#!/usr/bin/env python import os import sys import json import logging from cutlass import iHMPSession import settings from cutlass_utils import \ load_data, get_parent_node_id, list_tags, format_query, \ write_csv_headers, values_to_node_dict, write_out_csv, \ get_field_header, dump_args, log_it log = log_it('osdf_submit') log.info('Starting metadata submission to OSDF server.') # load username, password from files dcc_user = settings.auth.dcc_user dcc_pass = settings.auth.dcc_pass session = iHMPSession(dcc_user, dcc_pass) log.info('Loaded session: {}'.format(session.get_session())) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Main Actions ~~~~~ def main(): """make it happen!""" """ Project node """ # Predefined_id_from_osdf_for_overall_iHMP_project
#!/usr/bin/env python """ load Visit into OSDF using info from data file """ import os import re from cutlass.Visit import Visit import settings from cutlass_utils import \ load_data, get_parent_node_id, list_tags, format_query, \ write_csv_headers, values_to_node_dict, write_out_csv, \ load_node, get_field_header, dump_args, log_it filename=os.path.basename(__file__) log = log_it(filename) # the Higher-Ups node_type = 'visit' parent_type = 'subject' grand_parent_type = 'study' great_parent_type = 'project' node_tracking_file = settings.node_id_tracking.path class node_values: visit_id = '' visit_number = '' interval = '' clinic_id = '' tags = ['rand_subject_id: ','sub_study: ','study: ']
#!/usr/bin/env python import sys from cutlass import iHMPSession from settings import auth from settings import NodeRetrievalFiles from cutlass_utils import log_it, format_query from cutlass_search import retrieve_nodes, retrieve_query_all log = log_it('retrieve_osdf_nodes') log.info('Starting metadata download from OSDF server.') # load username, password from files session = iHMPSession(auth.dcc_user, auth.dcc_pass, ssl=False) log.info('Loaded session: {}'.format(session.get_session())) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Main Actions ~~~~~ def retrieve_node_type(session, node_type): data_file_name = NodeRetrievalFiles[node_type] qry = '&&'.join([format_query("prediabetes", field="tags"), format_query(node_type, field="node_type")]) log.debug("query: %s", qry) retrieve_query_all(session, qry, data_file_name) def main(): """make it happen!""" """ Subject node """
import os import re import json import yaml import logging import settings from cutlass_utils import \ load_data, get_parent_node_id, list_tags, format_query, \ write_csv_headers, values_to_node_dict, write_out_csv, \ load_node, get_field_header, dump_args, log_it log = log_it(__name__)
#!/usr/bin/env python import sys from cutlass import iHMPSession from settings import auth from settings import NodeUpdateFiles from cutlass_utils import log_it from cutlass_search import update_nodes, delete_nodes log = log_it('jax_osdf_update') log.info('Starting metadata submission to OSDF server.') # load username, password from files dcc_user = auth.dcc_user dcc_pass = auth.dcc_pass session = iHMPSession(dcc_user, dcc_pass, ssl=False) log.info('Loaded session: {}'.format(session.get_session())) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Main Actions ~~~~~ def main(): """make it happen!""" # study_name = 'prediabetes' # study_node_id = '194149ed5273e3f94fc60a9ba58f7c24' """ Subject node """ # update_nodes(session, NodeUpdateFiles['Subject'], 'subject') """ Visit node """
from cutlass.Study import Study from cutlass_utils import log_it import settings # filename=os.path.basename(__file__) # log = log_it(filename) # Log It! import os, logging # needed for LogIt function! def log_it(filename=os.path.basename(__file__)): """log_it setup""" logging.basicConfig(level=logging.DEBUG, format="%(asctime)s %(levelname)s %(funcName)s: %(message)s") return logging.getLogger(filename) log = log_it() node_type='study' parent_type = 'project' node_tracking_file = settings.node_id_tracking.path class node_values: name = 'prediabetes' description = 'Type 2 diabetes mellitus (T2D) is a significant health problem facing our nation. Close to 20 million individuals in the United States have T2D, and 79 million aged 20 years or older are clinically pre-diabetic, with a 5-year conversion rate of 10% to 23% from prediabetes to T2D. In a collaborative effort to systematically understand diabetes and its etiology, the team is comprised of leading experts in research on both the human host as well as the microbiome, as properties of both are likely relevant in ' #T2D development. For a better elucidation of mechanisms of onset and progression of T2D disease, the group is performing a detailed analysis of the biological processes that occur in the microbiome and human host by longitudinal profiling of patients at risk for T2D. Both microbiome and host profiles are being analyzed by state-of-the-art omics platforms, and these large-scale and diverse data sets will be integrated to determine the dynamic pathways that change during the onset and progression of T2D, especially during viral infections and other stresses. This longitudinal study is expected to reveal changes in the microbiome and host at an unprecedented level of detail, and identify molecules and pathways that play important roles in diabetes onset and progression.' center = 'Stanford University / Jackson Laboratory' contact = 'Wenyu Zhou <*****@*****.**>' subtype = 'prediabetes' tags = [ 'prediabetes', 'overeaters', ] # print("Required fields: {}".format(OSDFNode.required_fields()))
#!/usr/bin/env python import os import sys import json import logging from cutlass import iHMPSession import settings from cutlass_utils import \ load_data, get_parent_node_id, list_tags, format_query, \ write_csv_headers, values_to_node_dict, \ get_field_header, dump_args, log_it log = log_it('jax_osdf_submit') log.info('Starting metadata submission to OSDF server.') # load username, password from files dcc_user = settings.auth.dcc_user dcc_pass = settings.auth.dcc_pass session = iHMPSession(dcc_user, dcc_pass, ssl=False) log.info('Loaded session: {}'.format(session.get_session())) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Main Actions ~~~~~ def main(): """make it happen!""" """ Project node """ # Predefined_id_from_osdf_for_overall_iHMP_project