What's the magic sauce (if any) to get other superusers (not 100000) to tag templates for home page aspects???

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What's the magic sauce (if any) to get other superusers (not 100000) to tag templates for home page aspects???

Sam Hokin-3
This is clearly a bug, but I wonder if anyone has come across it.

If I (user 1000000, the initial superuser on the mine) tag a template with, say, im:aspect:genetics (one of my home page tabs), it
shows up as it should.

If another superuser (like Andrew, 4000000 on SoyMine, or another of my emails, 22000076 on SoyMine) tags a template like that, it
does NOT show up on the home page tabs.

What gives? Here's all the tags. ONLY the im:aspect:* tagged objects associated with user 1000000 actually show up on the front end
where they should.

     id    |          objectidentifier          |    type    |        tagname         | userprofileid
----------+------------------------------------+------------+------------------------+---------------
  18000021 | expression_gene                    | template   | im:aspect:expression   |       1000000
  22000057 | goterm_proteins                    | template   | im:aspect:function     |       1000000
  18000008 | goterm_genes                       | template   | im:aspect:function     |       1000000
  18000011 | toterm_qtl                         | template   | im:aspect:genetics     |       1000000
  18000016 | name_publication                   | template   | im:aspect:publications |       1000000
   1000004 | bioentity.relations                | collection | im:hidden              |       1000000
   1000003 | bioentity.objects                  | collection | im:hidden              |       1000000
   1000015 | bioentity.subjects                 | collection | im:hidden              |       1000000
   1000010 | evidence.relations                 | collection | im:hidden              |       1000000
  18000003 | goterm_genes                       | template   | im:public              |       1000000
  18000010 | toterm_qtl                         | template   | im:public              |       1000000
  18000015 | name_publication                   | template   | im:public              |       1000000
   1000007 | gotermidentifier_name              | template   | im:public              |       1000000
   1000002 | gene_particulargoannotation        | template   | im:public              |       1000000
   1000008 | gene_allgoterms                    | template   | im:public              |       1000000
   1000011 | gene_identifiers                   | template   | im:public              |       1000000
   1000013 | gene_go                            | template   | im:public              |       1000000
   1000017 | organism_goterm_gene               | template   | im:public              |       1000000
   1000019 | organism_goterm_genewithannotation | template   | im:public              |       1000000
  14000004 | genetic maps                       | bag        | im:public              |       1000000
  14000006 | qtls                               | bag        | im:public              |       1000000
  18000020 | expression_gene                    | template   | im:public              |       1000000
  19000002 | goterm_proteins                    | template   | im:public              |       1000000
   1000001 | gene.publications                  | collection | im:summary             |       1000000
   1000018 | bioentity.organism                 | reference  | im:summary             |       1000000
   1000006 | bioentity.synonyms                 | collection | im:summary             |       1000000
  22000008 | soybean_soybean_homologues         | template   | im:aspect:comparison   |       4000000
  22000042 | gene_homologues                    | template   | im:aspect:comparison   |       4000000
  22000046 | gene_goterms                       | template   | im:aspect:function     |       4000000
  22000072 | Gene_GOTerms                       | template   | im:aspect:function     |       4000000
  22000038 | gene_transcripts                   | template   | im:aspect:geneProducts |       4000000
  22000022 | region_gwas_qtl                    | template   | im:aspect:genomics     |       4000000
  22000032 | region_markers                     | template   | im:aspect:genomics     |       4000000
  22000018 | gene_proteins                      | template   | im:aspect:genomics     |       4000000
  22000074 | Gene_GOTerms                       | template   | im:frontpage           |       4000000
  22000045 | gene_goterms                       | template   | im:public              |       4000000
  22000017 | gene_proteins                      | template   | im:public              |       4000000
  22000006 | soybean_soybean_homologues         | template   | im:public              |       4000000
  22000073 | Gene_GOTerms                       | template   | im:public              |       4000000
  22000031 | region_markers                     | template   | im:public              |       4000000
  22000037 | gene_transcripts                   | template   | im:public              |       4000000
  22000041 | gene_homologues                    | template   | im:public              |       4000000
  22000021 | region_gwas_qtl                    | template   | im:public              |       4000000
  22000075 | Gene_GOTerms                       | template   | im:report              |       4000000
  23000003 | gene_description_match             | template   | im:aspect:genomics     |      22000076
  23000002 | gene_description_match             | template   | im:public              |      22000076
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Re: What's the magic sauce (if any) to get other superusers (not 100000) to tag templates for home page aspects???

