting_path = app.config.get('MTBLS_FTP_ROOT') + app.config.get('REPORTING_PATH') + 'global/'
msg = AnalyticalMethodBuilder(
original_study_location=study_location,
studytype=studytype,
slim=slim,
reporting_path=reporting_path,
verbose=verbose,
g_drive=drive
).build()
logger.info(msg)
return jsonify({'message': msg})
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
from flask import request, abort
from flask_restful import Resource
from flask_restful_swagger import swagger
from app.ws.mtblsWSclient import WsClient
from app.ws.utils import *
from app.ws.isaApiClient import IsaApiClient
logger = logging.getLogger('wslog')
wsc = WsClient()
iac = IsaApiClient()
class Convert2ISAtab(Resource):
@swagger.operation(
summary="Convert mzML files into ISA-Tab",
notes=
'''</P><B>Be aware that any ISA-Tab files will be overwritten for this study</P>
This process can run for a long while, please be patient</B>''',
parameters=[{
"name": "study_id",
"description":
"Existing Study Identifier for generating new ISA-Tab files",
"required": True,
"allowMultiple": False,
def __init__(self):
self.inv_filename = "i_Investigation.txt"
self.wsc = WsClient() # MetaboLights (Java-Based) WebService client
return
class IsaApiClient:
def __init__(self):
self.inv_filename = "i_Investigation.txt"
self.wsc = WsClient() # MetaboLights (Java-Based) WebService client
return
def get_isa_json(self, study_id, api_key, study_location=None):
"""
Get an ISA-API Investigation object reading directly from the ISA-Tab files
:param study_id: MTBLS study identifier
:param api_key: User API key for accession check
:param study_location: The filesystem location of the study
:return: an ISA-API Investigation object
"""
start = time.time()
if study_location is None:
logger.info(
"Study location is not set, will have load study from filesystem"
)
path = self.wsc.get_study_location(study_id, api_key)
else:
logger.info("Study location is: " + study_location)
path = study_location
# try the new parser first
isa_json = None
try:
isa_json = isatab2json.convert(path,
validate_first=False,
use_new_parser=True)
except Exception: # on failure, use the old one
try:
isa_json = isatab2json.convert(path,
validate_first=False,
use_new_parser=False)
except Exception:
# if it fails too
if isa_json is None:
abort(500)
else:
logger.info('... get_isa_json() processing (I): %s sec.',
time.time() - start)
return isa_json
else:
logger.info('... get_isa_json() processing (II): %s sec.',
time.time() - start)
return isa_json
@staticmethod
def create_new_study(title, description, sub_date, pub_rel_date,
mtbls_accession, technology):
"""
Create a new MTBLS Study
:param title:
:param description:
:param sub_date: Submission date (now)
:param pub_rel_date: Public release date
:param mtbls_accession: MTBLS id
:param technology: MS or NMR
:return: an ISA-JSON representation of the Study
"""
inv_file_name = 'i_investigation.txt'
study_file_name = 's_study.txt'
assay_file_name = 'a_assay.txt'
if mtbls_accession is not None:
study_file_name = 's_' + mtbls_accession + '_' + technology + '.txt'
assay_file_name = 'a_' + mtbls_accession + '_' + technology + '.txt'
# investigation file
investigation = Investigation(filename=inv_file_name)
investigation.title = title
investigation.description = description
investigation.submission_date = sub_date
investigation.public_release_date = pub_rel_date
# study file
study = Study(filename=study_file_name)
study.identifier = mtbls_accession
study.title = title
study.description = description
study.submission_date = sub_date
study.public_release_date = pub_rel_date
# investigation.studies.append(study)
protocol = Protocol()
# assay file
assay = Assay(filename=assay_file_name)
assay.technology_platform = technology
# TODO, ontology term
# assay.technology_type = technology
study.assays.append(assay)
# Add it all together
investigation.studies.append(study)
return investigation
def get_isa_study(self,
study_id,
api_key,
skip_load_tables=True,
study_location=None,
failing_gracefully=False):
"""
Get an ISA-API Investigation object reading directly from the ISA-Tab files
:param study_id: MTBLS study identifier
:param api_key: User API key for accession check
:param skip_load_tables: speed-up reading by skiping loading assay and sample tables
:param study_location: filessystem location of the study
:return: a tuple consisting in ISA-Study obj, ISA-Investigation obj
and path to the Study in the file system
"""
if skip_load_tables == 'false':
skip_load_tables = False
if study_location is None:
logger.info(
"Study location is not set, will have load study from filesystem"
)
std_path = self.wsc.get_study_location(study_id, api_key)
else:
