Person

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Revision as of 17:28, 20 May 2011 by Jchan (talk | contribs) (→‎To Do)
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Form URL

http://mangolassi.caltech.edu/~postgres/cgi-bin/cecilia/person_editor.cgi (sandbox for testing)

New postgreSQL Tables

table 'two' does not have history, only has joinkey (two#), two value (integer), two_timestamp (timestamp) Cecilia, you should comment on each table, what type of table it is, what kind of stuff you put in there.

all other tables have joinkey (two#), two_order (integer), two_

(data -- text), two_curator (two# -- text), two_timestamp (timestamp) :
  • two_firstname -- e.g. single value. always has a value
  • two_middlename
  • two_lastname
  • two_standardname
  • two_street -- e.g. multi value. always shows at least 4 fields.
  • two_city
  • two_state
  • two_post
  • two_country
  • two_institution
  • two_old_institution
  • two_old_inst_date
  • two_mainphone
  • two_labphone
  • two_officephone
  • two_otherphone
  • two_fax
  • two_email
  • two_old_email
  • two_old_email_date
  • two_pis
  • two_lab
  • two_oldlab
  • two_left_field
  • two_unable_to_contact
  • two_privacy
  • two_aka_firstname
  • two_aka_middlename
  • two_aka_lastname
  • two_webpage
  • two_wormbase_comment
  • two_hide
  • two_status
  • two_mergedinto
  • two_acqmerge
  • two_comment
  • two_usefulwebpage

Changes between old and new tables

  • Adding history tables as h_two_...
  • Removing two_apu_ tables, two_groups
  • Adding two_usefulwebpage, two_old_inst_date, two_old_email_date
  • Changing two_comment into normal table with order
  • Changing old_timestamp column to two_curator (all values will be 'two1')

Questions

Please confirm that no one uses this form http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/confirm_paper.cgi In the last year 111 IPs have used it (mostly once) but a couple of them over 100 each. If you don't use it, is it in the emails you send out or in the submit forms in WormBase ? -- J answer Please keep form, must be the one linking to old papers associated but not verified -- Ceci Sounds good, added to list of forms to check -- J thanks ceci

1681 two_middlename without value, is that okay ? SELECT * FROM two_middlename WHERE two_middlename = ' '; <-- no space in between the singlequotes --J answer It was from when we thoght that a data was needed in tag, please delete if not needed -- Ceci.

1004 two_middlename with NULL order, value, old_timestamp, what should we do with that ? SELECT * FROM two_middlename WHERE two_order IS NULL;

answer i've been adding aka_middlename = NULL to every aka entry, if it is not necessary them we can delete it, but if it is necessary please keep it. Talk tomorrow? Ceci. I am also fixing some typos showing searching in new Person editor Ceci I don't know if you need it to say 'NULL' or not, but I thought you were never supposed to have blank values, you can skype me whenever you want -- J will talk in person about all middle/aka names, empty values

1) two_aka_midlename always has NULL (when none middlename to fill) 2) two_middlename Primero dijimos all tags filled Mas adelante me parece recordar que habiamos dicho que cuando la gente no tiene middle name no se ponia. http://www.wormbase.org/db/misc/person?name=WBPerson1823;class=Person Si esto esta mal hay que volver a poner 1 espacio vacio a los que no tienen data en two_middename. C

I don't know if it needs to be a certain way, when I set it up I let you know how it should be and you should make a note of it so you can tell me if something is wrong later.


two427 had under wormbase_comment :

  • two427 | 1 | Due to illness, please get in touch with: Mark Edgley (edgley@interchange.ubc.ca) for gene knockout inquiries. Teresa Rogalski (rogalski@zoology.ubc.ca) for muscle lab matters. 2003-03-07 18:36:25.089309-08 | 2003-03-19 11:38:57.295736-08 |
  • two427 | 1 | Lab:DM or VC | 2003-03-10 16:23:56.877045-08 | 2003-03-19 11:38:57.295736-08
  • two427 | 2 | DM his own lab and VC head of the KO | 2008-01-31 00:00:00-08 | 2008-01-30 10:04:25.884154-08

Which has two order '1', I've deleted the first one, if you want to add it again as order '3' -- J. answer Deleted OK, thanks Ceci

Please comment on these changes :

