def build_initial_gene_model(server:str):
# server:str = 'localhost'
# server: str = '165.227.89.140'
# schema__graphql = 'schema.graphql'
users_dict = {'*****@*****.**':'manuel',
'*****@*****.**':'carrie',
'*****@*****.**':'paul',
'*****@*****.**':'mary',
'loader':'loader',
'updater':'updater'
}
# erase_neo4j(schema__graphql,server)
write_users(users_dict,server)
auto_user_id: str = get_editor_id('loader',server)
print(auto_user_id)
authors_dict = get_authors(server)
reference_dict = get_literature_references(server)
journals_dict = get_journals(server)
hgnc_gene_name_dict = create_hgnc_gene_name_dict()
write_jax_genes(server,reference_dict,journals_dict,authors_dict,auto_user_id,PMID_extractor)
gene_dict = get_jax_gene_ids(server)
omini_genes:list = read_omni_genes('data/tblOS_GLOBAL_GLOBAL_Ref_AllPanelsGenes.csv')
write_omni_genes(omini_genes,server,auto_user_id,gene_dict,PMID_extractor,PubMed_extractor,reference_dict,journals_dict,authors_dict,hgnc_gene_name_dict)
def write_omni_genes(omini_genes:list, server:str,editor_id:str,jax_gene_dict,pmid_extractor:callable,sp_pmid_extractor:callable, reference_dict:dict,journal_dict:dict,author_dict:dict,hgnc_gene_name_dict)->None:
hgnc_gene_name_dict = create_hgnc_gene_name_dict()
for omni_gene in omini_genes:
gene_name: str = omni_gene['symbol']
omni_gene['panel_name'] = gene_name
if gene_name in hgnc_gene_name_dict:
omni_gene['panel_name'] = gene_name
omni_gene['synonym'] = gene_name
gene_name = hgnc_gene_name_dict[gene_name]
omni_gene['symbol'] = gene_name
entrez_gene_id = fetch_gene_id_by_gene_name(gene_name)
omni_gene['entrez_gene_id'] = entrez_gene_id
if entrez_gene_id is None:
print("no entrz gene id for",gene_name)
else:
gene_info = fetch_gene_info_by_gene_id(entrez_gene_id)
if 'genomic_pos_hg19' in gene_info:
populate_omni_gene(gene_info, omni_gene)
print(gene_name)
s = create_myGeneInfo_gene(omni_gene, editor_id, pmid_extractor, reference_dict, journal_dict,
author_dict)
s += create_uniprot_entry(omni_gene, editor_id, sp_pmid_extractor, reference_dict, journal_dict,
author_dict)
m, omnigene_id, cat_id, syn_id = create_omniGene(omni_gene, jax_gene_dict, omni_gene['summary'], editor_id, pmid_extractor,
reference_dict, journal_dict, author_dict)
s += m
send_mutation(s,server)
else:
print('no gene_info for',gene_name)
def main():
server: str = 'localhost'
# server: str = '165.227.89.140'
editor: str = '*****@*****.**'
editor_id: str = get_editor_id(editor, server)
print(editor_id)
edits = read_edits('data/GeneDescriptions2.tsv')
authors_dict: dict = get_authors(server)
reference_dict: dict = get_literature_references(server)
journals_dict: dict = get_journals(server)
jax_gene_dict: dict = get_jax_gene_ids(server)
omnigene_dict = get_omnigene_descriptions(server)
hgnc_gene_name_dict = create_hgnc_gene_name_dict()
for edit in edits:
gene_name: str = edit['gene']
if gene_name in hgnc_gene_name_dict:
gene_name = hgnc_gene_name_dict[gene_name]
print(gene_name)
# gene_id, old_description_id,field = get_id_old_id_and_field(edit['gene'], server)
if gene_name not in omnigene_dict:
gene_description: str = edit['description']
s = create_omni_gene(edit['gene'], gene_description, editor_id,
jax_gene_dict, PMID_extractor,
PubMed_extractor, reference_dict,
journals_dict, authors_dict,
hgnc_gene_name_dict)
print(s)
send_mutation(s, server)
else:
item = omnigene_dict[gene_name]
s = write_new_gene_description(item['id'], item['statement'],
item['field'], edit['description'],
editor_id, PMID_extractor,
reference_dict, journals_dict,
authors_dict)
print(s)
send_mutation(s, server)
print()
return '165.227.89.140'
def write_to_dev():
return '161.35.115.213'
# server: str = 'localhost'
# server: str = '161.35.115.213'
server: str = write_to_dev()
editor_ids: dict = get_editor_ids(server)
authors_dict: dict = graphql_utils_extra.get_authors(server)
reference_dict: dict = graphql_utils_extra.get_literature_references(server)
journals_dict: dict = graphql_utils_extra.get_journals(server)
jax_gene_dict:dict = get_jax_gene_ids(server)
