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placeholder repo for issues migrating from JIRA system, to be moved to their appropriate places later
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CMap links have vanished from QTL pages #456

Closed adf-ncgr closed 8 years ago

adf-ncgr commented 8 years ago

[LEGUME-489] created by ecannon

adf-ncgr commented 8 years ago

not sure this is related, but in case it helps, I happened to notice this error displayed on
lis-dev/feature/Phaseolus/vulgaris/QTL/phavu.Root-length-2-3#pane=map_position

Notice: Undefined property: stdClass::$map_id in makeMapLink() (line 242 of /usr/local/www/drupal7/sites/all/modules/legume/legume_qtl/legume_qtl.module).
Notice: Undefined property: stdClass::$map_id in makeMapLink() (line 242 of /usr/local/www/drupal7/sites/all/modules/legume/legume_qtl/legume_qtl.module).
Notice: Undefined property: stdClass::$comments in include() (line 54 of /usr/local/www/drupal7/sites/all/modules/legume/legume_qtl/theme/templates/tripal_feature_QTL_base.tpl.php).
Notice: Undefined property: stdClass::$map_id in makeMapLink() (line 242 of /usr/local/www/drupal7/sites/all/modules/legume/legume_qtl/legume_qtl.module).
Notice: Undefined property: stdClass::$map_id in makeMapLink() (line 242 of /usr/local/www/drupal7/sites/all/modules/legume/legume_qtl/legume_qtl.module).
Notice: Undefined property: stdClass::$comments in include() (line 54 of /usr/local/www/drupal7/sites/all/modules/legume/legume_qtl/theme/templates/tripal_feature_QTL_base.tpl.php).
Notice: Undefined property: stdClass::$map_id in makeMapLink() (line 242 of /usr/local/www/drupal7/sites/all/modules/legume/legume_qtl/legume_qtl.module).
Notice: Undefined property: stdClass::$map_id in makeMapLink() (line 242 of /usr/local/www/drupal7/sites/all/modules/legume/legume_qtl/legume_qtl.module).

by adf_ncgr

adf-ncgr commented 8 years ago

NB: the aforementioned errors don't appear on lis-stage.
I did just notice that there are two active views defined for QTL, both using the same path, one in code and the other
database overriding code. Not sure that is causing any of these problems, but it seems unlikely to be a good thing:

this seems to be the same on all three servers (dev,stage,prod)

by adf_ncgr

adf-ncgr commented 8 years ago

OK, you probably already knew this, but I guess it is an issue with the database. Seems the materialized view isn't
picking up values for lis_map_accession or lis_lg_map_accession due to the absence of any appropriate dbxrefs pointing
to the db with name=LIS:cmap

so, presumably a loader issue? We didn't think reloading had been done of this data between BIC/NAPIA and now,
but perhaps we just missed it. Might be able to bulk-sql-insert them based on naming conventions but I'm loathe to confuse things further
without the go-ahead of the developer who knows how this is all supposed to work (though I do a pretty good imitation
of a bull in a china shop on occasion!).

will wait to hear further...

by adf_ncgr

adf-ncgr commented 8 years ago

Repopulating the MViews fixed the missing CMap links for PeanutBase.

There are no CMap links for the bean QTL in LegumeInfo because the data doesn't exist. Will need to check and possibly reload the original spreadsheets or fix by hand.

Also fixed notices and warnings, but they were not related to the problem.

by ecannon

adf-ncgr commented 8 years ago

Added CMap dbxref records and links for PvConsensus_GaleanoFernandez2011_a and BAT93_x_JALOEEP558_b and repopulated qtl_map_position. CMap links are now showing where they should.

by ecannon