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']