there is no https database

[dsenalik]

Tripal Version

4.x

Drupal Version

any

PostgreSQL Version

any

PHP Version

any

General Description

The Sequence Ontology obo file contains four cross references that get converted incorrectly to https database references. While not harmful, it is not creating valid entries, and most likely we should just skip these.

An example of one of the offending records in tripal_chado/files/so.obo - at line 20427

  20419 [Term]
  20420 id: SO:0002168
  20421 name: RNA_thermometer
  20422 def: "An RNA_thermometer is a cis element in the 5' end of an mRNA that can change its secondary structure in respo>
  20423 synonym: "RNA thermometer" EXACT []
  20424 synonym: "RNA thermoregulator" EXACT []
  20425 synonym: "RNAT" EXACT []
  20426 synonym: "thermoregulator" EXACT []
  20427 xref: https://en.wikipedia.org/wiki/RNA_thermometer "wiki"
  20428 is_a: SO:0000836 ! mRNA_region
  20429 relationship: part_of SO:0000234 ! mRNA
  20430 created_by: nicole
  20431 creation_date: 2017-07-17T10:07:45Z

Steps to reproduce

On any tripal 4 site you will see:

select * from db DB left join dbxref X on DB.db_id=X.db_id where DB.name='https';
 db_id | name  | description | urlprefix | url | dbxref_id | db_id |                                                  accession                                                   | version | description 
-------+-------+-------------+-----------+-----+-----------+-------+--------------------------------------------------------------------------------------------------------------+---------+-------------
    46 | https |             |           |     |      2764 |    46 | //en.wikipedia.org/wiki/RNA_thermometer                                                                      |         | 
    46 | https |             |           |     |      2852 |    46 | //www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/long-interspersed-nuclear-element |         | 
    46 | https |             |           |     |      2873 |    46 | //en.wikipedia.org/wiki/MtDNA_control_region                                                                 |         | 
    46 | https |             |           |     |      2910 |    46 | //epi.grants.cancer.gov/epigen/#\:~\:text=mail.nih.gov-\,Overview\,a%20cell%20or%20entire%20organism.        |         | 
(4 rows)

Error messages

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Screenshots

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