Error while running "sudo php symfony search:populate"

[Joel R Smith]

I am getting the error message "Error in one or more bulk request actions:"  This was after it was successfully upgraded from 1.3 to 2.2.  See below for full error log.

Error in one or more bulk request actions:                                                                                                                               
                                                                                                                                                                           
  index: /atom/QubitAccession/5166 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]   
  index: /atom/QubitAccession/5257 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]   
  index: /atom/QubitAccession/5269 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]   
  index: /atom/QubitAccession/5839 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]   
  index: /atom/QubitAccession/5922 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]   
  index: /atom/QubitAccession/6247 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]   
  index: /atom/QubitAccession/6302 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]   
  index: /atom/QubitAccession/6346 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]      
  index: /atom/QubitAccession/6354 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]      
  index: /atom/QubitAccession/6375 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]   
  index: /atom/QubitAccession/9218 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]      
  index: /atom/QubitAccession/12151 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]  
  index: /atom/QubitAccession/22929 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]     
                                                                                                                                                                           
                                                                                                                                                                           

PHP Fatal error:  Uncaught exception 'Elastica\Exception\Bulk\ResponseException' with message 'Error in one or more bulk request actions:

index: /atom/QubitAccession/5166 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/5257 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/5269 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/5839 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/5922 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/6247 caused StrictDynamicMappingExceptio in /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Bulk.php on line 395

Fatal error: Uncaught exception 'Elastica\Exception\Bulk\ResponseException' with message 'Error in one or more bulk request actions:

index: /atom/QubitAccession/5166 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/5257 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/5269 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/5839 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/5922 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/6247 caused StrictDynamicMappingExceptio in /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Bulk.php on line 395
archives@archives:/usr/share/nginx/atom$

[mi...@artefactual.com]

Hi Joel,

One thing to try is re-building the search index.

To do so, enter these commands into a command-line prompt (assuming you're running AtoM on Ubuntu), substituting "/path/to/atom/root/directory" with the path to your AtoM installation:

1) cd /path/to/atom/root/directory

2) php symfony search:populate

Cheers,

Mike Cantelon

Artefactual Systems

[Joel R Smith]

I made my original post because I am getting that error message AFTER running "php symfony search:populate"

[gs]

I'm getting exactly the same error after following the upgrade instructions.
Upgrading 2.1.2 to 2.2.0.

Fatal error: Uncaught exception 'Elastica\Exception\Bulk\ResponseException' with message 'Error in one or more bulk request actions:

index: /atom/QubitAccession/843861 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/845594 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/847156 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/861953 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/861993 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/861996 caused StrictDynamicMappingExceptio in /var/www/html/atom-2.2.0/vendor/Elastica/lib/Elastica/Bulk.php on line 395

[mi...@artefactual.com]

Hi Joel,

Apologies... one thing to try is deleting the ElasticSearch index entirely so it can be re-created from scratch, rather than updated. To do this you can follow these steps:

1) Install ElasticSearch Head (instructions at http://mobz.github.io/elasticsearch-head/).

2) Make sure your server's TCP/IP port 9200 is open so you can access ElasticSearch from your browser

3) Visit http://<your server's IP>:9200/_plugin/head/

4) Select the appropriate index then select the "Delete" option (for example here: http://i.imgur.com/OaNrnzc.png)

Cheers,

Mike

[gs]

Hi Mike,

Done that and still getting errors.

Regards,

George

PHP Fatal error:  Uncaught exception 'Elastica\Exception\Bulk\ResponseException' with message 'Error in one or more bulk request actions:

index: /atom/QubitAccession/843861 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/845594 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/847156 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/861953 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/861993 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]

index: /atom/QubitAccession/861996 caused StrictDynamicMappingExceptio in /var/www/html/atom-2.2.0/vendor/Elastica/lib/Elastica/Bulk.php on line 395

Fatal error: Uncaught exception 'Elastica\Exception\Bulk\ResponseException' with message 'Error in one or more bulk request actions:

index: /atom/QubitAccession/843861 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/845594 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [parallelNames] within [creators] is not allowed]
index: /atom/QubitAccession/847156 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/861953 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/861993 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]
index: /atom/QubitAccession/861996 caused StrictDynamicMappingExceptio in /var/www/html/atom-2.2.0/vendor/Elastica/lib/Elastica/Bulk.php on line 395

[Joel R Smith]

Thanks. elasticsearch-head installed successfully and I was able to delete the index.