logger.info("Study location is: " + study_location)
std_path = study_location
try:
i_filename = glob.glob(os.path.join(std_path, "i_*.txt"))[0]
fp = open(i_filename, encoding='utf-8', errors='ignore')
# loading tables also load Samples and Assays
isa_inv = load(fp, skip_load_tables)
# ToDo. Add MAF to isa_study
isa_study = isa_inv.studies[0]
except IndexError as e:
logger.exception("Failed to find Investigation file from %s",
study_id, std_path)
logger.error(str(e))
if failing_gracefully:
return None, None, None
else:
abort(417)
except Exception as e:
logger.exception("Failed to find Investigation file from %s",
study_id, std_path)
logger.error(str(e))
if failing_gracefully:
return None, None, None
else:
abort(417)
else:
return isa_study, isa_inv, std_path
def write_isa_study(self,
inv_obj,
api_key,
std_path,
save_investigation_copy=True,
save_samples_copy=False,
save_assays_copy=False):
"""
Write back an ISA-API Investigation object directly into ISA-Tab files
:param inv_obj: ISA-API Investigation object
:param api_key: User API key for accession check
:param std_path: file system path to destination folder
:param save_investigation_copy: Keep track of changes saving a copy of the unmodified i_*.txt file
:param save_samples_copy: Keep track of changes saving a copy of the unmodified s_*.txt file
:param save_assays_copy: Keep track of changes saving a copy of the unmodified a_*.txt and m_*.tsv files
:return:
"""
# dest folder name is a timestamp
update_path_suffix = app.config.get('UPDATE_PATH_SUFFIX')
update_path = os.path.join(std_path, update_path_suffix)
if save_investigation_copy or save_samples_copy or save_assays_copy: # Only create audit folder when requested
dest_path = new_timestamped_folder(update_path)
# make a copy before applying changes
if save_investigation_copy:
src_file = os.path.join(std_path, self.inv_filename)
dest_file = os.path.join(dest_path, self.inv_filename)
logger.info("Copying %s to %s", src_file, dest_file)
copy_file(src_file, dest_file)
if save_samples_copy:
for sample_file in glob.glob(os.path.join(std_path,
"s_*.txt")):
sample_file_name = os.path.basename(sample_file)
src_file = sample_file
dest_file = os.path.join(dest_path, sample_file_name)
logger.info("Copying %s to %s", src_file, dest_file)
copy_file(src_file, dest_file)
if save_assays_copy:
for assay_file in glob.glob(os.path.join(std_path, "a_*.txt")):
assay_file_name = os.path.basename(assay_file)
src_file = assay_file
dest_file = os.path.join(dest_path, assay_file_name)
logger.info("Copying %s to %s", src_file, dest_file)
copy_file(src_file, dest_file)
# Save the MAF
for maf in glob.glob(os.path.join(std_path, "m_*.tsv")):
maf_file_name = os.path.basename(maf)
src_file = maf
dest_file = os.path.join(dest_path, maf_file_name)
logger.info("Copying %s to %s", src_file, dest_file)
copy_file(src_file, dest_file)
logger.info("Writing %s to %s", self.inv_filename, std_path)
i_file_name = self.inv_filename
dump(inv_obj,
std_path,
i_file_name=i_file_name,
skip_dump_tables=False)
return
def __init__(self):
self.inv_filename = "i_Investigation.txt"
self.wsc = WsClient() # MetaboLights (Java-Based) WebService client
return
class IsaApiClient:
def __init__(self):
self.inv_filename = "i_Investigation.txt"
self.wsc = WsClient() # MetaboLights (Java-Based) WebService client
return
def get_isa_json(self, study_id, api_key, study_location=None):
"""
Get an ISA-API Investigation object reading directly from the ISA-Tab files
:param study_id: MTBLS study identifier
:param api_key: User API key for accession check
:param study_location: The filesystem location of the study
:return: an ISA-API Investigation object
"""
start = time.time()
if study_location is None:
logger.info("Study location is not set, will have load study from filesystem")
path = self.wsc.get_study_location(study_id, api_key)
else:
logger.info("Study location is: " + study_location)
path = study_location
# try the new parser first
isa_json = None
try:
isa_json = isatab2json.convert(path, validate_first=False, use_new_parser=True)
except Exception: # on failure, use the old one
try:
isa_json = isatab2json.convert(path, validate_first=False, use_new_parser=False)
except Exception:
# if it fails too
if isa_json is None:
abort(500)
else:
logger.info('... get_isa_json() processing (I): %s sec.', time.time() - start)
return isa_json
else:
logger.info('... get_isa_json() processing (II): %s sec.', time.time() - start)
return isa_json
@staticmethod
def create_new_study(title, description, sub_date, pub_rel_date, mtbls_accession, technology):
"""
Create a new MTBLS Study
:param title:
:param description:
:param sub_date: Submission date (now)
:param pub_rel_date: Public release date
