User talk:Diberri/Template filler

Bug reports

Ideally, please report bugs using this link. If you're not comfortable with that, please report the bug below. The more details, the better.

Missing titles

Resolved

In cases where there is no title retrieved for a URL (like this), could the title field be populated with the domain name instead of being left blank? --Arcadian (talk) 15:19, 5 November 2008 (UTC)

Great idea. Should be fixed now. See [1]. --David Iberri (talk) 02:40, 10 November 2008 (UTC)

Thanks! --Arcadian (talk) 03:32, 10 November 2008 (UTC)

Vertical pipes in page titles

Resolved

BBC articles like http://news.bbc.co.uk/2/hi/business/7732733.stm contain vertical bars in the data that will end up in the title field, terminating it early. So something like $title =~ s/|/|/g; to quote. RDBrown (talk) 13:49, 17 November 2008 (UTC)

Thanks for the report. I've added it to the ticket tracker as ticket #41005. I've uploaded a patched version. See [2] for an example. --David Iberri (talk) 01:29, 18 November 2008 (UTC)

PMCID/PMID

A PMC doesn't imply that a PMID exists (ie PMC 1247673), also older PMC PDF image articles - a more specific error in that case would help. RDBrown (talk) 13:49, 17 November 2008 (UTC)

I'm not sure I follow. Can you explain a bit more? --David Iberri (talk) 01:29, 18 November 2008 (UTC)

Using 1247673 in a PubMedCentral search give (me at least) "Internal Server Error" which is hard to distinguish from an other problem. Indicating that no PMID can be found so the PMC can't (yet) be formatted would help.

Similarly when an ISBN can't be found. -- RDBrown (talk) 12:53, 18 November 2008 (UTC)

Ah, I see. This has been filed as ticket 41053. I've mostly fixed the PubMed Central issue, but the error messages aren't quite as user-friendly as I'd like (see [3] for example). Do you have an example of an ISBN the template filler isn't grokking? --David Iberri (talk) 03:23, 19 November 2008 (UTC)

Journal abbreviations

The journal titles are back to a terser form (applause), but they sometimes don't match the Pubmed abbreviation, if that was your aim (ie 11319089 |journal=Appl. Environ. Microbiol. Pubmed: Appl Environ Microbiol.) This seems to depend on the Journal, but Pubmed seems to suppress internal periods for abbreviation. RDBrown (talk) 13:49, 17 November 2008 (UTC)

PubMed offers several journal titles and abbreviations. Arbitrarily, the template filler prefers the ISO abbreviation ("Appl. Environ. Microbiol."), followed by the Medline abbreviation ("Appl Environ Microbiol"), and then, if all else fails, the full title ("Applied and environmental microbiology"). Since the tool's been using the ISO abbreviation, and there doesn't appear to be a standard/preference on Wikipedia, I'd just as soon continue to use the ISO abbreviation. Do you have a compelling reason to switch to the Medline abbreviation? --David Iberri (talk) 01:29, 18 November 2008 (UTC)

No compelling reasons, but I had the impression that earlier versions of the filler (say 3 months ago) used the Medline form rather than the ISO form, though it looks like a number of journals give the terser Medline form for the ISO form if that's what the filler has been requesting. For articles with a lot of refs (I've seen 200 in a few), brevity may help. -- RDBrown (talk) 12:53, 18 November 2008 (UTC)

I see, but still I'm unsure whether this necessitates a change from ISO to Medline titles. There's actually some discussion somewhere on Wikipedia (possibly on my talk page, I'm not sure) about having the template filler return full journal titles instead of either abbreviation type (WP:PAPER and all that). I can see that argument, but as for switching between types of journal title abbreviations, I'm thinking there's probably too much inertia to motivate a change. --David Iberri (talk) 03:27, 19 November 2008 (UTC)

Partial PMID data

At least twice tonight, I've had PMID data return populating only the URL field, no others. Clicking Submit again, once more than once fully populated the cite journal fields. I have seen this before infrequently but I can't identify which PMID values gave problems from my browser history. If easy could you please check that the title and journal fields have data and go around again (once) if they don't. -- RDBrown (talk) 12:53, 18 November 2008 (UTC)

This appears to be a load issue with the NCBI/PubMed servers. I've been in contact with some of the folks there, and they tell me they're unable to replicate the problem. However, it invariably results when the load level is high (more than a few requests per second during EST business hours). I've thought about the solution you mention, but I'm afraid that would only exacerbate the load problem. --David Iberri (talk) 03:37, 19 November 2008 (UTC)

Feature requests

Would you like to see the template filler do a new trick? Post it here. The more details, the better.