Paulo Nuin
I have some ideas on that, and similar problems. I will get back to you when I am on my desk

Paulo

Sent from my iPhone

> On Aug 6, 2018, at 14:52, Sam Hokin <[hidden email]> wrote:
>
> This is clearly a bug, but I wonder if anyone has come across it.
>
> If I (user 1000000, the initial superuser on the mine) tag a template with, say, im:aspect:genetics (one of my home page tabs), it shows up as it should.
>
> If another superuser (like Andrew, 4000000 on SoyMine, or another of my emails, 22000076 on SoyMine) tags a template like that, it does NOT show up on the home page tabs.
>
> What gives? Here's all the tags. ONLY the im:aspect:* tagged objects associated with user 1000000 actually show up on the front end where they should.
>
>    id    |          objectidentifier          |    type    |        tagname         | userprofileid
> ----------+------------------------------------+------------+------------------------+---------------
> 18000021 | expression_gene                    | template   | im:aspect:expression   |       1000000
> 22000057 | goterm_proteins                    | template   | im:aspect:function     |       1000000
> 18000008 | goterm_genes                       | template   | im:aspect:function     |       1000000
> 18000011 | toterm_qtl                         | template   | im:aspect:genetics     |       1000000
> 18000016 | name_publication                   | template   | im:aspect:publications |       1000000
>  1000004 | bioentity.relations                | collection | im:hidden              |       1000000
>  1000003 | bioentity.objects                  | collection | im:hidden              |       1000000
>  1000015 | bioentity.subjects                 | collection | im:hidden              |       1000000
>  1000010 | evidence.relations                 | collection | im:hidden              |       1000000
> 18000003 | goterm_genes                       | template   | im:public              |       1000000
> 18000010 | toterm_qtl                         | template   | im:public              |       1000000
> 18000015 | name_publication                   | template   | im:public              |       1000000
>  1000007 | gotermidentifier_name              | template   | im:public              |       1000000
>  1000002 | gene_particulargoannotation        | template   | im:public              |       1000000
>  1000008 | gene_allgoterms                    | template   | im:public              |       1000000
>  1000011 | gene_identifiers                   | template   | im:public              |       1000000
>  1000013 | gene_go                            | template   | im:public              |       1000000
>  1000017 | organism_goterm_gene               | template   | im:public              |       1000000
>  1000019 | organism_goterm_genewithannotation | template   | im:public              |       1000000
> 14000004 | genetic maps                       | bag        | im:public              |       1000000
> 14000006 | qtls                               | bag        | im:public              |       1000000
> 18000020 | expression_gene                    | template   | im:public              |       1000000
> 19000002 | goterm_proteins                    | template   | im:public              |       1000000
>  1000001 | gene.publications                  | collection | im:summary             |       1000000
>  1000018 | bioentity.organism                 | reference  | im:summary             |       1000000
>  1000006 | bioentity.synonyms                 | collection | im:summary             |       1000000
> 22000008 | soybean_soybean_homologues         | template   | im:aspect:comparison   |       4000000
> 22000042 | gene_homologues                    | template   | im:aspect:comparison   |       4000000
> 22000046 | gene_goterms                       | template   | im:aspect:function     |       4000000
> 22000072 | Gene_GOTerms                       | template   | im:aspect:function     |       4000000
> 22000038 | gene_transcripts                   | template   | im:aspect:geneProducts |       4000000
> 22000022 | region_gwas_qtl                    | template   | im:aspect:genomics     |       4000000
> 22000032 | region_markers                     | template   | im:aspect:genomics     |       4000000
> 22000018 | gene_proteins                      | template   | im:aspect:genomics     |       4000000
> 22000074 | Gene_GOTerms                       | template   | im:frontpage           |       4000000
> 22000045 | gene_goterms                       | template   | im:public              |       4000000
> 22000017 | gene_proteins                      | template   | im:public              |       4000000
> 22000006 | soybean_soybean_homologues         | template   | im:public              |       4000000
> 22000073 | Gene_GOTerms                       | template   | im:public              |       4000000
> 22000031 | region_markers                     | template   | im:public              |       4000000
> 22000037 | gene_transcripts                   | template   | im:public              |       4000000
> 22000041 | gene_homologues                    | template   | im:public              |       4000000
> 22000021 | region_gwas_qtl                    | template   | im:public              |       4000000
> 22000075 | Gene_GOTerms                       | template   | im:report              |       4000000
> 23000003 | gene_description_match             | template   | im:aspect:genomics     |      22000076
> 23000002 | gene_description_match             | template   | im:public              |      22000076
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Re: What's the magic sauce (if any) to get other superusers (not 100000) to tag templates for home page aspects???

