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Update API call for GEO ids - still broken
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bin/sra_ids_to_runinfo.py

Lines changed: 7 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -261,9 +261,14 @@ def _id_to_srx(cls, identifier):
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def _gse_to_srx(cls, identifier):
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"""Resolve the identifier to SRA experiments."""
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ids = []
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params = {"acc": identifier, "targ": "gsm", "view": "data", "form": "text"}
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params = {
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"id": identifier,
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"db": "gds",
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"rettype": "runinfo",
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"retmode": "text"
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}
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response = fetch_url(
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f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?{urlencode(params)}"
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f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?{urlencode(params)}"
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)
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cls._content_check(response, identifier)
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gsm_ids = [

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