Person

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Form URL

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

New postgreSQL Tables

  1. Data tables
  2. History tables

Some data tables do not have history, only have joinkey (two#), value, two_timestamp (timestamp) :

  • two -- second column 'two' is an integer
  • two_unsubscribe -- second column is text
  • two_curator_ip -- second column is text
  • two_lineage - joinkey , two_sentname (not editable), two_othername (not editable), two_number (of the person connecting to), two_role, two_date1 (Beginning in the year), two_date2 (Through the year), two_sender (email of sender or REV- email for reverse connection). two_lineage is a 2 way connection table, connects to sender and recipient who is the other person role connecting identified by REV-.

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

(data -- text), two_curator (two# -- text), two_timestamp (timestamp). History tables have h_ in front to keep track of editing history (h_two_status) keeping same columns:
  • Data and History tables:
  • two_firstname -- single value. always has a value.
  • h_two_firstname -- single values. to keep track of editing history.
  • two_middlename -- single value.
  • h_two_middlename -- single value. to keep track of editing history.
  • two_lastname -- single value. always has a value.
  • h_two_lastname -- single values. to keep track of editing history.
  • two_standardname -- single value. always has a value.
  • h_two_standardname -- single values. to keep track of editing history.
  • two_street -- multi value.
  • h_two_street -- multi value. to keep track of editing history.
  • two_city -- single value.
  • h_two_city -- single value. to keep track of editing history.
  • two_state -- single value.
  • h_two_state -- single value. to keep track of editing history.
  • two_post -- single value.
  • h_two_post -- single value. to keep track of editing history.
  • two_country -- single value.
  • h_two_country -- single value. to keep track of editing history.
  • two_institution -- multi value.
  • h_two_institution -- multi value. to keep track of editing history.
  • two_old_institution -- multi value.
  • h_two_old_institution -- multi value. to keep track of editing history.
  • two_old_inst_date -- multi value. from time we knew it was current/got data
  • h_two_old_inst_date -- multi value. to keep track of editing history.
  • two_mainphone -- multi value.
  • h_two_mainphone -- multi value. to keep track of editing history.
  • two_labphone -- multi value.
  • h_two_labphone -- multi value. to keep track of editing history.
  • two_officephone -- multi value.
  • h_two_officephone -- multi value. to keep track of editing history.
  • two_otherphone -- multi value.
  • h_two_otherphone -- multi value. to keep track of editing history.
  • two_fax -- multi value.
  • h_two_fax -- multi value. to keep track of editing history.
  • two_email -- multi value.
  • h_two_email -- multi value. to keep track of editing history.
  • two_old_email -- multi value. (add to Person editor form section to log old_date from time we knew it was current/got data)
  • h_two_old_email_date -- multi value. to keep track of editing history.
  • two_pis -- multi value.
  • h_two_pis -- multi value. to keep track of editing history.
  • two_lab -- multi value.
  • h_two_lab -- multi value. to keep track of editing history.
  • two_oldlab -- multi value.
  • h_two_oldlab -- multi value. to keep track of editing history.
  • two_left_field -- single value.
  • h_two_left_field -- single value. to keep track of editing history.
  • two_unable_to_contact -- single value.
  • h_two_unable_to_contact -- single value. to keep track of editing history.
  • two_privacy -- single value.
  • h_two_privacy -- single value. to keep track of editing history.
  • two_aka_firstname -- multi value.
  • h_two_aka_firstname -- multi value. to keep track of editing history.
  • two_aka_middlename -- multi value.
  • h_two_aka_middlename -- multi value. to keep track of editing history.
  • two_aka_lastname -- multi value.
  • h_two_aka_lastname -- multi value. to keep track of editing history.
  • two_webpage -- multi value.
  • h_two_webpage -- multi value. to keep track of editing history.
  • two_wormbase_comment -- multi value.
  • h_two_wormbase_comment -- multi value. to keep track of editing history.
  • two_hide -- single value.
  • h_two_hide -- single value. to keep track of editing history.
  • two_status -- single value.
  • h_two_status -- single value. to keep track of editing history.
  • two_mergedinto -- single value.
  • h_two_mergedinto -- single value. to keep track of editing history.
  • two_acqmerge -- single value.
  • h_two_acqmerge -- single value. to keep track of editing history.
  • two_comment -- multi value.
  • h_two_comment -- multi value. to keep track of editing history.
  • two_usefulwebpage -- multi value.
  • h_two_usefulwebpage -- multi value. to keep track of editing history.

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.