:param mtbls_accession: MTBLS id
:param technology: MS or NMR
:return: an ISA-JSON representation of the Study
"""
inv_file_name = 'i_investigation.txt'
study_file_name = 's_study.txt'
assay_file_name = 'a_assay.txt'
if mtbls_accession is not None:
study_file_name = 's_' + mtbls_accession + '_' + technology + '.txt'
assay_file_name = 'a_' + mtbls_accession + '_' + technology + '.txt'
# investigation file
investigation = Investigation(filename=inv_file_name)
investigation.title = title
investigation.description = description
investigation.submission_date = sub_date
investigation.public_release_date = pub_rel_date
# study file
study = Study(filename=study_file_name)
study.identifier = mtbls_accession
study.title = title
study.description = description
study.submission_date = sub_date
study.public_release_date = pub_rel_date
# investigation.studies.append(study)
protocol = Protocol()
# assay file
assay = Assay(filename=assay_file_name)
assay.technology_platform = technology
# TODO, ontology term
# assay.technology_type = technology
study.assays.append(assay)
# Add it all together
investigation.studies.append(study)
return investigation
def get_isa_study(self, study_id, api_key, skip_load_tables=True, study_location=None):
"""
Get an ISA-API Investigation object reading directly from the ISA-Tab files
:param study_id: MTBLS study identifier
:param api_key: User API key for accession check
:param skip_load_tables: speed-up reading by skiping loading assay and sample tables
:param study_location: filessystem location of the study
:return: a tuple consisting in ISA-Study obj, ISA-Investigation obj
and path to the Study in the file system
"""
if study_location is None:
logger.info("Study location is not set, will have load study from filesystem")
std_path = self.wsc.get_study_location(study_id, api_key)
else:
logger.info("Study location is: " + study_location)
std_path = study_location
try:
i_filename = glob.glob(os.path.join(std_path, "i_*.txt"))[0]
fp = open(i_filename)
# loading tables also load Samples and Assays
isa_inv = load(fp, skip_load_tables)
isa_study = isa_inv.studies[0]
except IndexError as e:
logger.exception("Failed to find Investigation file from %s", study_id, std_path)
logger.error(str(e))
abort(400)
except Exception as e:
logger.exception("Failed to find Investigation file from %s", study_id, std_path)
logger.error(str(e))
abort(400)
else:
return isa_study, isa_inv, std_path
def write_isa_study(self, inv_obj, api_key, std_path,
save_investigation_copy=True, save_samples_copy=False, save_assays_copy=False):
"""
Write back an ISA-API Investigation object directly into ISA-Tab files
:param inv_obj: ISA-API Investigation object
:param api_key: User API key for accession check
:param std_path: file system path to destination folder
:param save_investigation_copy: Keep track of changes saving a copy of the unmodified i_*.txt file
:param save_samples_copy: Keep track of changes saving a copy of the unmodified s_*.txt file
:param save_assays_copy: Keep track of changes saving a copy of the unmodified a_*.txt and m_*.tsv files
:return:
"""
# dest folder name is a timestamp
update_path_suffix = app.config.get('UPDATE_PATH_SUFFIX')
update_path = os.path.join(std_path, update_path_suffix)
if save_investigation_copy or save_samples_copy or save_assays_copy: # Only create audit folder when requested
dest_path = new_timestamped_folder(update_path)
# make a copy before applying changes
if save_investigation_copy:
src_file = os.path.join(std_path, self.inv_filename)
dest_file = os.path.join(dest_path, self.inv_filename)
logger.info("Copying %s to %s", src_file, dest_file)
copy_file(src_file, dest_file)
if save_samples_copy:
for sample_file in glob.glob(os.path.join(std_path, "s_*.txt")):
sample_file_name = os.path.basename(sample_file)
src_file = sample_file
dest_file = os.path.join(dest_path, sample_file_name)
logger.info("Copying %s to %s", src_file, dest_file)
copy_file(src_file, dest_file)
if save_assays_copy:
for assay_file in glob.glob(os.path.join(std_path, "a_*.txt")):
assay_file_name = os.path.basename(assay_file)
src_file = assay_file
dest_file = os.path.join(dest_path, assay_file_name)
logger.info("Copying %s to %s", src_file, dest_file)
copy_file(src_file, dest_file)
# Save the MAF
for maf in glob.glob(os.path.join(std_path, "m_*.tsv")):
maf_file_name = os.path.basename(maf)
src_file = maf
dest_file = os.path.join(dest_path, maf_file_name)
logger.info("Copying %s to %s", src_file, dest_file)
copy_file(src_file, dest_file)
logger.info("Writing %s to %s", self.inv_filename, std_path)
i_file_name = self.inv_filename
dump(inv_obj, std_path, i_file_name=i_file_name, skip_dump_tables=False)
return