However, doing that didn't change anything, the same exact error message appears when I try running php symphony search:populate

Could this have to do with a corrupted row? Error always happens after this entry: [Actor] Lastname, Firstname inserted (2.91s) (334/696)

[Dan Gillean]

Hi all,

For anyone following this thread, one of our developers is following up with these users off-list, but we're looking into the AtoM 2.2 release to see if a patch is needed.

If so, we'll either provide a patch with some install instructions, or we'll prepare a 2.2.1 release in the near future so we can resolve this for anyone else who is encountering the same issue.

The work will be tracked on this issue ticket:

• https://projects.artefactual.com/issues/8744

Regards,

Dan Gillean, MAS, MLIS
AtoM Product Manager / Systems Analyst,
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[Gomes Silva]

Hello,

I'm having a similar trouble with AtoM 2.2.0 (I already replaced mapping.yml). I'm using Elasticsearch 1.7.2 and everything went fine for months.

Today, however, some founds and digital objects did not appear, so I run php symfony search:populate && php symfony cc and everything seems fine until this error appear:

Error in one or more bulk request actions:                                                                                                                            

                                                                                                                                                                        

  index: /atom/QubitAccession/68567 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]  

                                                                                                                                                                        

                                                                                                                                                                        

PHP Fatal error:  Uncaught exception 'Elastica\Exception\Bulk\ResponseException' with message 'Error in one or more bulk request actions:

index: /atom/QubitAccession/68567 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]

' in /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Bulk.php:395

Stack trace:

#0 /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Bulk.php(345): Elastica\Bulk->_processResponse(Object(Elastica\Response))

#1 /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Client.php(284): Elastica\Bulk->send()

#2 /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Index.php(147): Elastica\Client->addDocuments(Array)

#3 /usr/share/nginx/atom/plugins/arElasticSearchPlugin/lib/arElasticSearchPlugin.class.php(113): Elastica\Index->addDocuments(Array)

#4 [internal function]: arElasticSearchPlugin->__destruct()

#5 {main}

  thrown in /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Bulk.php on line 395

Fatal error: Uncaught exception 'Elastica\Exception\Bulk\ResponseException' with message 'Error in one or more bulk request actions:

index: /atom/QubitAccession/68567 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]

' in /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Bulk.php:395

Stack trace:

#0 /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Bulk.php(345): Elastica\Bulk->_processResponse(Object(Elastica\Response))

#1 /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Client.php(284): Elastica\Bulk->send()

#2 /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Index.php(147): Elastica\Client->addDocuments(Array)

#3 /usr/share/nginx/atom/plugins/arElasticSearchPlugin/lib/arElasticSearchPlugin.class.php(113): Elastica\Index->addDocuments(Array)

#4 [internal function]: arElasticSearchPlugin->__destruct()

#5 {main}

  thrown in /usr/share/nginx/atom/vendor/Elastica/lib/Elastica/Bulk.php on line 395

Is there a fix for this? I'm using ubuntu 14.04, nginx1.8.0.

Thankyou for your support.

[Gomes Silva]

Hello,

I think I figured out what the problem was. I just had to delete the accession corresponding to this ID 68567 and now everything works fine.

I apologize for any trouble.

[Dan Gillean]

Hi Gomes,

Well, I'm glad that you got everything sorted out! Do you know what caused the issue in the first place? In any case, thanks for updating the thread.

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[Gomes Silva]

Hello,

Apparently on last Friday I imported a CSV with some accessions. I only noticed the problem when I did search:populate and ElasticSearch stopped at that  index: /atom/QubitAccession/68567 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]  message. On phpmyadmin I searched for 68567 number and found out the associated slug. Writing the slug on the URL made me able to access that accession page (it was an accession that did did not appear on Accessions list after running populate task). 

There are three ways to solve the problem:

1. Delete the accession

2. Delete the association that links the accession with the creator

3. Delete "Other form(s) of name" fields from the creator (the creator that is associated with that accession)

My conclusion is that having "Other form(s) of name" on a creator that is associated with an accession with cause problems and that's why Elasticsearch was telling us that "[otherNames] within [creators] is not allowed]".

So, to avoid this problem we simply cannot associate any "creator" with "Other form(s) of name" to an accession. Even if that field is left blank it will cause problems (the field cannot exist). I hope it was a bug, otherwise I messed up something.