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


  • 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
  • Like the grey background, 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 institutions - 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_institution? 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_institution 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 institution
  • 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 people see their contact data to update, does it link to two_display? http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person.cgi?action=Display&number=WBPerson1 no, the person.cgi gets its own person display independent from the two_display.cgi People outside Caltech don't ever use the two display, so we can get rid of it an just use the new person editor in display vs. edit mode.
  • Confirm paper: 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.


  • 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

http://tazendra.caltech.edu/~postgres/cgi-bin/cecilia/two_display.cgi I like to to-display because it shows only data, and I can do searches 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. search 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

Ceci, please fix the multiple entries in the postgres table two by running /home/cecilia/work/gaps_in_twos/get_recent.pl which now looks for gaps and tells you of multiples :

  • testdb=# SELECT * FROM two WHERE two = 871;
    • two871 | 871 | 2002-08-12 09:25:21.17393-07
    • two871 | 871 | 2004-11-27 14:44:38.614083-08
  • testdb=# SELECT * FROM two WHERE two = 871 AND two_timestamp > '2004-11-26' AND two_timestamp < '2004-11-28';
    • two871 | 871 | 2004-11-27 14:44:38.614083-08

Once you do the SELECT, you can do the DELETE to get rid of just that one Thanks, fixed.

Just recording your oral response. all Paper search in mangolassi are showing as: pap_curation_done author_person in red bold letters Just for me to see if it is the way i'd like it to show. Yes, i like it, impossible to miss it.

*Person_lineage: 2011-06-17 /home/postgres/work/pgpopulation/two_people/two_lineage/update_twos_in_two_lineage.pl output files /home/postgres/work/pgpopulation/two_people/two_lineage/ vim lineage_psql_commands Veo dos posibles soluciones al problema de IGNORE Dr. Chris Link IGNORE Dr. Chris Link UPDATE two_lineage SET joinkey = 'NO' WHERE two_sentname = 'Dr. Chris Link' AND two_othername = 'Dr. Andreas Kampktter' AND two_role = 'Lab_visitor' AND two_sender = 'REV - kampkoet@uni-duesseldorf.de'; UPDATE two_lineage SET two_number = 'NO' WHERE two_othername = 'Dr. Chris Link' AND two_sentname = 'Dr. Andreas Kampktter' AND two_role = 'withLab_visitor' AND two_sender = 'kampkoet@uni-duesseldorf.de'; IGNORE Dr. David Hall 1a Is it possible for the script to not ignore data and only ignore titles? 1b Add under line Lineage Connections with(Please do not add titles to names, script will ignore your data)??? 2 Changes in Person_lineage form: 2a red letters (Your Email) and (Your Full name) change them for black color 2b in section 'LINEAGE CONNECTIONS WITH ' Relationship 1 :(keep relation I trained...etc) Change instead of 1 large blank space split it into 3 spaces, labeled First, Middle and Last names I like solution #2

To Do

For new person editor

Check these forms / scripts (get rid of two_fullname view and replace with code looking at firstname middlename and lastname) :

  • /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/postgres/work/pgpopulation/two_people/two_lineage/update_twos_in_two_lineage.pl
  • /home/azurebrd/public_html/cgi-bin/forms/paper_display.cgi
  • /home/azurebrd/public_html/cgi-bin/forms/person.cgi # DONE
  • /home/azurebrd/public_html/cgi-bin/forms/person_lineage.cgi
  • /home/azurebrd/public_html/cgi-bin/forms/confirm_paper.cgi
  • /home/azurebrd/public_html/cgi-bin/forms/generic.cgi?action=VerifyPaper&two_number=two11941&aid=125345&pap_join=1&yes_no=YES
  • /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/acedb/cecilia/citace_upload/get_pap_person_ace.pl
  • /home/cecilia/work/gaps_in_twos/get_recent.pl # DONE
  • /home/postgres/work/pgpopulation/pap_papers/author_person/email_connected_authors.pl
  • /home/acedb/cecilia/citace_upload/get_pap_person_ace.pl

Creando :

  • /home/acedb/cecilia/citace_upload/errors_in_pap_person.ace (vim this and get two# with no status)

Cecilia, put range of papers to mark as curated for author_person here to populate pap_curation_done with value 'author_person' for those WBPaperIDs's joinkeys 33058-33200 33201-33300 33301-33400 33401-33500 33501-33586 33601-33644 34636-34641 35601-35700 35701-35800 35801-35900 35901-36000 36738 36750 36765 36796 36870 37108-37109 37135 37144 34157-37161 37637 37909 37923 37998 38037 38126 38142 38144 38152 38193 38341 When Person curation is done a message will show at top of Person editor page-> Search paper = as pap_curation_done author_person, in bold red letters.

