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isarest_client.py
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import requests
import json
import os
class IsaRestClient:
def __init__(self, baseurl='http://localhost:5000', dl_folder='/tmp'):
self.baseurl = baseurl
self.dl_folder = dl_folder
def convert_tab_to_json(self, zipped_tab_bytes):
"""
:param zipped_tab_bytes: Bytes of zip file containing ISA tabs to sent to converter service
:return: Absolute path for local JSON file returned by converter service called out.json
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient(dl_folder='tmp/')
client.convert_tab_to_json(open('testdata/BII-S-3.zip', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/convert/tab-to-json',
headers={'Content-type': 'application/zip'}, data=zipped_tab_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
data = response.json()
outpath = os.path.join(self.dl_folder, 'out.json')
with open(outpath, 'w') as f:
json.dump(data, f)
return os.path.abspath(f.name)
def convert_json_to_tab(self, isa_json_bytes):
"""
:param isa_json_bytes: Bytes of zip file containing ISA tabs to sent to converter service
:return: Absolute path for local ZIP file named out.zip returned by converter service
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient(dl_folder='tmp/')
client.convert_json_to_tab(open('testdata/BII-S-3.json', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/convert/json-to-tab',
headers={'Content-type': 'application/json'}, data=isa_json_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
data = response.content
outpath = os.path.join(self.dl_folder, 'out.zip')
with open(outpath, 'wb') as f:
f.write(data)
return os.path.abspath(f.name)
def convert_json_to_sra(self, isa_json_zip_bytes):
"""
:param isa_json_zip_bytes: Bytes of zip file containing ISA JSON and data files to sent to converter service
:return: Absolute path for local ZIP file named out.zip returned by converter service
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient(dl_folder='tmp/')
client.convert_json_to_tab(open('testdata/BII-S-3_json.zip', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/convert/json-to-sra',
headers={'Content-type': 'application/zip'}, data=isa_json_zip_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
data = response.content
outpath = os.path.join(self.dl_folder, 'out.zip')
with open(outpath, 'wb') as f:
f.write(data)
return os.path.abspath(f.name)
def convert_tab_to_sra(self, zipped_tab_bytes):
"""
:param isa_json_zip_bytes: Bytes of zip file containing ISA JSON and data files to sent to converter service
:return: Absolute path for local ZIP file named out.zip returned by converter service
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient(dl_folder='tmp/')
client.convert_json_to_tab(open('testdata/BII-S-3_json.zip', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/convert/tab-to-sra',
headers={'Content-type': 'application/zip'}, data=zipped_tab_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
data = response.content
outpath = os.path.join(self.dl_folder, 'out.zip')
with open(outpath, 'wb') as f:
f.write(data)
return os.path.abspath(f.name)
def convert_tab_to_cedar(self, zipped_tab_bytes):
"""
:param zipped_tab_bytes: Bytes of zip file containing ISA tabs to sent to converter service
:return: Absolute path for local CEDAR JSON file returned by converter service called out.json
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient(dl_folder='tmp/')
client.convert_tab_to_json(open('testdata/BII-S-3.zip', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/convert/tab-to-cedar',
headers={'Content-type': 'application/zip'}, data=zipped_tab_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
data = response.json()
outpath = os.path.join(self.dl_folder, 'out.json')
with open(outpath, 'w') as f:
json.dump(data, f)
return os.path.abspath(f.name)
def validate_json(self, isa_json_bytes):
"""
:param isa_json_bytes: Bytes of ISA JSON to sent to converter service
:return: JSON validation report: Validation report as JSON
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient()
client.validate_json(open('testdata/BII-S-3.json', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/validate/json',
headers={'Content-type': 'application/json'}, data=isa_json_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
print(response.content)
def validate_isatab(self, isatab_zip_bytes):
"""
:param isatab_zip_bytes: Bytes of zip file containing ISA tabs to sent to converter service
:return: JSON validation report: Validation report as JSON
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient()
client.validate_tab(open('testdata/BII-S-3.zip', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/validate/isatab',
headers={'Content-type': 'application/zip'}, data=isatab_zip_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
print(response.content)
def convert_sampletab_to_tab(self, sampletab_bytes):
"""
:param sampletab_bytes: Bytes of SampleTab input file to sent to converter service
:return: Absolute path for local ZIP file named out.zip returned by converter service
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient(dl_folder='tmp/')
client.convert_sampletab_to_tab(open('testdata/GSB-3.txt', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/convert/sampletab-to-isatab',
headers={'Content-type': 'text/tab-separated-values'}, data=sampletab_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
data = response.content
outpath = os.path.join(self.dl_folder, 'out.zip')
with open(outpath, 'wb') as f:
f.write(data)
return os.path.abspath(f.name)
def convert_sampletab_to_json(self, sampletab_bytes):
"""
:param sampletab_bytes: Bytes of SampleTab input file to sent to converter service
:return: Absolute path for local JSON file returned by converter service called out.json
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient(dl_folder='tmp/')
client.convert_sampletab_to_json(open('testdata/GSB-3.txt', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/convert/sampletab-to-json',
headers={'Content-type': 'text/tab-separated-values'}, data=sampletab_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
data = response.json()
outpath = os.path.join(self.dl_folder, 'out.json')
with open(outpath, 'w') as f:
json.dump(data, f)
return os.path.abspath(f.name)
def import_mw_to_tab(self, accession):
"""
:param accession: Accession ID for study in MetabolomicsWorkbench
:return: Absolute path for local ZIP file named out.zip returned by converter service
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient(dl_folder='tmp/')
client.import_mw_to_tab('ST000367')
"""
response = requests.get(self.baseurl + '/api/v1/import/mw/' + accession)
print("HTTP response code: " + str(response.status_code))
if response.ok:
data = response.content
outpath = os.path.join(self.dl_folder, 'out.zip')
with open(outpath, 'wb') as f:
f.write(data)
return os.path.abspath(f.name)
def convert_tab_to_sampletab(self, zipped_tab_bytes):
"""
:param isa_json_zip_bytes: Bytes of zip file containing ISA JSON and data files to sent to converter service
:return: Absolute path for SampleTab file named out.txt returned by converter service
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient(dl_folder='tmp/')
client.convert_tab_to_sampletab(open('testdata/BII-S-3_json.zip', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/convert/isatab-to-sampletab',
headers={'Content-type': 'application/zip'}, data=zipped_tab_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
data = response.content
outpath = os.path.join(self.dl_folder, 'out.txt')
with open(outpath, 'wb') as f:
f.write(data)
return os.path.abspath(f.name)
def convert_json_to_sampletab(self, isa_json_bytes):
"""
:param isa_json_bytes: Bytes of zip file containing ISA tabs to sent to converter service
:return: Absolute path for local ZIP file named out.zip returned by converter service
Example usage
from isarest_client import IsaRestClient
client = IsaRestClient(dl_folder='tmp/')
client.convert_json_to_sampletab(open('testdata/BII-S-3.zip', 'rb').read())
"""
response = requests.post(self.baseurl + '/api/v1/convert/json-to-sampletab',
headers={'Content-type': 'application/json'}, data=isa_json_bytes, verify=False)
print("HTTP response code: " + str(response.status_code))
if response.ok:
data = response.content
outpath = os.path.join(self.dl_folder, 'out.txt')
with open(outpath, 'wb') as f:
f.write(data)
return os.path.abspath(f.name)