  • I've added history tables, and changed the postgres tables to store the curator in the 4th column where the old_timestamp used to be. Updating data updates the data table with current timestamp ; removes any history data for that table-joinkey-order in the last 10 minutes, and inserts with current timestamp. answer OK Ceci
  • Street field always has at least 4 fields. answer YES ceci
  • name and aka_name now show first/middle/last in a row with timestamp below them. answer Like it Ceci
  • old_email shows data from old_email_date horizontally with timestamp. answer OK ceci
  • old_institution shows old_inst_date data, and webpage shows usefulwebpage vertically because I assume you need more space, if you'd rather display them horizontally like old_email, let me know. answer OK ceci
  • All changes to the person editing section of the person editor are done, please let me know if I overlooked something. answer looks ok, will look more in detail, thanks Juancarlos ceci Cool, let me know. Thanks -- J two_comment is missing ceci// added - J// thanks, c
  • In the Search Paper (to create people from XML) section, do you want to see input fields to create new people for authors that are already verified 'YES' ? Right now people that are verified 'YES' have a grey background, if you don't want to see the inputs, do you still want the grey background ? Probably easier to talk about this in person / skype. Some papers I tried were 00003865 00026893 -- J
  • wow thanks, looks really great, will look in more detail. Yes talk in person, lots of new stuffs, when do you have time? I have to be in Pasadena on Friday, is that OK with you? See email, we can talk until around 1pm OK answered email
  • I like the grey part. Paper 00026893 is showing aid77392 Davis J - xml Jerel C. Davis - 1 matches two4351 (Ralph E. Davis) -> Are matches to last names even when it doesn't match first initial or first name? ceci no, it's the same matching script that we wrote a few weeks ago, it matches to fullname exactly, we went over how that worked, right ? If not we can go over it in person OK, but Ralhp E. Davis in in no way exact match to Jerel C. Davis


  • Last name Davis, first initial J shouldn't it match to two3329 Justin R Davis, two4914 Jamie Davis, two7656 Joseph S. Davis? ceci It matches exactly on xml first+last not initials, the single_match and histogram script you run manually matches with initials and creates them automatically, this is for manual curation First Last is no match Ralhp E. Davis to Jerel C. Davis
  • Like the grey backgroud, but when clicked on Create people from XML volvio a crear Nadia D. Singh, va a haber un boton para marcar Do not create or ignore it?. Really love the multiple instititions - addresses (hide-show-assign), really like it!!! cec If you assign an institution it does something, if you don't it ignores the person. Yes, I noticed after trying several different things, it is in may notes to talk to you tomorrow
  • could you add old_instition? it will be useful when creating Persons form oldpapers,o when pdf shows currently at different affiliation, I could add both datas. c - Create new people from XML. Please add old_institution to this part (some people no longer at inst) Just 1 line, no address. Are those two issues the same thing ? If so the old institutions would be one of the 20 normal institutions, but you'd assign it under an old_inst dropdown instead of the normal inst dropdown. So you're saying that if selected in the old_inst dropdown, it would only take the institution line from that inst# and add it to the two_old_instutition and the current date to two_old_inst_date. Would there only ever be one old institution ? Would you ever want to add both old institution and current institution ? yes. sometimes i'd add both current and old instituion
  • WBPaper00026893. When editing another institution, it is showing street from 1st institution at creating people from XML fixed OK, thanks
  • We only need to change this script for person stats: /home/postgres/work/get_stuff/for_paul/curation_stats/wbperson_creation_stats/get_recent.pl which keys off of the two_display.cgi (unless we change the two_display.cgi to keep working,do you want it to ?) YES from To Do below it's decided that we'll have a display and editor in the person_editor with a checkbox for display mode (default off), and links between display - editor and editor - display. New question : Sometimes outside people have to look at the paper display, will they ever need to look at some kind of person display ? Because if so we don't want them to see the editor, so we should keep the two forms separate in that case. ok good idea, when peole see their contat data to update, does it link to two_display? http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person.cgi?action=Display&number=WBPerson1

To Do

Check these forms / scripts :

