def test_efetch_no_history(small_esearch_results): ids = small_esearch_results.ids for result in entrez.efetch(DB, ids, api_key=API_KEY): for experiment in parsers_sra_xml.parse_sra_efetch_result(result): assert (experiment.accn.startswith("SRX") | experiment.accn.startswith("DRX") | experiment.accn.startswith("ERX"))
def test_efetch_pubmed(small_esearch_results): webenv = small_esearch_results.webenv query_key = small_esearch_results.query_key link = entrez.elink("pubmed", "sra", webenv=webenv, query_key=query_key, api_key=API_KEY, retmax=RETMAX) for result in entrez.efetch("pubmed", webenv=link.webenv, query_key=link.query_key, api_key=API_KEY, retmax=RETMAX): for document in parsers_pubmed_xml.parse_pubmed_efetch_result(result): assert isinstance(document.accn, str)
def test_efetch_biosample(small_esearch_results): webenv = small_esearch_results.webenv query_key = small_esearch_results.query_key link = entrez.elink("biosample", "sra", webenv=webenv, query_key=query_key, api_key=API_KEY, retmax=RETMAX) for result in entrez.efetch("biosample", webenv=link.webenv, query_key=link.query_key, api_key=API_KEY, retmax=RETMAX): for document in parsers_biosample_xml.parse_biosample_efetch_result( result): assert document.accn.startswith("SAMN")
def pubmed_efetch(webenv, query_key, count, defaults): for result in entrez.efetch( "pubmed", webenv=webenv, query_key=query_key, count=count, **defaults ): yield from parsers_pubmed_xml.parse_pubmed_efetch_result(result)
def biosample_efetch(webenv, query_key, count, defaults): for result in entrez.efetch( "biosample", webenv=webenv, query_key=query_key, count=count, **defaults ): yield from parsers_biosample_xml.parse_biosample_efetch_result(result)
def sra_efetch(webenv, query_key, count, defaults): for docs in entrez.efetch("sra", webenv=webenv, query_key=query_key, count=count, **defaults): yield from parsers_sra_xml.parse_sra_efetch_result(docs)