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tripal / mainlab_chado_loader

Mainlab Chado Loader
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install required vocabulary? #7

Open bradfordcondon opened 6 years ago

bradfordcondon commented 6 years ago

Each of the loaders requires a number of CVterms installed on the site. For example, the featuremap loader requires the below cvterms

>Required cvterms
Error : Could not find cvterm : alias [cv_id = 21695].
Error : Could not find cvterm : analysis_method [cv_id = 21695].
Error : Could not find cvterm : software [cv_id = 21695].
Error : Could not find cvterm : map_type [cv_id = 21695].
Error : Could not find cvterm : population_type [cv_id = 21695].
Error : Could not find cvterm : population_size [cv_id = 21695].
Error : Could not find cvterm : source_url [cv_id = 21695].
Error : Could not find cvterm : comments [cv_id = 21695].
Error : Could not find cvterm : genome_group [cv_id = 21695].

Is there a separate module or command that sets up this site CV with all the terms the loader expects? Should they have been inserted on installing this module?

I can otherwise insert the terms manually as I get the errors. I see you have a nice drush command that automatically inserts the term into the right CV, ie , drush mcl-add-cvterm comments

leetaei commented 6 years ago

Hi Bradford,

Yes, we have a drush command 'mcl-add-cveterm cvterm_name cv_name' to add a cvterm as you said. But it is pain to add all the cvterms one by one. I can work on creating a drush command to add all cvterms for a particluar template. For example, if you want to add all the cvterm for stock, type 'drush mcl-add-cvterm-by-template stock'.

bradfordcondon commented 6 years ago

that might be helpful. It might also be a good idea to list the needed cvterms in the requirements/setup. For example, this module requires the relationship ontology. I also had to insert an extra term (marker_locus) into the sequence ontology. Or I've had to create specific databases ('dbSNP', 'DB:genbank'). It would be create if these things could be inserted on install or at least added to the README instructions.

leetaei commented 6 years ago

Thank you for suggestions. Yes, some templates use sequence / relationship ontology. However, I think this module should not insert or change the these ontology terms. I believe Tripal has ontology loader to add terms so I should recommend to use the loader to add terms into Chado table. I definitely need to add 'prerequisites' section in README file.

bradfordcondon commented 6 years ago

Yes, some templates use sequence / relationship ontology. However, I think this module should not insert or change the these ontology terms.

Which version of the sequence ontology includes the term marker_locus ? I can't find it in the EBI OLS and it was not included in my install.

Mine is: http://purl.obolibrary.org/obo/so.obo which does not have a term named marker_locus

So, my point is, I have to insert this extra terms into the ontology in order to use this module.