Paulo Nuin
In reply to this post by Sam Hokin-3
Hi Sam

This definitely a bug and we are having problems with this for a long time, but I was never able to get some traction for a full fix. Basically in our case templates that are tagged by someone that not the “super” superuser don’t show in the main page tabs.

We have tried everything possible, from changing the template in the back end, deleting the templates from the “super” superuser and add identical templates and tags to another superuser, and nothing worked. The only thing missing in our tests was to modify the superuser in the configuration file and try again.

Our plan was to have a “generic” superuser that curators and devs would be able to access and modify templates here and there. I tried everything of the above with a complete new superuser and even with identical templates and tags they never appeared on the front page.

The latest solution provide by Julie was this (I haven’t tested yet)

"Is the other older superuser still marked as a superuser?

That code on the front page is likely still looking at the old superuser account given you were able to see its template.

For a quick fix, make that superuser not a superuser. You can toggle superusers on the UI (but maybe not the original superuser?) or edit directly in the database.

        userprofile.superuser = false

PLEASE PLEASE make backups first!”

Seems like a hack, and as I said, not tested.

Cheers
Paulo




> On Aug 6, 2018, at 2:52 PM, Sam Hokin <[hidden email]> wrote:
>
> This is clearly a bug, but I wonder if anyone has come across it.
>
> If I (user 1000000, the initial superuser on the mine) tag a template with, say, im:aspect:genetics (one of my home page tabs), it shows up as it should.
>
> If another superuser (like Andrew, 4000000 on SoyMine, or another of my emails, 22000076 on SoyMine) tags a template like that, it does NOT show up on the home page tabs.
>
> What gives? Here's all the tags. ONLY the im:aspect:* tagged objects associated with user 1000000 actually show up on the front end where they should.
>
>    id    |          objectidentifier          |    type    |        tagname         | userprofileid
> ----------+------------------------------------+------------+------------------------+---------------
> 18000021 | expression_gene                    | template   | im:aspect:expression   |       1000000
> 22000057 | goterm_proteins                    | template   | im:aspect:function     |       1000000
> 18000008 | goterm_genes                       | template   | im:aspect:function     |       1000000
> 18000011 | toterm_qtl                         | template   | im:aspect:genetics     |       1000000
> 18000016 | name_publication                   | template   | im:aspect:publications |       1000000
>  1000004 | bioentity.relations                | collection | im:hidden              |       1000000
>  1000003 | bioentity.objects                  | collection | im:hidden              |       1000000
>  1000015 | bioentity.subjects                 | collection | im:hidden              |       1000000
>  1000010 | evidence.relations                 | collection | im:hidden              |       1000000
> 18000003 | goterm_genes                       | template   | im:public              |       1000000
> 18000010 | toterm_qtl                         | template   | im:public              |       1000000
> 18000015 | name_publication                   | template   | im:public              |       1000000
>  1000007 | gotermidentifier_name              | template   | im:public              |       1000000
>  1000002 | gene_particulargoannotation        | template   | im:public              |       1000000
>  1000008 | gene_allgoterms                    | template   | im:public              |       1000000
>  1000011 | gene_identifiers                   | template   | im:public              |       1000000
>  1000013 | gene_go                            | template   | im:public              |       1000000
>  1000017 | organism_goterm_gene               | template   | im:public              |       1000000
>  1000019 | organism_goterm_genewithannotation | template   | im:public              |       1000000
> 14000004 | genetic maps                       | bag        | im:public              |       1000000
> 14000006 | qtls                               | bag        | im:public              |       1000000
> 18000020 | expression_gene                    | template   | im:public              |       1000000
> 19000002 | goterm_proteins                    | template   | im:public              |       1000000
>  1000001 | gene.publications                  | collection | im:summary             |       1000000
>  1000018 | bioentity.organism                 | reference  | im:summary             |       1000000
>  1000006 | bioentity.synonyms                 | collection | im:summary             |       1000000
> 22000008 | soybean_soybean_homologues         | template   | im:aspect:comparison   |       4000000
> 22000042 | gene_homologues                    | template   | im:aspect:comparison   |       4000000
> 22000046 | gene_goterms                       | template   | im:aspect:function     |       4000000
> 22000072 | Gene_GOTerms                       | template   | im:aspect:function     |       4000000
> 22000038 | gene_transcripts                   | template   | im:aspect:geneProducts |       4000000
> 22000022 | region_gwas_qtl                    | template   | im:aspect:genomics     |       4000000
> 22000032 | region_markers                     | template   | im:aspect:genomics     |       4000000
> 22000018 | gene_proteins                      | template   | im:aspect:genomics     |       4000000
> 22000074 | Gene_GOTerms                       | template   | im:frontpage           |       4000000
> 22000045 | gene_goterms                       | template   | im:public              |       4000000
> 22000017 | gene_proteins                      | template   | im:public              |       4000000
> 22000006 | soybean_soybean_homologues         | template   | im:public              |       4000000
> 22000073 | Gene_GOTerms                       | template   | im:public              |       4000000
> 22000031 | region_markers                     | template   | im:public              |       4000000
> 22000037 | gene_transcripts                   | template   | im:public              |       4000000
> 22000041 | gene_homologues                    | template   | im:public              |       4000000
> 22000021 | region_gwas_qtl                    | template   | im:public              |       4000000
> 22000075 | Gene_GOTerms                       | template   | im:report              |       4000000
> 23000003 | gene_description_match             | template   | im:aspect:genomics     |      22000076
> 23000002 | gene_description_match             | template   | im:public              |      22000076
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Re: What's the magic sauce (if any) to get other superusers (not 100000) to tag templates for home page aspects???

