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placeholder repo for issues migrating from JIRA system, to be moved to their appropriate places later
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analysis for phylotree #57

Closed adf-ncgr closed 9 years ago

adf-ncgr commented 9 years ago

this probably reflects my ignorance of tripal more than anything else, but putting it as an issue so as not to forget. In lis-adf (my sandbox dev) I added an analysis row for the phytozome-derived gene families, and linked it to all the trees. I expected that it would show up via the Analysis TOC (is that the correct term?) but it did not (even after syncing the new Analysis row).
Probably something I haven't seen yet, so just noting here so as not to lose track.

[LEGUME-89] created by adf_ncgr

adf-ncgr commented 9 years ago

just noticed that my db update was applied to lis-dev instead of lis-adf. Probably no real harm done,
although now that I've applied it both places, it still hasn't made the analysis info appear in the TOC,
and we are now getting some nasties from drupal in the phylotree display:

Warning: Invalid argument supplied for foreach() in element_children() (line 6433 of /usr/local/www/drupal7/includes/common.inc).
Warning: Illegal string offset '#children' in drupal_render() (line 5898 of /usr/local/www/drupal7/includes/common.inc).
Warning: Illegal string offset '#children' in drupal_render() (line 5908 of /usr/local/www/drupal7/includes/common.inc).
Warning: Illegal string offset '#children' in drupal_render() (line 5946 of /usr/local/www/drupal7/includes/common.inc).
Warning: Illegal string offset '#printed' in drupal_render() (line 5953 of /usr/local/www/drupal7/includes/common.inc).
Warning: Invalid argument supplied for foreach() in element_children() (line 6433 of /usr/local/www/drupal7/includes/common.inc).
Warning: Illegal string offset '#children' in drupal_render() (line 5898 of /usr/local/www/drupal7/includes/common.inc).
Warning: Illegal string offset '#children' in drupal_render() (line 5908 of /usr/local/www/drupal7/includes/common.inc).
Warning: Illegal string offset '#children' in drupal_render() (line 5946 of /usr/local/www/drupal7/includes/common.inc).
Warning: Illegal string offset '#printed' in drupal_render() (line 5953 of /usr/local/www/drupal7/includes/common.inc).

hopefully, this will be the grist of a good learning experience for me...

by adf_ncgr

adf-ncgr commented 9 years ago

turns out that analysis.description is not retrieved by default, but must be accessed via a call to expand_vars (or similar). The drupal nasties appear to have been due to an incorrect level of nesting of arrays in the representation of the analysis row data in the template file.

by adf_ncgr