Tripal Plant PopGen Submit
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Defines module schema and install/uninstall processes.
Definition in file tpps.install.
tpps_add_dryad | ( | ) |
Creates the dryad DB.
Definition at line 1279 of file tpps.install.
tpps_alter_genotype_call | ( | ) |
Add foreign key constraints to the chado.genotype_call table.
Definition at line 718 of file tpps.install.
tpps_alter_tpps_project_file_managed | ( | ) |
Add foreign key constraints to the tpps_project_file_managed table.
Definition at line 773 of file tpps.install.
tpps_alter_tpps_submission_dbxref | ( | ) |
Add foreign key constraints to the tpps_submission_dbxref table.
Definition at line 760 of file tpps.install.
tpps_alter_tpps_submission_tag | ( | ) |
Add foreign key constraints to the tpps_submission_tag table.
Definition at line 786 of file tpps.install.
tpps_alter_tpps_submissions | ( | ) |
Add foreign key constraints to the tpps_submission table.
Definition at line 746 of file tpps.install.
tpps_create_entities | ( | ) |
Creates Tripal Entity types if they do not already exist.
Definition at line 1002 of file tpps.install.
tpps_create_genotype_entity | ( | ) |
Creates the Genotype Tripal Entity type.
Definition at line 1024 of file tpps.install.
tpps_create_genotype_search_views | ( | ) |
Create the chado.tpps_search_genotype_name materialized view.
Definition at line 860 of file tpps.install.
tpps_create_plusgeno_view | ( | ) |
Create the chado.plusgeno_view materialized view.
Definition at line 799 of file tpps.install.
tpps_create_stock_entity | ( | ) |
Creates the Stock Tripal Entity type.
Definition at line 1164 of file tpps.install.
tpps_default_permissions | ( | ) |
Sets default TPPS module permissions.
Definition at line 891 of file tpps.install.
tpps_default_tags | ( | ) |
tpps_install | ( | ) |
Implements hook_install().
Define local cvterms, add necessary foreign keys to schema tables, create necessary materialized views.
Definition at line 14 of file tpps.install.
tpps_install_cvterms | ( | ) |
tpps_install_miappe_ontology | ( | ) |
Install the MIAPPE ontology using via the obo file and tripal_cv_load_obo().
The MIAPPE ontology obo file was created using http://robot.obolibrary.org/ on the owl file found here: https://github.com/MIAPPE/MIAPPE-ontology.
Definition at line 659 of file tpps.install.
tpps_schema | ( | ) |
Implements hook_schema().
This function defines and creates the tpps_submission table that TPPS uses to keep track of submissions.
Definition at line 315 of file tpps.install.
tpps_uninstall | ( | ) |
Implements hook_uninstall().
Removes TPPS variables from the public.variable table. Also removes TPPS file usage from public.file_usage.
Definition at line 287 of file tpps.install.
tpps_update_7100 | ( | ) |
Implements hook_update_N().
Convert old submissions to new form_state structure.
Definition at line 1292 of file tpps.install.
tpps_update_7101 | ( | ) |
Implements hook_update_N().
Populate top-level state info for old submissions.
Definition at line 1328 of file tpps.install.
tpps_update_7102 | ( | ) |
tpps_update_7103 | ( | ) |
Implements hook_update_N().
Add DOI dbxref to old TPPSc submissions.
Definition at line 1418 of file tpps.install.
tpps_update_7104 | ( | ) |
Implements hook_update_N().
Populate pub_organism table for old TPPS submissions.
Definition at line 1449 of file tpps.install.
tpps_update_7105 | ( | ) |
Implements hook_update_N().
Create materialized views for genotype search functions.
Definition at line 1483 of file tpps.install.
tpps_update_7106 | ( | ) |
Implements hook_update_N().
Create last-updated timestamps for old submissions.
Definition at line 1492 of file tpps.install.
tpps_update_7107 | ( | ) |
Implements hook_update_N().
Load MIAPPE ontology to chado.
Definition at line 1506 of file tpps.install.
tpps_update_7108 | ( | ) |
Implements hook_update_N().
Set default cvterms version and migrate to 1.2.
Definition at line 1518 of file tpps.install.
tpps_update_7109 | ( | ) |
Implements hook_update_N().
Corrects file path records for renamed files in the db.
Definition at line 1528 of file tpps.install.
tpps_update_7110 | ( | ) |
Implements hook_update_N().
Initializes alternative accessions for each submission.
Definition at line 1583 of file tpps.install.
tpps_update_7111 | ( | ) |
Implements hook_update_N().
Removes old entries in project_pub linking table for replaced submissions.
Definition at line 1609 of file tpps.install.
tpps_update_7112 | ( | ) |
Implements hook_update_N().
Converts old species page information to new structure.
Definition at line 1627 of file tpps.install.
tpps_update_7113 | ( | ) |
Implements hook_update_N().
Add species names to file_info names for existing submissions.
Definition at line 1659 of file tpps.install.
tpps_update_7114 | ( | ) |
Implements hook_update_N().
Add tpps_project_file_managed table if it does not exist.
Definition at line 1710 of file tpps.install.
tpps_update_7115 | ( | ) |
Implements hook_update_N().
Populate tpps_project_file_managed for approved submissions.
Definition at line 1730 of file tpps.install.
tpps_update_7116 | ( | ) |
Implements hook_update_N().
Add TPPS tag tables if they do not exist.
Definition at line 1823 of file tpps.install.
tpps_update_7117 | ( | ) |
Implements hook_update_N().
Adds approx/none coordinate tags to old submissions.
Definition at line 1888 of file tpps.install.
tpps_update_7118 | ( | ) |
Implements hook_update_N().
Adds normal-check field to old submissions where applicable.
Definition at line 1943 of file tpps.install.