Julie Sullivan-2
In reply to this post by Sam Hokin-3
Related to this I think:

https://github.com/intermine/intermine/issues/701

Basically the home page is looking at the initial super user only for
templates.

On 06/08/18 21:52, Sam Hokin wrote:

> This is clearly a bug, but I wonder if anyone has come across it.
>
> If I (user 1000000, the initial superuser on the mine) tag a template
> with, say, im:aspect:genetics (one of my home page tabs), it shows up as
> it should.
>
> If another superuser (like Andrew, 4000000 on SoyMine, or another of my
> emails, 22000076 on SoyMine) tags a template like that, it does NOT show
> up on the home page tabs.
>
> What gives? Here's all the tags. ONLY the im:aspect:* tagged objects
> associated with user 1000000 actually show up on the front end where
> they should.
>
>      id    |          objectidentifier          |    type    |        
> tagname         | userprofileid
> ----------+------------------------------------+------------+------------------------+---------------
>
>   18000021 | expression_gene                    | template   |
> im:aspect:expression   |       1000000
>   22000057 | goterm_proteins                    | template   |
> im:aspect:function     |       1000000
>   18000008 | goterm_genes                       | template   |
> im:aspect:function     |       1000000
>   18000011 | toterm_qtl                         | template   |
> im:aspect:genetics     |       1000000
>   18000016 | name_publication                   | template   |
> im:aspect:publications |       1000000
>    1000004 | bioentity.relations                | collection |
> im:hidden              |       1000000
>    1000003 | bioentity.objects                  | collection |
> im:hidden              |       1000000
>    1000015 | bioentity.subjects                 | collection |
> im:hidden              |       1000000
>    1000010 | evidence.relations                 | collection |
> im:hidden              |       1000000
>   18000003 | goterm_genes                       | template   |
> im:public              |       1000000
>   18000010 | toterm_qtl                         | template   |
> im:public              |       1000000
>   18000015 | name_publication                   | template   |
> im:public              |       1000000
>    1000007 | gotermidentifier_name              | template   |
> im:public              |       1000000
>    1000002 | gene_particulargoannotation        | template   |
> im:public              |       1000000
>    1000008 | gene_allgoterms                    | template   |
> im:public              |       1000000
>    1000011 | gene_identifiers                   | template   |
> im:public              |       1000000
>    1000013 | gene_go                            | template   |
> im:public              |       1000000
>    1000017 | organism_goterm_gene               | template   |
> im:public              |       1000000
>    1000019 | organism_goterm_genewithannotation | template   |
> im:public              |       1000000
>   14000004 | genetic maps                       | bag        |
> im:public              |       1000000
>   14000006 | qtls                               | bag        |
> im:public              |       1000000
>   18000020 | expression_gene                    | template   |
> im:public              |       1000000
>   19000002 | goterm_proteins                    | template   |
> im:public              |       1000000
>    1000001 | gene.publications                  | collection |
> im:summary             |       1000000
>    1000018 | bioentity.organism                 | reference  |
> im:summary             |       1000000
>    1000006 | bioentity.synonyms                 | collection |
> im:summary             |       1000000
>   22000008 | soybean_soybean_homologues         | template   |
> im:aspect:comparison   |       4000000
>   22000042 | gene_homologues                    | template   |
> im:aspect:comparison   |       4000000
>   22000046 | gene_goterms                       | template   |
> im:aspect:function     |       4000000
>   22000072 | Gene_GOTerms                       | template   |
> im:aspect:function     |       4000000
>   22000038 | gene_transcripts                   | template   |
> im:aspect:geneProducts |       4000000
>   22000022 | region_gwas_qtl                    | template   |
> im:aspect:genomics     |       4000000
>   22000032 | region_markers                     | template   |
> im:aspect:genomics     |       4000000
>   22000018 | gene_proteins                      | template   |
> im:aspect:genomics     |       4000000
>   22000074 | Gene_GOTerms                       | template   |
> im:frontpage           |       4000000
>   22000045 | gene_goterms                       | template   |
> im:public              |       4000000
>   22000017 | gene_proteins                      | template   |
> im:public              |       4000000
>   22000006 | soybean_soybean_homologues         | template   |
> im:public              |       4000000
>   22000073 | Gene_GOTerms                       | template   |
> im:public              |       4000000
>   22000031 | region_markers                     | template   |
> im:public              |       4000000
>   22000037 | gene_transcripts                   | template   |
> im:public              |       4000000
>   22000041 | gene_homologues                    | template   |
> im:public              |       4000000
>   22000021 | region_gwas_qtl                    | template   |
> im:public              |       4000000
>   22000075 | Gene_GOTerms                       | template   |
> im:report              |       4000000
>   23000003 | gene_description_match             | template   |
> im:aspect:genomics     |      22000076
>   23000002 | gene_description_match             | template   |
> im:public              |      22000076
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Re: What's the magic sauce (if any) to get other superusers (not 100000) to tag templates for home page aspects???

