Tripal upgrade to 2.1 trial at LIS

[adf-ncgr]

Task: Upgrade Tripal from 2.0 to 2.1 as a trial at LIS. Also upgrade Chado from 1.2 to 1.3.
The sandbox for the purpose is at lis-chado-update.

Instructions at: http://tripal.info/tutorials/v2.x/upgrade_2.0_to_2.1

[LEGUME-710] created by sdash-legume

[adf-ncgr]

The following steps for Tripal has already been done at the sandbox:

1. Site backup: pgdump of drupal on 20170719
2. Tripal 7.x-2.1 downloaded
3. Tripal update applied
4. Site renabled
5. Upgraded Extension Modules (pm-update, updatedb)
6. Site checked-- OK (not detailed check)
Next TO DO: Chado upgrade

by sdash-legume

[adf-ncgr]

Chado Upgrade Issues

1. Postgres version : Not an issue in our case.

2. ?? If your site has custom materialized views: change to bigint:
Couldn’t find out, with certainty, any mat-views. (select relname from pg_class where relkind='v'

Identify and alter the views to change the fields from integers to big integers and repopulate those views.

3. **Custom PL/pgSQL functions: change to bigint:
LIS chado has many functions (\df chado.*). So, need to identify the custom functions.
Those functions will need to be altered to accept big integers.

4.** PostgreSQL Views: change to bigint:
[LIS has many views: Needs to remove those views; upgrade; then recreate those views with change to bigint. Need to sequester the custom views ]

5. ** ?? Do we have Chado 1.3 tables added to our Chado v1.2 installation.:
--Find out if we have these tables added
(PB has some of these.)

Next: Ask Andrew and Ethy, if they are aware of any of the above items at LIS

by sdash-legume

[adf-ncgr]

Questions for Andrew and Ethy

Are you aware of any at LIS of the following items. If so please list as many as you can remember or find out. (CUSTOM is the key here).
1. Custom Tripal Materialized views
2. Custom PL/pgSQL functions
3. Custom PostgreSQL Views
4. Chado 1.3 Tables in our LIS Chado 1.2 (like PB has some)

We will find some of these in other ways but want to verify if our method identies the ones you list.
Thanks.
Assigning to Ethy now.

by sdash-legume

[adf-ncgr]

1. Custom Tripal Materialized views
qtl_search, qtl_map_pos, marker_search, gene2domain, gene, domain, tree2domain, phylotree_count

2. Custom PL/pgSQL functions
One or more of these may have been changed (but no record of which, if any; repairs were likely all in Tripal code, not these functions) _fill_cvtermpath4node, _fill_cvtermpath4root, fill_cvtermpath(INTEGER), fill_cvtermpath(cv.name%TYPE)

3. Custom PostgreSQL Views
None

4. Chado 1.3 Tables in our LIS Chado 1.2
new tables: stock_eimage, analysis_dbxref, project_analysis, project_dbxref, featurelocprop, featuremapprop, featuremap_dbxref, featuremap_stock, featureposprop, feature_project, feature_stock, stock_organism

by ecannon

[adf-ncgr]

Assigning to Andrew.
Please add to the list Ethy has started above(please see the above comments).

by sdash-legume

[adf-ncgr]

I've generated diffs between lists of tables and views defined in the chado distribution
/opt/chado/1.23+/src/chado/modules/complete.sql
and our legumeinfo db at:
~adf/chado_distro_vs_legumeinfo

see tables.diffs and views.diffs for results, notes file shows process used to generate

there's some overlap with what Ethy has listed, but also some discrepancies. note that if any tables
have had columns added or changes to their definitions, this method won't account for it.

Note that this ignores tables in the public schema which are either drupal or added by tripal or other tools;
a few that catch my eye from \dt public.*:
gene_family_assignment
gene_order
(both used by GCV)
gff_sort_tmp
tmp_gff_load_cache
(perl loader tables I think, but I also think they will get recreated by the loader everytime you use it, so probably not needing any changes)

chado_gene (not stock tripal, IIRC)

let me know if you have questions- it's not exactly clear to me what the upgrade process does, so not sure how
superfluous these lists may be, but figured it might be worth attempting such a list of diffs using some marginal
attempt at being methodical - if nothing else, it might trigger some further memories...

by adf_ncgr

[adf-ncgr]

After discussion with Andrew:
I will be away for a month. Can be be assigned to somebody else to continue tackling the issue from here. Andrew will assign it to specific individuals.

by sdash-legume

[adf-ncgr]

thanks, was hoping this might be something Malachy O'Connell could take on, but didn't want to presume to assign it without discussion; note that Sudhansu was working in a dedicated VM that Nathan set up for this purpose, so maybe you can ask Nathan to give you access if you don't already have it; relevant info from him:

OK, I've created a sandbox (hostname "lis-chado-update") accessible at

127.0.0.14 after tunneling into one of the other sites. Home

directories for Andrew, Connor, Sudhansu, and Ethy are mounted in this

instance.

by adf_ncgr