PDQ Issues

Issue Number	705
Summary	Import Page - no indication of related citations ready to import following a batch import
Created	2023-01-19 13:26:32
Issue Type	Task
Submitted By	Boggess, Cynthia (NIH/NCI) [C]
Assigned To	Kline, Bob (NIH/NCI) [C]
Status	Closed
Resolved	2023-01-20 12:33:06
Resolution	Fixed
Path	/home/bkline/backups/jira/oceebms/issue.336627

Description

From the Import page, when a user imports a batch of citations that has a related citation, there is no indication to the user that there is a related citation available for import. However, the pmid is put into the pmid field but all other import criteria is reset (related to ticket 704). Can we add a similar notification like we currently have in prod to alert users that related citations have been identified and are available for import and retain the import criteria from the original batch import?

Comment entered 2023-01-19 13:41:07 by Boggess, Cynthia (NIH/NCI) [C]

Also, the related citation links/info were not added to the record after import.

The citation in the previous screenshot was identified from today's import of adult Rx, renal cell, Jan 2023 batch import. After the import, the pmid was added to the blank form. When I added the original import criteria back into the form and imported, the citation did not get treated as a related citation should have. See added screenshot of citation.

Comment entered 2023-01-19 17:07:24 by Kline, Bob (NIH/NCI) [C]

Sounds like a separate problem, so separate ticket, please.

Comment entered 2023-01-19 17:35:47 by Boggess, Cynthia (NIH/NCI) [C]

Ok I'll add a new ticket and will reference this ticket.

Comment entered 2023-01-20 12:33:06 by Kline, Bob (NIH/NCI) [C]

Implemented on https://ebms.rksystems.com.

Comment entered 2023-01-20 13:07:23 by Boggess, Cynthia (NIH/NCI) [C]

I'm not seeing any notification on erc. The pmids are added to the pmid field and all other original import criteria is retained but no notification.

See screenshot.

Note: Testing this requires recreating a unique import environment. I have very limited data and therefore limited opportunities to test this. And I am trying to test this ticket and 707 together.

Comment entered 2023-01-20 13:31:11 by Kline, Bob (NIH/NCI) [C]

Sorry, I had done the initial implementation and testing in a private virtual server, and I had committed the code changes and pushed them to GitHub (the cloud storage of our version control system). I thought I had pulled the changes down to e.r.c., but clearly I hadn't. I've really installed the changes now. 😛

I agree that this corner of the system is tricky to test. I haven't really found a way to query PubMed for articles which have CommentsCorrections elements, which would be a big help. If you have any tips, please share. 🙂

Comment entered 2023-01-20 13:36:28 by Boggess, Cynthia (NIH/NCI) [C]

ok I am seeing the notification now. I am not sure if you just fixed it again or if my page finally loaded the new stuff. Regardless, the notification is working on erc.

Comment entered 2023-01-20 13:46:47 by Kline, Bob (NIH/NCI) [C]

Here are some relationships I can see (from querying the database) which were created after the migration to the servers we're using for testing EBMS4. Some of them may have been imported already on the EBMS4 servers, but others may be usable candidates for this purpose.

SELECT created, from_id, to_id
  FROM ebms_related_article
 WHERE comment LIKE 'linked programmatically%'
   AND created > '2022-12-20'
 ORDER BY created;
+---------------------+---------+--------+
| created             | from_id | to_id  |
+---------------------+---------+--------+
| 2022-12-28 21:49:41 |  885421 | 885450 |
| 2022-12-28 21:49:41 |  885446 | 885451 |
| 2022-12-28 21:51:03 |  884425 | 885517 |
| 2022-12-28 22:04:35 |  878653 | 886579 |
| 2022-12-28 22:05:32 |  886607 | 886641 |
| 2022-12-28 22:07:01 |  886752 | 886801 |
| 2022-12-28 22:07:01 |  884489 | 886802 |
| 2022-12-28 22:12:29 |  862513 | 887210 |
| 2022-12-28 22:18:46 |  887350 | 887358 |
| 2022-12-28 22:23:10 |  878399 | 887425 |
| 2022-12-29 14:04:21 |  888257 | 888326 |
| 2022-12-29 14:04:21 |  888282 | 888327 |
| 2022-12-29 14:04:21 |  888311 | 888328 |
| 2022-12-29 14:08:03 |  888408 | 888718 |
| 2022-12-29 14:08:03 |  888408 | 888719 |
| 2022-12-29 14:08:19 |  888719 | 888720 |
| 2022-12-29 14:13:51 |  889132 | 889161 |
| 2022-12-29 14:13:51 |  889141 | 889162 |
| 2022-12-29 14:13:51 |  884498 | 889163 |
| 2022-12-29 14:13:51 |  884488 | 889164 |
| 2023-01-09 09:43:23 |  889908 | 889909 |
+---------------------+---------+--------+
21 rows in set (0.01 sec)