[Dan Gillean]

Ahhh, thanks for clarifying, Gomes.

Yes, the CSV template for accessions in 2.2 does include new columns for creation dates, and one field for a creator name, but no otherNames column. If you want to supplement the creator's authority record, you cannot add additional columns to the Accessions CSV - AtoM simply won't know what to do with them. Instead, there are 2 ways you can do this:

1) Prepare an authority record CSV import with your creators, and import it first. Then import the accessions CSV - if the creator names match those in the authority record CSV exactly, then they should link to the imported authority records.

2) Import your accessions CSV data, and then manually supplement the related authority records via the user interface.

You will find our CSV templates, along with a change log listed for each different version, on our wiki, here:

• https://wiki.accesstomemory.org/Resources/CSV_templates

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[Gomes Silva]

Hello,

I apologize for my late reply. I believe AtoM 2.2.0 has a bug in accessions, because recently I reinstalled it in both windows and ubuntu (clean install following your instructions as always) and noticed the same issue in both cases.

What happens?

When elasticsearch (ES) starts indexing an accession that has a creator with 'otherNames' field filled, ES will stop indexing of the remaining documents and don't even index that accession (AtoM won't show on the accession list, making difficult to delete it which is one solution for that problem). Also, ES will give a message like this:

Fatal error: Uncaught exception 'Elastica\Exception\Bulk\ResponseException' with message 'Error in one or more bulk request actions:

index: /atom/QubitAccession/432 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [otherNames] within [creators] is not allowed]

How does the problem appear?

When you add "creator" and fill its "otherNames" field and add that creator to an accession.

How to avoid that problem?

Make sure there is not a single creator linked to an accession that has two "otherNames" fields and that the only "otherNames" field remaining is completely empty. Ideally a creator should have a single and empty "otherNames" field to avoid future problems.

[Dan Gillean]

Hi Gomes,

Thanks for this report. I just tested this through the user interface, and by importing a CSV (in 2.3), and I was not able to reproduce it. However, I have seen this error a couple times now in the forum, so there must be something going on. What I did:

• Create a new authority record for "John Smith" via the user interface
  
• Give the authority some data in the "Other forms of name" field - 2 alternative forms of name - Dick Clark, and Jane Doe
• Save the authority record
• Create a new accession via the user interface - add "John Smith" as the creator via the creators autocomplete drop-down

All of that worked. Next:

• Create an accessions CSV using the AtoM 2.2 accessions CSV sample on our wiki: https://wiki.accesstomemory.org/Resources/CSV_templates#AtoM_2.2_CSV_templates_2
• In the accessions CSV, add "John Smith" to the creators column; add other data as necessary
• Import the CSV

Again, that seems to have worked without any issue. Is this what you were doing as well?

I repeated these steps on our stable/2.2.x test site as well, and they worked. This either means that it is already fixed in our upcoming 2.2.1 release, or we need to identify exactly how we can reproduce it.

I will be away for the rest of the week, but if you can provide further information, I can do more testing when I return!

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[Gomes Silva]

Hello,

I repeated your procedure:

• Create a new authority record for "John Smith" via the user interface
  

• Give the authority some data in the "Other forms of name" field - 2 alternative forms of name - "Somedata", and "Somedata"
• Saved the authority record
• Created a new accession via the user interface - add "John Smith" as the creator via the creators autocomplete drop-down (I also filled the title field with "title" and filed the immediate source of acquisition field with "asd" (after saving the system also placed today's date and gave me this accession number "2016/5" -- note that my accession mask is %Y/#i)
• On terminal:
• cd /usr/share/nginx/atom
• sudo php symfony search:populate
• It gave me that same red error (I'm using AtoM 2.2.0 Ubuntu or Windows)

[Dan Gillean]

Thanks for the update, Gomes - I've been away on a work trip this week. Early next week,  I'll repeat the tests and try repopulating the index after. I will let you know what I find.

Regards,

Dan Gillean, MAS, MLIS

AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[Dan Gillean]

Gomes, I'm running out of ideas! I tried this again in our stable/2.2.x test site, as well as my local 2.3.x instance, and was unable to reproduce the issue with the steps above, even after re-indexing. Could it be that there is a bug in 2.2.0 that has been fixed in 2.2.1? Now that the 2.2.1 release is available, maybe you can upgrade?