Fix two10121 has no status, two11402 has no status, two11917 has no status, FIXED

For Person verification


Change subject letter to email author for verification to show standard name instead of WBPerson id NO email to Cecilia standard automatic reply to paper verification, Yes to cronjobs to keep track of response instead of email to cecilia Possibly we could get rid of that and implement a separate way to track who's responded. 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. Cecilia, please clarify what you want to change and how to change it Updated subject of confirm paper to not show WBPerson id and to not email me a copy of the of the thank you automatic reply.

  • script to check last 24 hours of YES/NO Cecilia, tell me when you want this to run, and how you want the data grouped (by person / by paper / by yes/no ?)

Run at noon. Data grouped by Papers verified NO, showing aid# + Person#. At the end of run, count of Persons verified YES and count of #Papers.

Person Update Form

Update contact information form to have extra lines for old_institution, to not show akas, I don't want it to be editable, we'll talk about this later ok

  • UPDATED May 25, 2011: Changed colors. Deleted extra timestamp boxes, extra lines from city, state, post, country. Added old_timestamp with at lest 3 lines.

Full name (discontinued) changed to manually get values

  • Table full_name sees 3 tables, First + middle + last names, if a table is missing it doesn't see it.
  • Changed to manually get 3 values (first_name, middle_name, last_name) if available and combine them instead of full_name. This will resolve problem of people with no middle name, adding an empty value to middle_name tag.

two_display -> Person editor

Old two_display replaced by this really awesome multi tasking new one. Can do multiple combination searches.

Person editor: display mode, edit mode

  • Functionality:
  1. Search - Display or Edit mode - Results Links to Person_editor
    1. Priority = two#, will ignore rest.
    2. Combine search = unlimited search fields
      1. example- email + caltech + case insensitive = Will give results of all People with caltech in email address.
      2. example- ^ (carat) Li (last_name) substring = will give results of all last names starting with Li
      3. example- ard$ (last_name) + caltech (email) substring = two699 Alison Claire Woollard lastname : Woollard
  2. Create New Person: Manual curation, New autofill for some tags.
  3. Search Paper: Individual discriminate paper curation. Will show data from Pubmed xml. Required data: lastname, instituion and either inst or old_inst. Check curation_flags: author_person, if not flagged do not Person curate.
    1. Curation_flags
    2. Bold red message Person curation done.
    3. WBPaper00026893 paper editor link.
    4. Identifiers and pdf links
    5. pmid 15965246 xml found
    6. Affiliation : Stanford University, Stanford, California 94305, USA. ndsingh@stanford.edu
    7. Inst1 - click to show another institution - hide another institution
      1. institution : create all institutions linked to paper, current or old clicking to show another institution. This is a required data to create new Persons.
      2. street - auto fill. Data manually entered.
      3. street - auto fill. Data manually entered.
      4. street - auto fill. Data manually entered.
      5. street - auto fill. Data manually entered.
      6. city - auto fill. Data manually entered.
      7. state - auto fill. Data manually entered.
      8. post - auto fill. Data manually entered.
      9. country - auto fill. Data manually entered.
    8. Under this section will show data from xml and postgres pap_ tables:
      1. From postgres pap_ tables: aid,author, possible two#,sent, verified.
      2. From pubmed xml and Cecilia manual curation: standard name, firstname, middlename, lastname (required data to create new Person).
      3. From Cecilia manual curation: email, inst, old inst (either inst or old_inst is required to create new Person).
    9. Enter each author's data (only new Persons to create), Under inst select #1, #2 etc, as well of oldinst. NO# institution will not create new Person (For existing Person do not mark any Institution here).
    10. CREATE people from XML. Required lastname, institution, either inst or old_inst. Will mark Paper as Person-verified. If paper is in the list but was already Person curated, click here without adding any inst or oldinst to mark paper as already curated. Clicking 'Create people from xml' will make a new entry in pap_curation_done for "author_person".
    11. Creating persons from authors in WBPaper00026893 paper editor link.
    12. Checkout next paper id WBPaper00026894 - check out previous paper - checkout page.
  4. Checkout Papers: Will show papers not yet Person curated, flagged from 'author_person' priority in pap_curation_flags, Valid papers.