Comment entered 2023-01-20 13:48:00 by Kline, Bob (NIH/NCI) [C]

Our comments are crossing paths. 😃

Comment entered 2023-01-20 13:53:45 by Kline, Bob (NIH/NCI) [C]

Here's a more useful query (it has the PMIDs):

SELECT r.created, 
       r.from_id, 
       f.source_id AS from_pmid,
       r.to_id,
       t.source_id AS to_pmid
  FROM ebms_related_article r
  JOIN ebms_article f
    ON f.article_id = r.from_id
  JOIN ebms_article t
    ON t.article_id = r.to_id
 WHERE r.comment LIKE 'linked programmatically%'
   AND r.created > '2022-12-20'
 ORDER BY r.created;
+---------------------+---------+-----------+--------+----------+
| created             | from_id | from_pmid | to_id  | to_pmid  |
+---------------------+---------+-----------+--------+----------+
| 2022-12-28 21:49:41 |  885421 | 36332647  | 885450 | 36455569 |
| 2022-12-28 21:49:41 |  885446 | 36301581  | 885451 | 36301585 |
| 2022-12-28 21:51:03 |  884425 | 36477032  | 885517 | 36477037 |
| 2022-12-28 22:04:35 |  878653 | 36400098  | 886579 | 36400104 |
| 2022-12-28 22:05:32 |  886607 | 36522207  | 886641 | 36522196 |
| 2022-12-28 22:07:01 |  886752 | 36480221  | 886801 | 35772005 |
| 2022-12-28 22:07:01 |  884489 | 36507686  | 886802 | 36507665 |
| 2022-12-28 22:12:29 |  862513 | 35969835  | 887210 | 36520477 |
| 2022-12-28 22:18:46 |  887350 | 35797472  | 887358 | 36520478 |
| 2022-12-28 22:23:10 |  878399 | 36306810  | 887425 | 36306811 |
| 2022-12-29 14:04:21 |  888257 | 35849791  | 888326 | 36054870 |
| 2022-12-29 14:04:21 |  888282 | 36520473  | 888327 | 35857899 |
| 2022-12-29 14:04:21 |  888311 | 35984905  | 888328 | 36454593 |
| 2022-12-29 14:08:03 |  888408 | 35394824  | 888718 | 35786962 |
| 2022-12-29 14:08:03 |  888408 | 35394824  | 888719 | 35786975 |
| 2022-12-29 14:08:19 |  888719 | 35786975  | 888720 | 35787109 |
| 2022-12-29 14:13:51 |  889132 | 35960849  | 889161 | 36480220 |
| 2022-12-29 14:13:51 |  889141 | 36548016  | 889162 | 35700381 |
| 2022-12-29 14:13:51 |  884498 | 36508741  | 889163 | 36534980 |
| 2022-12-29 14:13:51 |  884488 | 36507690  | 889164 | 36507659 |
| 2023-01-09 09:43:23 |  889908 | 36603541  | 889909 | 9704735  |
+---------------------+---------+-----------+--------+----------+
21 rows in set (0.01 sec)

Comment entered 2023-01-20 14:09:30 by Boggess, Cynthia (NIH/NCI) [C]

Yes, these are related citations. I matched them up with my records. Very good to know that you can do this query.

Jeff creates a list of all the pmids for all the related citations each month. It started with Minaxi as a QC of this feature when it was new and then became part of our routine. And it was handy to have when testing.

Comment entered 2023-01-20 14:10:34 by Boggess, Cynthia (NIH/NCI) [C]

Current status: looks good on erc.

Comment entered 2023-01-31 13:00:04 by Boggess, Cynthia (NIH/NCI) [C]

verified on ebms4

Attachments

File Name	Posted	User
image-2023-01-19-13-25-16-837.png	2023-01-19 13:25:17	Boggess, Cynthia (NIH/NCI) [C]
image-2023-01-19-13-38-16-617.png	2023-01-19 13:38:17	Boggess, Cynthia (NIH/NCI) [C]
image-2023-01-20-13-02-51-570.png	2023-01-20 13:02:52	Boggess, Cynthia (NIH/NCI) [C]

Elapsed: 0:00:00.000842

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