A translator for GEO, Gene Expression Omnibus #3299
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AbeJellinek
requested changes
Apr 22, 2024
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| return "dataset"; | ||
| // if (url.includes("acc.cgi?acc")) { | ||
| // return "dataset"; | ||
| // } | ||
| // return false; |
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We need to actually check if the page matches here (and ideally support search pages, if this site has them)
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| newItem.title = text(doc, '#ui-ncbiexternallink-1 > table > tbody > tr > td > table:nth-child(6) > tbody > tr:nth-child(3) > td:nth-child(2) > table > tbody > tr > td > table > tbody > tr > td > table:nth-child(6) > tbody > tr > td > table:nth-child(1) > tbody > tr:nth-child(3) > td:nth-child(2)'); | ||
| newItem.abstractNote = text(doc, '#ui-ncbiexternallink-1 > table > tbody > tr > td > table:nth-child(6) > tbody > tr:nth-child(3) > td:nth-child(2) > table > tbody > tr > td > table > tbody > tr > td > table:nth-child(6) > tbody > tr > td > table:nth-child(1) > tbody > tr:nth-child(6) > td:nth-child(2)'); | ||
| newItem.url = url; | ||
| // url is of format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE251923 | ||
| // subset the last part of the url to get the accession number | ||
| const acc = url.split("acc=")[1]; | ||
| newItem.identifier = acc; | ||
| // status is of format: Public on Dec 27, 2023 | ||
| // subset it to get the date | ||
| const status_str = text(doc, '#ui-ncbiexternallink-1 > table > tbody > tr > td > table:nth-child(6) > tbody > tr:nth-child(3) > td:nth-child(2) > table > tbody > tr > td > table > tbody > tr > td > table:nth-child(6) > tbody > tr > td > table:nth-child(1) > tbody > tr:nth-child(2) > td:nth-child(2)'); | ||
| newItem.date = status_str.split("on")[1].trim(); | ||
| // authors is of format: Chen J, Song Y, Huang J, Wan X, Li Y | ||
| // push into newItem.creators | ||
| const author_str = text(doc, '#ui-ncbiexternallink-1 > table > tbody > tr > td > table:nth-child(6) > tbody > tr:nth-child(3) > td:nth-child(2) > table > tbody > tr > td > table > tbody > tr > td > table:nth-child(6) > tbody > tr > td > table:nth-child(1) > tbody > tr:nth-child(10) > td:nth-child(2)'); |
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These aren't reasonable - I'm guessing output from Chrome/Firefox devtools? We need selectors that will remain stable between pages. It's possible that we'll have to walk through cells in the table and look at the labels ("Status", "Title") to figure out which field is which.
| newItem.url = url; | ||
| // url is of format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE251923 | ||
| // subset the last part of the url to get the accession number | ||
| const acc = url.split("acc=")[1]; |
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Breaks if there's more in the query string/an anchor on the URL.
Suggested change
| const acc = url.split("acc=")[1]; | |
| const acc = new URL(url).searchParams.get("acc"); |
| // status is of format: Public on Dec 27, 2023 | ||
| // subset it to get the date | ||
| const status_str = text(doc, '#ui-ncbiexternallink-1 > table > tbody > tr > td > table:nth-child(6) > tbody > tr:nth-child(3) > td:nth-child(2) > table > tbody > tr > td > table > tbody > tr > td > table:nth-child(6) > tbody > tr > td > table:nth-child(1) > tbody > tr:nth-child(2) > td:nth-child(2)'); | ||
| newItem.date = status_str.split("on")[1].trim(); |
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I think ZU.strToISO(status_str) will extract the date fine, no need to split.
(Also rename to use camelCase, not snake_case.)
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| { | |||
| "translatorID": "5a325508-cb60-42c3-8b0f-d4e3c6441059", | |||
| "label": "GEO", | |||
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Let's call this NCBI GEO for clarity.
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Thanks for your detailed review. I will refine the code when I have time
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