def get_response_dict(id_type, ids, pmc_query): response_dict = {} num_ids = len(ids) id_counter = 0 geo_instance = geo.GEO() for accession in ids: print accession, id_counter += 1 reuse_pmcids = get_accession_in_pmc_fulltext(id_type, accession, pmc_query) if ((not reuse_pmcids) or ("<ERROR>" in "".join(reuse_pmcids))): print " Nope" continue stripped_accession = geo.get_stripped_accession(accession) if id_type == "GSE": gse_accessions = [stripped_accession] gds_accessions = [ geo.get_stripped_accession(acc) for acc in geo.get_gds_from_gse("GSE" + stripped_accession) ] else: gds_accessions = [stripped_accession] gse_accessions = [ geo.get_stripped_accession(acc) for acc in geo.get_gse_from_gds("GDS" + stripped_accession) ] try: submit_pmids = geo_instance.pmids("GSE" + gse_accessions[0]) except Exception: continue print id_counter, "of", num_ids, ":", stripped_accession, "--", ( submit_pmids), "; ", len(reuse_pmcids) for reuse_pmcid in reuse_pmcids: reuse_pmids_for_pmcid = pubmedcentral.pmcids_to_pmids(reuse_pmcid) dict_key = (id_type + stripped_accession, reuse_pmcid) this_submit_contributors = flatten_unique([ geo_instance.contributors("GSE" + gse_accession) for gse_accession in gse_accessions ]) this_submit_authors = get_authors_and_submittors_from_accession( submit_pmids, this_submit_contributors) this_reuse_authors = get_authors_and_submittors_from_accession( reuse_pmids_for_pmcid) intersect = get_author_intersect_submit_reuse( this_submit_authors, this_reuse_authors) submit_affiliation = affiliation.institution(submit_pmids) release_date = geo_instance.release_date("GSE" + gse_accession) response_dict[dict_key] = (id_type + stripped_accession, gse_accessions, gds_accessions, submit_pmids, reuse_pmcid, reuse_pmids_for_pmcid, this_submit_authors, this_reuse_authors, intersect, submit_affiliation, release_date) #print response_dict[dict_key] return (response_dict)
def get_response_dict(id_type, ids, pmc_query): response_dict = {} num_ids = len(ids) id_counter = 0 geo_instance = geo.GEO() for accession in ids: print accession, id_counter += 1 reuse_pmcids = get_accession_in_pmc_fulltext(id_type, accession, pmc_query) if ((not reuse_pmcids) or ("<ERROR>" in "".join(reuse_pmcids))): print " Nope" continue stripped_accession = geo.get_stripped_accession(accession) if id_type=="GSE": gse_accessions = [stripped_accession] gds_accessions = [geo.get_stripped_accession(acc) for acc in geo.get_gds_from_gse("GSE"+stripped_accession)] else: gds_accessions = [stripped_accession] gse_accessions = [geo.get_stripped_accession(acc) for acc in geo.get_gse_from_gds("GDS"+stripped_accession)] try: submit_pmids = geo_instance.pmids("GSE"+gse_accessions[0]) except Exception: continue print id_counter, "of", num_ids, ":", stripped_accession, "--", (submit_pmids), "; ", len(reuse_pmcids) for reuse_pmcid in reuse_pmcids: reuse_pmids_for_pmcid = pubmedcentral.pmcids_to_pmids(reuse_pmcid) dict_key = (id_type+stripped_accession, reuse_pmcid) this_submit_contributors = flatten_unique([geo_instance.contributors("GSE"+gse_accession) for gse_accession in gse_accessions]) this_submit_authors = get_authors_and_submittors_from_accession(submit_pmids, this_submit_contributors) this_reuse_authors = get_authors_and_submittors_from_accession(reuse_pmids_for_pmcid) intersect = get_author_intersect_submit_reuse(this_submit_authors, this_reuse_authors) submit_affiliation = affiliation.institution(submit_pmids) release_date = geo_instance.release_date("GSE"+gse_accession) response_dict[dict_key] = (id_type+stripped_accession, gse_accessions, gds_accessions, submit_pmids, reuse_pmcid, reuse_pmids_for_pmcid, this_submit_authors, this_reuse_authors, intersect, submit_affiliation, release_date) #print response_dict[dict_key] return(response_dict)
def get_pmc_results(query): pmcids = pubmedcentral.search(query) pmids = pubmedcentral.pmcids_to_pmids(pmcids) return(pmids)
def get_pmc_results(query): pmcids = pubmedcentral.search(query) pmids = pubmedcentral.pmcids_to_pmids(pmcids) return (pmids)