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

tables for Person submition form

  • two_firstname -- 1 field. Required.
  • two_middlename -- (if not middle name, empty value?, 1 empty space?). Will talk later.
  • two_lastname -- 1 field. Required.
  • two_standardname -- 1 field. Name as people would like to be addressed. Example: Tuco.
  • two_street -- always shows at least 4 fields.
  • two_city -- 1 field.
  • two_state -- 1 field.
  • two_post -- 1 field.
  • two_country -- 1 field.
  • two_institution -- multi value.
  • two_old_institution -- always shows at least 3 fields.
  • two_old_inst_date -- Should submitters enter old-date ???
  • two_mainphone -- 2 fields.
  • two_labphone -- 2 fields.
  • two_officephone -- 2 fields.
  • two_otherphone -- 2 fields.
  • two_fax -- 2 fields.
  • two_email -- 2 fields. Required.
  • two_old_email -- 2 fields.
  • two_old_email_date - Should submitters enter old-date???
  • two_oldlab -- 2 fields.
  • two_left_field -- 1 field.
  • two_webpage -- 2 fields.
  • two_lab -- 2 fields.
  • two_oldlab -- 2 fields.
  • two_left_field -- 1 field.
  • two_webpage -- 2 fields.

tables for Person editor form

http://mangolassi.caltech.edu/~postgres/cgi-bin/cecilia/person_editor.cgi

  • two_number -- single value. Enter WBPerson number to edit data.
  • two_firstname -- single value. always has a value.
  • two_middlename -- single value. if not middle name, empty value?, 1 empty space?
  • two_lastname -- single value. always has a value. Required.
  • two_standardname -- single value. always has a value.
  • two_street -- always shows at least 4 fields.
  • two_city -- single value.
  • two_state -- single value.
  • two_post -- single value.
  • two_country -- single value.
  • two_institution -- multi value.
  • two_old_institution -- multi value. always shows at least 3 fields. do not forget to log old_date when entering old_institution data
  • two_old_inst_date -- multi value. log old_date from time we knew it was current/got data.
  • two_mainphone -- multi value.
  • two_labphone -- multi value.
  • two_officephone -- multi value.
  • two_otherphone -- multi value.
  • two_fax -- multi value.
  • two_email -- multi value.
  • two_old_email -- multi value. Do not forget to log old_date.
  • two_old_email_date -- multi value. Log old_date from time we knew it was current/got data.
  • two_pis -- multi value.
  • two_lab -- multi value.
  • two_oldlab -- multi value.
  • two_left_field -- single value.
  • two_unable_to_contact -- single value.
  • two_privacy -- single value. Person do not show in WormBase, only Suplemental information (not linked to Person).
  • two_aka_firstname -- multi value.
  • two_aka_middlename -- multi value.
  • two_aka_lastname -- multi value.
  • two_webpage -- multi value.
  • two_wormbase_comment -- multi value.
  • two_hide -- single value. Hyde data, usually email when people don't want their email addresses showing in our webpage. Do not send emails. Email deleted from two_email and entered into two_hide.
  • two_status -- single value.
  • two_mergedinto -- single value. Enter two# of the profile I want to keep. When Person were created double, I pick to delete the one with least papers connected. Transfer all current data to the selected profile (acqmerge), mark each paper connected to this profile in Paper_editor as NOT his/her and enter new join - possible two. And mark this Person as INVALID.
  • two_acqmerge -- single value. Enter two# of the profile you want to delete. When Person were created double, I pick to keep the one with more papers connected, and update contact data, lineage, papers connections and verify them if verified.
  • two_comment -- multi value.
  • two_usefulwebpage -- multi value. Tag where you can write 'useful' or 'not useful'. Not useful means webpage doesn't show lab members data, do no open it to look for lab member info. Note: this is for future data (when new Person-editor is Live), prior to this all webpages will have empty tag. I will manually check each webpage in the future as extra time is available or when curating papers and have to refer to PI webpage. In Person display will show under same order: above webpage and below usefulness.
  • two_status -- single value. Entered automatically at Person creation. Manually mark as INVALID when created double. Don't forget to add values to mergeinto and acqmerfe. Invalid will show in bold red letters at top of two_display form.

