loading chinese chestnut genetic map

[bradfordcondon]

• [x] create dev

• [ ] create live

Separating this from #234 since its not the same issue.

Abstract to summarize:

Two mapping populations were established with three Chinese chestnut parents, ‘Mahogany’, ‘Nanking’, and ‘Vanuxem’, totaling 337 progeny. The transcriptome-based genetic map was created with 329 simple sequence repeat and 1,064 single nucleotide polymorphism markers all derived from expressed sequence tag sequences. Genetic maps for each parent were developed and combined to establish 12 consensus linkage groups spanning 742 cM.

We don't have featuremap_organism loaded in our chado for some reason. It's defined in chado v1.3....

In theory the tripal_manage_analyses module provides the organism linker, and the cmap linker, ot make this work.

All (hah) that needs to be created is the front end component that reads in the cmap.js file.

cmap file here.

map publication

[bradfordcondon]

adding publication:

• identifier. it needs a unique identifier for some reason. let's juse use the DOI.
• If publication type is only null, you need to run cvtermpath update for tripal_pub.

Creating pubs is a bit of a pain... we should delete some of the fields we dont care about to simplify this page.

[bradfordcondon]

now that featuremap_organism #268 is on dev we can move forward.

[bradfordcondon]

Map is loaded at http://160.36.205.61:8095/Map/2288669

cmap file loaded to sites/default/files/cmap/c_mollissima/c_moll_kubisiak_2013_cmap.csv

• publication created and linked
• organism linked (obi__organism field from tripal_manage_analyses)
• map linker field displays map on organism (from tripal_cmap_loader)
• description contains download link

[bradfordcondon]

<a name="download"></a><h5 class="mb-4">Download Map Data</h4>
<table class="table table-valign-middle table-sm table-hover">
  <tbody>
  <tr class="no-border">
    <td class="text-muted download-td"><i class="fa fa-file-text-o"></i></td>
    <th>
      <div>
        <a class="text-sm text-muted font-normal" href="/sites/default/files/cmap/c_mollissima/c_moll_kubisiak_2013_cmap.csv">c_moll_kubisiak_2013_cmap.csv</a>
      </div>
    </th>
    <td class="text-right"><a href="/sites/default/files/cmap/c_mollissima/c_moll_kubisiak_2013_cmap.csv" class="btn btn-primary"><i class="fa fa-download"></i></a></td>
  </tr>
  </tbody>
</table>

[bradfordcondon]

This requires https://github.com/statonlab/hardwoods_site/issues/234 to be resolved. Then we can either further load the map into chado and/or create a viewer field for it...

Otherwise I consider this finished, so ill repeat on live.

[bradfordcondon]

Live tasks

https://www.hardwoodgenomics.org/Map/2192028

(physical map here: https://www.hardwoodgenomics.org/Map/2209425 #269 )

• [x] Create map

• [x] Copy raw file to server

• [x] Add pub

• [x] Link pub

• [ ] Install organism linker field

• [x] Link map

[bradfordcondon]

Get this error when linking pub on live.

Could not save the entity: SQLSTATE[25P02]: In failed sql transaction: 7 ERROR: current transaction is aborted, commands ignored until end of transaction block
Cannot save entity

[bradfordcondon]

loading publications: I upgraded lacey's loader to be Tripal 3 compatible. You can now drush cli bibtex. its a little finicky on formatting but it will make adding publications MUCH less tedious.

[bradfordcondon]

Reviewed in meeting. We're happy with this format, although we'd like some nicer publication links: #288

[bradfordcondon]

This error on live preventing enabling map linker field.

https://github.com/statonlab/tripal_manage_analyses/issues/36

[bradfordcondon]

ok. so deleting fields isnt working right, so this was throwing a wrench. I was updating the field, deleting it, and reattaching.. but seeing no changes!

need to remmeber to use the drush command for now: drush field-delete obi__organism_linker

i made changes to the field which affects a few bundles, so lets readd them eveyrwhere:

live:

 [2]  :  bio_data_2
 [3]  :  bio_data_21
 [4]  :  bio_data_20

dev:

 [2]  :  bio_data_27
 [3]  :  bio_data_2
 [4]  :  bio_data_21
 [5]  :  bio_data_20

[bradfordcondon]

oops! we need the chado 1.3 on live for this to work!!!!

https://github.com/statonlab/hardwoods_site/issues/268

[bradfordcondon]

note: you can import hte pub via drush trp-import-pubs --dbxref=PMID:29220446 --username=admin if theres a pubmed ID.

[bradfordcondon]

OK everything is abotu set. one last thing:

• update publication citations to use URL.
• fix file url?

[bradfordcondon]

• completed map record. https://www.hardwoodgenomics.org/Map/2192028 (note citation has URL link but field needs to be cache cleared to show up).
• enabled tirpal_cmap_loader live. note this module isnt ready to display maps yet, but the field that simple lists maps is fine.

pending

(doing drupal things is really slow right now...)

• enabled and placed field on organism.
• deleted the text-based map entry for C. mollissima. not deleting the field yet because otehr organisms are still using it.

[bradfordcondon]

i moved the text-based map entry to "social behavior" to prevent term overlap.