Citation format of the open access journals of Plos

How about a setup that gives back alternatively the template in the way that Plos journals provide their citations? Would be neat to try improving readability in citations. I think, they did a good job in that. Bollisee (German Wikipedia) —Preceding unsigned comment added by 217.227.237.248 (talk) 19:56, 16 November 2008 (UTC)

I'm not terribly familiar with PLoS, and I'm certainly not familiar with their citation style. Can you provide some additional details and/or links? Skimming the website didn't turn up much. Thanks, David Iberri (talk) 20:19, 16 November 2008 (UTC)

Would this help, formatting instruction and an example?

• Author_Surname Author_Initial, further_Autors (Year) Titel. Journal. Number: First_PageMinus_SignLast_Page. DOI_or_PMID_or_Onlinelink.
• Lee KB, Liu CT, Anzai Y, Kim H, Aono T, Oyaizu H (2005) The hierarchical system of the 'Alphaproteobacteria': description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol. 55: 1907−19. PMID 16166687.

And I almost forgot, it would be nice to have no truncation of the authors list. The last author is in newer publications in natural sciences usually the most important one. Bollisee (German Wikipedia)

Really? In most publications I'm aware of, the last author list is the PhD in whose lab the study was performed, and first author is usually the postdoc who wrote the majority of the paper, did most of the experiments, etc. --David Iberri (talk) 00:39, 25 November 2008 (UTC)

Patents

Hello again - I realise this is a bit out of the scope of your template filler wizard, but I was wondering if you would be interested in adding functionality to build the {{US patent reference}} given only a patent number? Regards—G716 <^T·_C> 05:06, 22 November 2008 (UTC)

There is some similarity. {{ref patent}} is likely the best case in point. Given a country and patent number it will link to the full patent data, which could then in principle be autoextracted to populate the several other fields, including the required "title=". I'm sure this would be a popular tool amongst patent fans.LeadSongDog (talk) 06:22, 22 November 2008 (UTC)

This would make a great addition to the template filler. As I don't use work on patent-related articles, it'd be helpful to know how one typically goes about obtaining patent information. I understand esp@cenet and uspto.gov are useful; are there others? In particular, I'm looking for a database that allows exporting; esp@cenet's CSV exporting might suffice, but XML would be much preferable. Any suggestions? --David Iberri (talk) 18:24, 22 November 2008 (UTC)

Have a look at the EPO portal. It can generate downloadable XML results, though I'm not sure just how to automate the query.LeadSongDog (talk) 20:51, 22 November 2008 (UTC)

Looks promising. Thanks for the link. --David Iberri (talk) 00:39, 25 November 2008 (UTC)

{{Chembox new}} → {{Chembox}}

Resolved

Heya

Could you code the following change into your pubchemid tool? {{Chembox new}} has been deprecated in favor of {{Chembox}}; the former now exists as a redirect to the latter. Thanks! --Rifleman 82 (talk) 11:37, 23 January 2009 (UTC)

I haven't been keeping up with these discussions. Is {{chembox}} completely backwards compatible with {{chembox new}}? If so, I'll happily update the template filler to use the former rather than the latter. Cheers, David Iberri (talk) 20:23, 25 January 2009 (UTC)

I did a run with User:Chem-awb to convert everything over to Chembox, but Physchim62 tells me that we still need a history. No article should be using Chembox new any more. --Rifleman 82 (talk) 03:35, 26 January 2009 (UTC)

Got it. I guess my real question is regarding what change(s) I need to make; is it as simple as changing "chembox new" to "chembox"? Or are some of the parameters a bit different as well? --David Iberri (talk) 23:45, 26 January 2009 (UTC)

Sorry for the late reply, yes, just change "chembox new" to "chembox"; everything else will work. --Rifleman 82 (talk) 12:54, 28 January 2009 (UTC)

Great. Should be all fixed now, for example [4]. --David Iberri (talk) 01:24, 30 January 2009 (UTC)

Great, thanks! --Rifleman 82 (talk) 03:45, 30 January 2009 (UTC)

IUPAC names

Also, the IUPAC names from PubChem are not reliable; could your template filler not fill that field? Thanks! --Rifleman 82 (talk) 11:54, 23 January 2009 (UTC)

That's a shame. If there is a general consensus that PubChem's IUPAC names are unreliable, I'll gladly remove them from the template filler. So far, you're the first one to mention it to me; are there others who have similar experiences? Are you aware of any other sources of IUPAC names? That way, we can remove the PubChem IUPAC name and replace it with a more reliable source. Cheers, David Iberri (talk) 20:23, 25 January 2009 (UTC)

There might be something at [5] or [6] or [7] that helps. Have a boo.LeadSongDog (talk) 02:15, 26 January 2009 (UTC)

Since Rifleman was the first, let me be the second :)

IUPAC names from PubChem are often "unreliable", as are the structures themselves, though much less frequently. I usually generate names manually with ACD/ChemSketch. I've found that ChemSpider consistently provides reliable IUPAC names. Fvasconcellos (t·c) 20:51, 26 January 2009 (UTC)

Hey David, would you mind removing the IUPAC field? Thanks. --Rifleman 82 (talk) 11:20, 19 February 2009 (UTC)