auto_user_id: str = get_editor_id('loader', server)
hgnc_gene_name_dict = create_hgnc_gene_name_dict()
@app.route('/new_gene/<string:gene_name>', methods=['GET'])
def new_gene(gene_name):
id = graphql_utils_extra.get_omnigene_ID_by_name(gene_name, server)
if id==None:
curation_item = {'gene': gene_name, 'description': None, 'oncogenic_category': None, 'synonmyms': None}
s = graphql_utils_extra.create_omni_gene(gene_name, curation_item, editor_ids, jax_gene_dict,
PMID_extractor,
PubMed_extractor, reference_dict, journals_dict,
authors_dict,
hgnc_gene_name_dict)
# print(s)
if s != '':
m = send_mutation(s, server)
if gene_name in hgnc_gene_name_dict:
def update(server: str):
editor_ids: dict = get_editor_ids(server)
curation_data = read_curation_data()
authors_dict: dict = get_authors(server)
reference_dict: dict = get_literature_references(server)
journals_dict: dict = get_journals(server)
jax_gene_dict: dict = get_jax_gene_ids(server)
omnigene_dict = get_omnigene_descriptions(server)
hgnc_gene_name_dict = create_hgnc_gene_name_dict()
for curation_item in curation_data:
gene_name: str = curation_item['gene']
if gene_name in hgnc_gene_name_dict:
gene_name = hgnc_gene_name_dict[gene_name]
print(gene_name)
if gene_name not in omnigene_dict:
print(gene_name + ' not in omnigene_dict')
s = create_omni_gene(gene_name, curation_item, editor_ids,
jax_gene_dict, PMID_extractor,
PubMed_extractor, reference_dict,
journals_dict, authors_dict,
hgnc_gene_name_dict)
print(s)
send_mutation(s, server)
else:
omnigene_id = omnigene_dict[gene_name]['id']
if curation_item['description'] is not None:
old_description_id = omnigene_dict[gene_name]['description'][
'id']
field = omnigene_dict[gene_name]['description']['field']
gene_description = curation_item['description']['statement']
editor_id = editor_ids[curation_item['description']['editor']]
edit_date = curation_item['description']['edit_date']
# def write_new_gene_description(gene_id, old_description_id:str, field:str, statement:str, editor_id,edit_date:str,pmid_extractor:callable,reference_dict:dict,journal_dict:dict,author_dict:dict )->str:
s = write_new_gene_description(omnigene_id, old_description_id,
field, gene_description,
editor_id, edit_date,
PMID_extractor, reference_dict,
journals_dict, authors_dict)
print(s)
send_mutation(s, server)
if curation_item['oncogenic_category'] is not None:
old_category_id = omnigene_dict[gene_name][
'oncogenic_category']['id']
field = omnigene_dict[gene_name]['oncogenic_category']['field']
oncogenic_category = curation_item['oncogenic_category'][
'statement']
editor_id = editor_ids[curation_item['oncogenic_category']
['editor']]
edit_date = curation_item['oncogenic_category']['edit_date']
s = write_new_oncogenic_category(omnigene_id, old_category_id,
field, oncogenic_category,
editor_id, edit_date,
PMID_extractor,
reference_dict, journals_dict,
authors_dict)
print(s)
send_mutation(s, server)
if curation_item['synonmyms'] is not None:
old_synonmyms_id = omnigene_dict[gene_name]['synonyms']['id']
field = omnigene_dict[gene_name]['synonyms']['field']
synonmyms = curation_item['synonmyms']['statement']
editor_id = editor_ids[curation_item['synonmyms']['editor']]
edit_date = curation_item['synonmyms']['edit_date']
s = write_new_synonym_string(omnigene_id, old_synonmyms_id,
field, synonmyms, editor_id,
edit_date, PMID_extractor,
reference_dict, journals_dict,
authors_dict)
print(s)
send_mutation(s, server)
# gene_id, old_description_id,field = get_id_old_id_and_field(edit['gene'], server)
# if gene_name not in omnigene_dict:
# gene_description:str = edit['description']
# s = create_omni_gene(edit['gene'],gene_description,editor_id,jax_gene_dict,PMID_extractor,PubMed_extractor,reference_dict,journals_dict,authors_dict,hgnc_gene_name_dict)
# print(s)
# send_mutation(s,server)
# else:
# item = omnigene_dict[gene_name]
# s = write_new_gene_description(item['id'],item['statement'],item['field'],edit['description'], editor_id,PMID_extractor,reference_dict,journals_dict,authors_dict)
# print(s)
# send_mutation(s,server)
print()