  • /home/postgres/public_html/cgi-bin/cecilia/two_display.cgi
  • /home/postgres/public_html/cgi-bin/cecilia/twoeditor.cgi
  • /home/postgres/public_html/cgi-bin/paper_editor.cgi
  • /home/postgres/work/get_stuff/for_paul/curation_stats/wbperson_creation_stats/get_recent.pl
  • /home/azurebrd/public_html/cgi-bin/forms/paper_display.cgi
  • /home/azurebrd/public_html/cgi-bin/forms/person.cgi
  • /home/azurebrd/public_html/cgi-bin/forms/person_lineage.cgi
  • /home/azurebrd/public_html/cgi-bin/forms/confirm_paper.cgi
  • /home/azurebrd/work/parsings/authorperson/citaceLineage/update_twos_in_two_lineage.pl
  • /home/cecilia/UPLOAD/new-upload/connect_single_match_authors_and_get_histogram.pl
  • /home/cecilia/UPLOAD/new-upload/verify_by_labs_or_lineage.pl
  • /home/cecilia/UPLOAD/new-upload/email_connected_authors.pl
  • /home/cecilia/work/gaps_in_twos/get_recent.pl
  • /home/acedb/cecilia/citace_upload/get_pap_person_ace.pl
  • cecilia/home/postgres/work/pgpopulation/pap_papers/author_person -- directory to associate single match, verify papers by lineage and labs, sent emails for verification:
  • /home/postgres/work/pgpopulation/pap_papers/author_person/email_connected_authors.pl

for upload: /home/acedb/cecilia/citace_upload/get_pap_person_ace.pl Creando : /home/acedb/cecilia/citace_upload/errors_in_pap_person.ace

Change subject letter to email author for verification to show standard name instead of WBPerson id http://tazendra.caltech.edu/~azurebrd/cgibin/forms/generic.cgi?action=VerifyPaper&two_number=two11941&aid=125345&pap_join=1&yes_no=YES NO email to Cecilia standard automatic reply to paper verification, Yes to crojobs to keep track of responce instead of email to cecilia Possibly we could get rid of that and implement a separate way to track who's reponded. We're already planning to have a cronjob check all the 'NO' verification in a 24 hour period, we could have it check all the verifications and sort that into 'NO' and 'YES', or some other system that she'll device.

Update contact information form to have extra lines for old_instituion, to not show akas, I don't want it to be editable, http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person.cgi?action=Editor&number=two6742

Work in progress Paper - Person track I'd like to have: Showing only: papers flagged from Person curation by Kimberly. Ignore: For functional annotations only, Invalid papers


WBPaper00000000 identifier link_to_paper_editor curated What's curated ? -- J Person curation, ceci does this work now ?

New script: that looks at all the stuff that was verified in the last 24 hours or by day, except for those exceptions below. I want to receive daily email notifications or list for every time a paper is verified NOT mine. Unless: - pap_author_verified 'NO Cecilia Nakamura' - pap_author_verified YES after verified NOT same day - do not read NOT if there is a YES in latest timestamp We'd get data from pap_author_verified, we can't tell what came in to there from generic.cgi as opposed to confirm_paper.cgi, we can only know the values and their timestamps. Thanks, ceci And also filter out the papers you've already done, right ? Do you want to give me the range or papers that you've already done so I can enter them ? done, but I don't have documented all I have already curated, will mark them done/delete when I see them. ceci

change two_display.cgi to keep working keys off means that it gets values from. In this case, it means that it knows what tables to look at by looking at the code of the two_display which lists the tables. So the two_display would need to list all the new tables and not the old tables.

Yo si quiero seguir usando el two_display! What's the advantage of the two_display vs. the future paper_editor ? J

Thanks for explaining it. I like to to-display because it shows only data, and I can do searches http://tazendra.caltech.edu/~postgres/cgi-bin/cecilia/two_display.cgi I use it all the time.

Ok, the searches should be better in the future person_editor, but the only-data display would be better in the two_display.cgi Or we could add a section in the paper_editor to do only display.

Would this section be able to do also searches? Otherwise I'd like a two_display.cgi where I can both. seach and display. c You could probably toggle in the front page whether you wanted to use it in editor mode, or in display mode. But once you were in the search results page you couldn't change your mind at that point. Or maybe in the editor there could be a link to the display and viceversa. What would you prefer ? (think about it, let me know in wiki) J I'd prefer a link to the display and viceversa. c ok

<scripts that run automatically>

Note: make sure to keep it updated when adding new scripts and forms, or when I stop using others. (also let Juancarlos know when stop using some so he can remove them from tazendra.)

script for person stats : run to get stats, and they're called by this script /home/postgres/work/get_stuff/for_paul/curation_stats/wrapper.sh which runs every monday at 2am.

