Understand the pipeline by looking at all scripts and forms

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List of scripts and forms to talk about

Paper Editor

/home/postgres/public_html/cgi-bin/paper_editor.cgi

URL: http://tazendra.caltech.edu/~postgres/cgi-bin/paper_editor.cgi

    Associated scripts:  script that checks PubMed daily for new papers
                         script that checks PubMed monthly for completing bibliographic data (i.e., to make PubMed final)

    Editor functions: approve, reject, remove papers
                      create paper objects for approved papers
                      add and edit paper-associated data

    Adding and Editing Paper-Associated Data
         Genes: added via script from abstract when paper is approved
                     see Attaching Genes to Papers for more details on this and proposed changes
                added manually via a curator
                added via script from the first-pass form with evidence 'curator first pass cfp_genesymbol'

  The perl module to create papers from pubmed IDs or abstracts
 /home/postgres/work/pgpopulation/pap_papers/new_papers/pap_match.pm

CRONJOBS :

 Get .ace file for Michael (how does the citace upload work

differently ?) /home/postgres/public_html/michael/get_all_papers.pl

 I don't know what this does, something about concise description and

invalid papers : /home/postgres/work/pgpopulation/wpa_papers/update_wbpaper_merging/postgres_fixing/find_merged_entries.pl

 gets merged papers from :

http://tazendra.caltech.edu/~postgres/cgi-bin/merged_papers.cgi

 (we should probably look at that CGI)

 Not sure, probably get list of new pubmed entries for form

verification and sorting : /home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/get_new_elegans_xml.pl

I don't know if first pass / author first pass is part of what we need to discuss.

 cronjob

/home/postgres/work/pgpopulation/textpresso/wrapper.sh

 calls

/home/postgres/work/pgpopulation/afp_papers/find_passwd_@.pl

 to get emails from textpresso for author first pass

 mails authors for first pass (?)
/home/postgres/work/pgpopulation/afp_papers/assign_passwd.pl

I'm sure there are more scripts and forms like :

(looking at site map) http://tazendra.caltech.edu/~postgres/cgi-bin/wpa_xref.cgi http://tazendra.caltech.edu/~postgres/cgi-bin/wpa_xref_backwards.cgi

(???) genefunction.cgi Checkout papers to curate gene_function only. http://tazendra.caltech.edu/~postgres/cgi-bin/genefunction.cgi

confirm_paper.cgi Verify grouped Authors and Persons. http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/confirm_paper.cgi

generic.cgi Generic public tasks. (show ip, verify papers, update obo_ for app_tempname) http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi

paper_display.cgi display pap tables's paper data http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_display.cgi

paper_obo.cgi display WBPaper's obo http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi

pmid_wo_pdf.cgi Table of WBPapers with PMID without a PDF http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/pmid_wo_pdf.cgi

paper.cgi Group Person data with Paper with help form Author http://tazendra.caltech.edu/~postgres/cgi-bin/cecilia/paper.cgi

but the Genetics pipeline isn't in that list. And there's nothing about scripts for organizing or downloading PDFs. And I'm sure there's other people that have some paper-related forms and scripts.

We need to find out what all of them are so that it can be documented and proposed changes can make sense.

I think once we have a list we can decide where to start going through it.