- To create the new Person after entering data: NO button, NO reload page (will create a new two#). - Link to Person display.

history tables are invisible. keeping track of old_email and old_institution history.
http://www.wormbase.org/db/misc/person?name=WBPerson3680;class=Person
See under Tracking, old email and old institution are dated, showing history date (two_old_email_date and two_old_inst_date)

Tables for Confirm paper

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

It is not showing some papers, example WBPerson : 11871, it shows no papers.

http://tazendra.caltech.edu/~postgres/cgi-bin/paper_editor.cgi?curator_id=two1&action=Person+Author+Curation&two_number_search=11871 Shows WBPaper00036637

Tables for Person Lineage submission form

Person Model

Revised and approved for sign off on the 16th June. 2011

?Person PostgreSQL_id UNIQUE Text // for linking to internal RDB

                                       // Text instead of Int so it says WBperson####
       Name    First_name    UNIQUE  Text    // prefered first name
               Middle_name   Text            // middle name(s)
               Last_name     UNIQUE  ?Person_name XREF Last_name_of    // prefered last name
               Standard_name UNIQUE  ?Person_name XREF Standard_name_of   // name to be used for displays
                                             // default is "First_name Last_name"
               Full_name     UNIQUE  ?Person_name XREF Full_name_of // field for storing long name [030321 krb]
               Also_known_as   ?Person_name XREF Other_name_of // new XREF added [030310 krb]
       CGC_representative_for ?Laboratory XREF Representative
       Laboratory ?Laboratory XREF Registered_lab_members
       Affiliation Text
       Conducted ?Analysis XREF Conducted_by
       Address #Address
       Tracking        Old_laboratory ?Laboratory XREF Past_lab_members      // Lab(s) the person previously worked in
                       Last_verified UNIQUE DateType                         // Last time the name/contact information in this record was actively verified
                       Last_attempt_to_contact UNIQUE DateType UNIQUE Text   // Text is method of attempt to contact
                       Old_address DateType #Address   // for history
                       Left_the_field Text
                       History        Merged_into       UNIQUE ?Person XREF Acquires_merge
                                      Acquires_merge    ?Person XREF Merged_into
                       Status  Valid
                               Invalid
       Comment Text
       Lineage Supervised    ?Person XREF Supervised_by #Role
               Supervised_by ?Person XREF Supervised #Role
               Worked_with   ?Person XREF Worked_with #Role
       Publication     Paper ?Paper XREF Person #Evidence
                       Not_paper ?Paper XREF Not_person #Evidence
                       Publishes_as ?Author    // confirmed author names (curated) can't XREF because of paper model
                       Possibly_publishes_as ?Author XREF Possible_person
                                               // curated for Author->Paper->Person
                                               // connection but not yet verified by
                                               // the Person
  1. Address Street_address Text // multiple lines including town, state, zip/postcode, whatever
         Country UNIQUE Text
         Institution UNIQUE Text
         Email Text                 // multiple emails allowed
         Main_phone    Text         // phone number for the institution, I presume
         Lab_phone     Text
         Office_phone  Text
         Other_phone   Text UNIQUE Text  // second text can be used to indicate type
         Fax           Text
         Web_page      Text    // web page is part of the address info I think

Notes

  • update to Paper editor (2011-05-18)Updated to add the author_person priority flag, creating the table pap_curation_done and moving the genestudied_done to

pap_curation_done as 'genestudied'. 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.

  • sandbox, mangolasi is only for testing. Tazendra is Live. all Paper search in mangolassi are showing as:

pap_curation_done author_person in red bold letters Just for me to see if it is the way i'd like it to show. Yes, i like it, impossible to miss it.

  • 2011-06-03 Cecilia, I've moved the script to update lineage names to WBPerson#### to the postgres account to :

/home/postgres/work/pgpopulation/two_people/two_lineage/update_twos_in_two_lineage.pl You should add that to the list of scripts to update when we change the person tables. 2011-06-07 missed a line, re -ran output at /home/postgres/work/pgpopulation/two_people/two_lineage/


  • 2001-06-06 Person editor in tazendra (development database)

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

We don't have the mangolassi sandbox, so I've made a development database, separate from the database with real data (devdb for developtment vs. testdb for real data), and copied the person_editor.cgi to tazendra, to access the development database. So you can test it, and it should work just like it used to, and you can mess with the data. Don't forget that any links to the paper editor and so forth are real links and data in those forms will make real changes.

  • 2001-06-07 Person_lineage:

http://tazendra.caltech.edu/~azurebrd/cgi-bin/data/person_lineage.ace aqui se ven todos los lineage mandados

/home/postgres/work/pgpopulation/two_people/two_lineage/update_twos_in_two_lineage.pl output files /home/postgres/work/pgpopulation/two_people/two_lineage/

cd /home/postgres/work/pgpopulation/two_people/two_lineage/ ls lineage_psql_commands not_found update_twos_in_two_lineage.pl*

vim lineage_psql_commands : ve los datos, como los ve, que pone y que no pone. vim not-found : lista de los que no encuentra vim update_twos_in_two_lineage.pl* : es el programa

Useful links

http://www.mediawiki.org/wiki/Help:Formatting