/home/postgres/work/get_stuff/for_paul/curation_stats/wbperson_creation_stats/get_recent.pl

This one for person lineage stats : /home/postgres/work/get_stuff/for_paul/curation_stats/wbperson_lineage_stats/get_recent.pl

This one for paper-author-person stats : /home/postgres/work/get_stuff/for_paul/curation_stats/wbpaper_author_person_stats/get_recent.pl

Note: April 17, 2011 We only need to change the first one, which keys off of the two_display.cgi (unless we change the two_display.cgi to keep working,do you want it to ?)YES. keys off means that it gets values from. In this case, it means that it knows what tables to look at by looking at the code of the two_display which lists the tables. So the two_display would need to list all the new tables and not the old tables

<scripts and forms>

Current May 18, 2011

  • /home/postgres/public_html/cgi-bin/cecilia/two_display.cgi
  • /home/postgres/public_html/cgi-bin/cecilia/twoeditor.cgi
  • /home/postgres/public_html/cgi-bin/paper_editor.cgi
  • /home/postgres/work/get_stuff/for_paul/curation_stats/wbperson_creation_stats/get_recent.pl
  • /home/azurebrd/public_html/cgi-bin/forms/paper_display.cgi
  • /home/azurebrd/public_html/cgi-bin/forms/person.cgi
  • /home/azurebrd/public_html/cgi-bin/forms/person_lineage.cgi
  • /home/azurebrd/public_html/cgi-bin/forms/confirm_paper.cgi
  • /home/azurebrd/work/parsings/authorperson/citaceLineage/update_twos_in_two_lineage.pl
  • /home/cecilia/UPLOAD/new-upload/connect_single_match_authors_and_get_histogram.pl
  • /home/cecilia/UPLOAD/new-upload/verify_by_labs_or_lineage.pl
  • /home/cecilia/UPLOAD/new-upload/email_connected_authors.pl
  • /home/cecilia/work/gaps_in_twos/get_recent.pl
  • /home/acedb/cecilia/citace_upload/get_pap_person_ace.pl

http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/confirm_paper.cgi http://tazendra.caltech.edu/~azurebrd/cgi-bin/index.cgi (site map)

When they connect papers through confirm_paper.cgi (always) It says ``WBPerson$two Thank you for updating your Author Person Paper connection When they connect papers through confirm_paper.cgi (saying 'NO') It says ``assigned new join $join to author $aid because said no to paper $joinkey When they comment through confirm_paper.cgi It says ``$two $curator comment for paper connections

When someone verifies a paper through generic.cgi It says ``${wbperson}, thank you for updating your Author Person Paper connection but only if /home/postgres/public_html/cgi-bin/data/confirm_paper_mailing.txt hasn't changed any data in the last day.

1.- generic.cgi (where is it?) You can see almost all the forms (including this one) in the sitemap http://tazendra.caltech.edu/~azurebrd/cgi-bin/index.cgi You can also see it in the emails that you send people to verify papers, when anyone clicks yes or no it's a link to that form

Looking at site map/ generic http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi shows: Your IP is :

I clicked yes to a paper http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=VerifyPaper&two_number=two10606&aid=105080&pap_join=1&yes_no=YES

So when you ask me where is the generic.cgi should i tell you the above link or is there a shorter generic version?

The generic.cgi has multiple uses. The default is to show the IP, the one that relates to person verification is http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=VerifyPaper

but the whole link is more useful because it makes it clear what values need to be passed in, and in what format.

2.- confirm_paper.cgi http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/confirm_paper.cgi yes


Kimberly - Flag papers for Person curation She's going to flag them in the table pap_curation_flags as 'author_person_priority' if they're priority and it will not have a value if they're not priority. So when you look at the checkout you can just look at the ones that are 'author_person_priority'.

Kimberly, this made me realize that since it's going into curation_flags the value can only either be there or not be there, so we might want to get rid of the 'blank' value because it implies that blank and not-priority are different, when they're stored the same way. We could make it a checkbox like functional annotation. Also, to both of you, should I just set all existing papers to 'priority' ? Sounds good to me, c

I'm fine with leaving it as a drop-down but with only two values and priority as the default. We could set all existing papers to priority for now, but that doesn't preclude us from re-categorizing some if we decide at a later time that Reviews, for example, could reasonably be set to not_priority, right? Kimberly

in the Enter New Papers section : - the author-person select at the top with the box for free pmids has an author-person dropdown with values priority and not_priority which populate pap_curation_flags with 'author_person' - each pmid has an aut-per_priority dropdown that works the same way

I've updated the pap_match.pm to allow the extra flag

I'll now work on populating all the papers except for those with functional_annotation as 'author_person' priority in pap_curation_flags. Cecilia, this means that in the future Kimberly will always flag this for you and not set that for those that are functional annotation, so you don't need to think about functional annotation anymore, just whether it's flagged as priority or not.

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