I'm going to ask our developers if they have any further ideas. It seems strange that 2 users have reported this issue, and there definitely could be a bug - but if we can't reproduce it ourselves, we don't know how to fix it, so I'm hoping that perhaps one of our devs more familiar with ES might have some ideas.

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/7d5dcdc3-b353-475c-8194-c6df4f708dce%40googlegroups.com.

[Dan Gillean]

Hi again Gomes,

It does sound like this might be a bug that has been fixed in the 2.2.1 release, as part of this issue:

• https://projects.artefactual.com/issues/8744

See also:

• https://github.com/artefactual/atom/commit/bc9ffdf9a0b438923f17e94e9ebdc0fd7cc85a87

Sorry it's taken us so long to figure this out! I hope that upgrading will resolve this issue for you.

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

[Gomes Silva]

Dear Dan,

It seems this problem was solved in v2.2.1. The error is gone.
You and your team are doing an amazing work. Thank you very much for your support!

[Dan Gillean]

Ah, I'm so glad to hear that, Gomes! Thanks for reporting back, and for your patience as we figured this out; thank you as well for your kind words about AtoM :)

Cheers,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/343ef093-5aac-4249-bbc7-a02d6b0353b4%40googlegroups.com.

[wes...@gmail.com]

Dear, I am using Atom 2.3.1 version, and when i try "sudo php symfony search:populate" i get following error:

i suppose this is a errror in field date, but i don't know how fix it. Can you help, please??

[Dan Gillean]

Hi Wesin, 

It looks like it is possible that you have entered time values (00:00:00) into one of the controlled date fields (Start date). Currently AtoM only accepts YYYY-MM-DD values. Are you able to locate the record and remove the time data?

Regards, 

Dan Gillean, MAS, MLIS

AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[wes...@gmail.com]

Hi Dan, thanks for information.

I looked for start_data in database and i found just in 'event','object_term_relation','relation', 'rights', and 'granted-right' tables. Only 'event' table seems to have time values, but i didn't find the same format in the error ("1991-01-01 00:00:00"), i found only '0000-00-00 00:00:00' format. Before i try to update it, are there other tables that i have to look for?

[Dan Gillean]

Hi Wesin, 

Let me see if I can have one of our developers take a look at this thread and offer suggestions - I'm not a developer myself and don't want to give you bad advice! No matter what, please make sure you make a backup of your database before making changes, just in case! 

Hopefully I can get further suggestions for you soon. 

Regards, 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[sbr...@artefactual.com]

It looks like Elasticsearch is issuing that error because it is receiving a 'datetime' field from AtoM event table instead of a 'date' field as it is expecting.  In the events table, the dates and times are stored in separate fields. 

e.g.

event.start_date  (should be a 'date' type)

event.start_time  (should be a 'time' type)

Are you able to access the mysql console or have a utility like MYSQL Workbench to view the database?  If so, what is the mysql database column type for event.start_date in your database?

From the CLI you can do this by:

1) connect to mysql admin interface

  mysql -u <your_db_user> -p

2) once you've entered your password and are on the mysql admin console, select your atom database:

  use <your_db_name>;

3) get your table details:

  describe event;

You should see a table displayed like the following - I have highlighted the start_date column - it should be a 'date' type:

mysql> describe event;
+----------------+------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+----------------+------------+------+-----+---------+-------+
| id | int(11) | NO | PRI | NULL | |
| start_date | date | YES | | NULL | |
| start_time | time | YES | | NULL | |
| end_date | date | YES | | NULL | |
| end_time | time | YES | | NULL | |
| type_id | int(11) | NO | MUL | NULL | |
| object_id | int(11) | YES | MUL | NULL | |
| actor_id | int(11) | YES | MUL | NULL | |
| source_culture | varchar(7) | NO | | NULL | |
+----------------+------------+------+-----+---------+-------+
9 rows in set (0.00 sec)



Steve
 

[wes...@gmail.com]

Hi Steve, my event table looks like this:

Start_date is a datetime filed. I am replacing a another developer in this job, so i don't know why it is a datetime field.

Do i need change it to date field?

Hello,

<blockquote class="gmail_quote" style="ma

[sbr...@artefactual.com]

Hello!

Yes, the column 'start_date' should be a 'date' type in mysql.  That is strange!

After you update that column type, you can try running search:populate again.  I would also test that you can successfully add/modify event dates on an archival description.

Steve

Hello,

Dan Gillean, MAS, MLIS

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