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 update_jax(server: str):
# server:str = 'localhost'
# server: str = '165.227.89.140'
editor = 'updater'
editor_id = get_editor_id(editor, server)
print(editor_id)
jax_dict = get_jax_descriptions(server)
authors_dict = get_authors(server)
reference_dict = get_literature_references(server)
journals_dict = get_journals(server)
omnigene_dict = get_omnigenes(server)
json_files = get_list_of_files(JAX_PATH + 'genes')
print('total=', len(json_files))
change_count = 0
new_count = 0
for json_file in json_files:
jax: dict = read_one_gene_jax_json(json_file)
if jax is not None:
gene = jax['gene']
description = jax['description']
if gene in jax_dict:
item = jax_dict[gene]
statement = item['statement']
if description != statement:
change_count += 1
print(change_count, 'description changed for', gene)
print('new:' + description)
print('old:' + statement)
# pmid_extractor:callable,reference_dict:dict,journal_dict:dict,author_dict:dict
s = create_jax_description(item['id'], item['field'],
description, editor_id,
PMID_extractor, reference_dict,
journals_dict, authors_dict)
print(s)
send_mutation(s, server)
print()
else:
new_count += 1
print(new_count, '***new entry', gene)
s = write_one_jax_gene(jax, editor_id, PMID_extractor,
reference_dict, journals_dict,
authors_dict, omnigene_dict)
print(s)
send_mutation(s, server)
print()
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()
def write_to_prod():
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)