Sam Hokin-3
Ah, indeed, I hadn't searched for the issue. +1 I guess I'll start digging into the code.... And thanks, Paulo!

On 08/07/2018 01:01 AM, Julie Sullivan wrote:
> Related to this I think:
>
> https://github.com/intermine/intermine/issues/701
>
> Basically the home page is looking at the initial super user only for templates.
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Re: What's the magic sauce (if any) to get other superusers (not 100000) to tag templates for home page aspects???

Sam Hokin-3
OK, so it turns out that ALL of template/tag code is built around a SINGLE superuser. There is no easily-updateable way of
implementing multiple superuser support. Here's an obvious tell:

im.getProfileManager().getSuperuserProfile()

That's one profile. Not many. That's used throughout.

I think to make this clearer in the future, InterMine should only allow creation of a single (initial) superuser, which happens
during the userprofileDB build, so there should NOT be a checkbox to make users superusers on the UI. Anyone you tag as being a
super user is a superuser in name only and does NOT have working superuser functions. A mine really has only one superuser, the
initial one, presumably with an id of 1000001. That's it.

On 08/07/2018 06:39 AM, Sam Hokin wrote:
> Ah, indeed, I hadn't searched for the issue. +1 I guess I'll start digging into the code.... And thanks, Paulo!
>
> On 08/07/2018 01:01 AM, Julie Sullivan wrote:
>> Related to this I think:
>>
>> https://github.com/intermine/intermine/issues/701
>>
>> Basically the home page is looking at the initial super user only for templates.
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Re: What's the magic sauce (if any) to get other superusers (not 100000) to tag templates for home page aspects???

Paulo Nuin
I would have advocated for a “super” superuser, and maybe have an easy solution to modify this superuser as people move from the project, or are not involved in different aspects of the mine. That would make management better in the future.

Paulo

> On Aug 8, 2018, at 10:35 AM, Sam Hokin <[hidden email]> wrote:
>
> OK, so it turns out that ALL of template/tag code is built around a SINGLE superuser. There is no easily-updateable way of implementing multiple superuser support. Here's an obvious tell:
>
> im.getProfileManager().getSuperuserProfile()
>
> That's one profile. Not many. That's used throughout.
>
> I think to make this clearer in the future, InterMine should only allow creation of a single (initial) superuser, which happens during the userprofileDB build, so there should NOT be a checkbox to make users superusers on the UI. Anyone you tag as being a super user is a superuser in name only and does NOT have working superuser functions. A mine really has only one superuser, the initial one, presumably with an id of 1000001. That's it.
>
> On 08/07/2018 06:39 AM, Sam Hokin wrote:
>> Ah, indeed, I hadn't searched for the issue. +1 I guess I'll start digging into the code.... And thanks, Paulo!
>> On 08/07/2018 01:01 AM, Julie Sullivan wrote:
>>> Related to this I think:
>>>
>>> https://github.com/intermine/intermine/issues/701
>>>
>>> Basically the home page is looking at the initial super user only for templates.
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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