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)