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UofS-Pulse-Binfo / analyzedphenotypes

Tripal/Drupal support for analyzed phenotypic data including data loaders, exporters, trait pages and summaries on germplasm pages.
GNU General Public License v2.0
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vocabulary error and foreach error on install #71

Closed bradfordcondon closed 5 years ago

bradfordcondon commented 5 years ago 
[TRIPAL ERROR] [TRIPAL_CHADO] chado_select_record: the foreign key definition for 'cv_id' on table 'cvterm' returned no results where the definition supplied was Array(    [name] => NCIT)
Invalid argument supplied for foreach() analyzedphenotypes.install:131                                                         [warning]

I think this the vocabulary error is due to the NCIT cv only being created "on demand" in tripal core- once you use the organism importer. I'll test this theory.

I dont know if the invalid foreach is related, looks like it originates from ap_construct_variablenames perhaps not returning whats expected.

bradfordcondon commented 5 years ago

My site has NCIT cv and terms though- unless these were created by this module.

select * from chado.cv where name ='NCIT';
cv_id   name    definition
58  NCIT    The NCIT OBO Edition project aims to increase integration of the NCIt with OBO Library ontologies
      NCIt is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases,
      findings and abnormalities. NCIt OBO Edition releases should be considered experimental.
(1 row)
select cvt.name from chado.cv cv INNER JOIN chado.cvterm cvt ON cvt.cv_id = cv.cv_id where cv.name ='NCIT';
name
Collected By
replicate
method
(3 rows)
laceysanderson commented 5 years ago

@reynoldtan was able to reproduce your error by trying install on a site without any organisms. He has fixed the install to remove that assumption and move the organism check to the configuration form. Can you test install again?

bradfordcondon commented 5 years ago

my permissions are bad so i manually created the required folders.

The following extensions will be enabled: analyzedphenotypes, trpdownload_api, dragndrop_upload, dragndrop_upload_element
Do you really want to continue? (y/n): y
[site http://default] [TRIPAL ERROR] [TRIPAL_CHADO] chado_select_record: the foreign key definition for 'cv_id' on table 'cvterm' returned no results where the definition supplied was Array(    [name] => NCIT)
analyzedphenotypes was enabled successfully.                                                                                        [ok]
analyzedphenotypes defines the following permissions: administer tripal, upload analyzed phenotypes, download analyzed phenotypes, access analyzed phenotypes
dragndrop_upload was enabled successfully.                                                                                          [ok]
dragndrop_upload_element was enabled successfully.                                                                                  [ok]
trpdownload_api was enabled successfully.                                                                                           [ok]
Custom table, 'mview_phenotype' ,  created successfully.                                                                            [status]
Materialized view 'mview_phenotype' created                                                                                         [status]
Custom table, 'mview_phenotype_summary' ,  created successfully.                                                                    [status]
Materialized view 'mview_phenotype_summary' created                                                                                 [status]
Analyzed Phenotypes needs to be configured here in order to be specific to your system.                                             [warning]

So looks like we install successfully now.

laceysanderson commented 5 years ago

Great! Just let us know if you run into anything else :-)