def get_omnigene_ID_by_name(name: str, server: str) -> str:
id: str = None
query = f''' {{ OmniGene(name: \"{name}\") {{ id, name }} }}'''
response = send_query(query, server)
if len(response['data']['OmniGene']) > 0:
for item in response['data']['OmniGene']:
id: str = item['id']
break
return id
def get_literature_references(server: str) -> dict:
reference_dict: dict = {}
query = f'{{ LiteratureReference {{ id,PMID }} }}'
response = send_query(query, server)
if len(response['data']['LiteratureReference']) > 0:
for item in response['data']['LiteratureReference']:
id = item['id']
pmid = item['PMID']
reference_dict[pmid] = id
return reference_dict
def get_journals(server: str) -> dict:
journal_dict: dict = {}
query = f'{{ Journal {{ id,name }} }}'
response = send_query(query, server)
if len(response['data']['Journal']) > 0:
for item in response['data']['Journal']:
id = item['id']
name = item['name']
journal_dict[name] = id
return journal_dict
def get_history(server: str) -> list:
query = f'''{{EditableStatement{{
field
statement
edit_date
editor{{
name
}}
}}
}}'''
response = send_query(query, server)
return response['data']['EditableStatement']
def get_authors(server: str) -> dict:
author_dict: dict = {}
query = f'{{ Author {{ id,surname,firstInitial }} }}'
response = send_query(query, server)
if len(response['data']['Author']) > 0:
for item in response['data']['Author']:
id = item['id']
surname = item['surname']
first_initial = item['firstInitial']
key = fix_author_id(surname + '_' + first_initial)
author_dict[key] = id
return author_dict
def get_current_data(server: str) -> list:
query = '''
{
OmniGene(orderBy: name_asc) {
name
geneDescription {
...es_fields
}
oncogenicCategory {
...es_fields
}
synonymsString {
...es_fields
}
}
}
fragment es_fields on EditableStatement {
field
statement
editor {
name
}
edit_date
references {
... on LiteratureReference {
PMID
DOI
title
journal {
name
}
volume
first_page
last_page
publication_Year
abstract
authors {
surname
first_initial
}
}
}
}
'''
response = send_query(query, server)
return response['data']['OmniGene']
def get_current_data_fields(server: str) -> list:
query = '''
{
OmniGene(orderBy: name_asc) {
name
geneDescription {
field
}
oncogenicCategory {
field
}
synonymsString {
field
}
}
}
'''
response = send_query(query, server)
return response['data']['OmniGene']
def get_current_user_data(server: str) -> list:
query = '{ User {id, name, password, isAdmin } }'
response = send_query(query, server)
return response['data']['User']
def get_current_author_data(server: str) -> list:
query = '{Author { id, surname, first_initial } }'
response = send_query(query, server)
return response['data']['Author']
def get_current_omnigene_data(server: str) -> list:
query = '{ OmniGene {id, name, panelName, geneDescription {id}, oncogenicCategory {id }, synonymsString {id }, myGeneInfoGene {id}, jaxGene {id}, uniprot_entry { id }} }'
response = send_query(query, server)
return response['data']['OmniGene']
def get_current_uniprot_entry_data(server: str) -> list:
query = '{ Uniprot_Entry {id, name, accessionNumber, uniprot_id, function { id }, gene { id} }}'
response = send_query(query, server)
return response['data']['Uniprot_Entry']
def get_current_myGene_info_gene_data(server: str) -> list:
query = '{ MyGeneInfo_Gene {id, name, chromosome, strand, start, end, entrezId, description { id }}}'
response = send_query(query, server)
return response['data']['MyGeneInfo_Gene']
def get_current_jax_gene_data(server: str) -> list:
query = '{ JaxGene { id, name, canonicalTranscript, chromosome, entrezId, jaxId, synonyms, description { id } } }'
response = send_query(query, server)
return response['data']['JaxGene']
def get_current_editable_statement_data(server: str) -> list:
query = '{ EditableStatement { id, field, statement, edit_date, deleted, editor { id }, references { id, __typename } } }'
response = send_query(query, server)
return response['data']['EditableStatement']
def get_current_internet_reference_data(server: str) -> list:
query = '{ InternetReference { id, accessed_date,web_address,shortReference} }'
response = send_query(query, server)
return response['data']['InternetReference']
def get_current_literature_reference_data(server: str) -> list:
query = '{ LiteratureReference { id, PMID,DOI,title,journal{id},volume,first_page,last_page,publication_Year,shortReference,abstract,authors {id}} }'
response = send_query(query, server)
return response['data']['LiteratureReference']
def get_current_journal_data(server: str) -> list:
query = '{ Journal { id,name } }'
response = send_query(query, server)
return response['data']['Journal']
