Inheritance diagram for Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml:

Collaboration diagram for Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml:

[legend]

Public Member Functions
	chadoCheckTermsAreAsExpected ($options=['chado_schema'=> NULL, 'auto-expand'=> FALSE, 'auto-fix'=> FALSE, 'no-fix'=> FALSE])

Protected Member Functions
	chadoCheckTerms_findProblems (&$problems, &$solutions, &$summary_rows, $options)

	chadoCheckTerms_findCVProblems (&$problems, &$solutions, &$summary_rows, $options)

	chadoCheckTerms_reportProblems ($problems, $solutions, $summary_rows, $options)

	chadoCheckTerms_checkVocab (array $vocab_info, array &$problems, array &$solutions)

	chadoCheckTerms_checkIdSpaces (array $vocab_info, array &$problems, array &$solutions)

	chadoCheckTerms_checkTerm (array $term_info, array &$problems, array &$solutions)

	chadoCheckTerms_printSummaryTable (array $summary_rows)

	updateChadoTermRecords (string $table_name, string $pkey, array $records)

	migrateObsoleteVocabularies (array $cv_ids)

	chadoCheckTerms_reportProblem_yamlDuplication ($problems, $solutions, $options)

	chadoCheckTerms_reportProblem_missingDbYaml ($problems, $solutions, $options)

	chadoCheckTerms_reportProblem_obsoleteCv ($problems, $solutions, $options)

	chadoCheckTerms_reportProblem_terms ($problems, $solutions, $options)

	chadoCheckTerms_reportProblem_eccentricCv ($problems, $solutions, $options)

	chadoCheckTerms_reportProblem_eccentricDb ($problems, $solutions, $options)

	chadoCheckTerms_reportProblem_eccentricCVTerm ($problems, $solutions, $options)

Protected Attributes
	$chado_schema

ChadoConnection	$chado

string	$red_format = "\033[31;40m\033[1m %s \033[0m"

string	$yellow_format = "\033[1;33;40m\033[1m %s \033[0m"

Detailed Description

Drush command specific to checking the cv/db/cvterm/dbxref records in a specific chado schema against the expected terms in the Tripal Content Terms YAML.

DO NOT ADD ADDITION DRUSH COMMANDS TO THIS CLASS.

Member Function Documentation

◆ chadoCheckTerms_checkIdSpaces()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_checkIdSpaces	(	array	$vocab_info,
		array &	$problems,
		array &	$solutions
	)

protected

Checks that the id space metadata in the YAML matches this chado instance.

Parameters

array	$vocab_info
array	$problems
array	$solutions

Returns

array

summary_dbs: an array where the key is the id space name and the value summarizes its status.
defined_idspaces: an array where the key is the id space name and the value is the db_id found or NULL if not.

◆ chadoCheckTerms_checkTerm()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_checkTerm	(	array	$term_info,
		array &	$problems,
		array &	$solutions
	)

protected

Checks that the term metadata in the YAML matches this chado instance.

Parameters

array	$term_info
array	$problems
array	$solutions

Returns

array

summary_cvterm: the value to print in the summary table
summary_dbxref: the value to print in the summary table

◆ chadoCheckTerms_checkVocab()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_checkVocab	(	array	$vocab_info,
		array &	$problems,
		array &	$solutions
	)

protected

Checks that the vocabulary metadata in the YAML matches this chado instance.

Parameters

array	$vocab_info
array	$problems
array	$solutions

Returns

array

summary_cv: the value to print in the summary table
existing_cv: the cv object selected from the database or NULL if there wasn't one.

◆ chadoCheckTerms_findCVProblems()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_findCVProblems	(	&	$problems,
		&	$solutions,
		&	$summary_rows,
			$options
	)

protected

Checks for obsolete vocabularies in the database.

Parameters

array	$problems	Array containing details for either errors or warnings
array	$solutions	Array containing possible solutions for either errors or warnings
array	$summary_rows	Infomation for the output table
array	$options	Options from drush command line

◆ chadoCheckTerms_findProblems()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_findProblems	(	&	$problems,
		&	$solutions,
		&	$summary_rows,
			$options
	)

protected

Checks all YAML specifications and compares to current chado state.

Parameters

array	$problems	Array containing details for either errors or warnings
array	$solutions	Array containing possible solutions for either errors or warnings
array	$summary_rows	Infomation for the output table
array	$options	Options from drush command line

◆ chadoCheckTerms_printSummaryTable()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_printSummaryTable ( array $summary_rows )

protected

Prints a beautiful summary table showing the status of all terms.

Parameters

array $summary_rows

Returns: void No need to return as we are printing directly.

◆ chadoCheckTerms_reportProblem_eccentricCv()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_reportProblem_eccentricCv	(	$problems,
		$solutions,
		$options
	)

protected

Reports warnings and potential solutions for the "cv" warning type.

Trigger Example: Imagine there is a vocabulary defined whose

definition in the YAML is different from in your chado instance

Parameters

array	$problems	An array describing instances with this type of warning with the following format: [Existing cv_id]: an array of reports describing how this cv differs in your chado instance from what is defined in the YAML. Each report has the following structure: vocab-name: the name of the vocabulary in the YAML which must match the cv in your chado instance. column: the chado column showing a difference property: the yaml property being compared YOURS: the value in your chado instance THEIRS: the value in the YAML
array	$solutions	An array describing possible solutions with the following format: [Existing cv_id]: an array of columns in the cv table to update. Each entry has the following structure: [column name]: [value in YAML]

Returns: void This function interacts through command-line input/output directly and as such, does not need to return anything to the parent Drush command.

◆ chadoCheckTerms_reportProblem_eccentricCVTerm()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_reportProblem_eccentricCVTerm	(	$problems,
		$solutions,
		$options
	)

protected

Reports warnings and potential solutions for the "cvterm" warning type.

Trigger Example: Imagine there is a cvterm defined whose

definition in the YAML is different from in your chado instance

Parameters

array	$problems	An array describing instances with this type of warning with the following format: [Existing cvterm_id]: an array of reports describing how this cvterm differs in your chado instance from what is defined in the YAML. Each report has the following structure: term-name: the name of the term in the YAML which must match the cvterm in your chado instance. term-id: the full id of the term in the YAML which must match the connected dbxref in your database. column: the chado column showing a difference property: the yaml property being compared YOURS: the value in your chado instance THEIRS: the value in the YAML
array	$solutions	An array describing possible solutions with the following format: [Existing cvterm_id]: an array of columns in the cvterm table to update. Each entry has the following structure: [column name]: [value in YAML]

Returns: void This function interacts through command-line input/output directly and as such, does not need to return anything to the parent Drush command.

◆ chadoCheckTerms_reportProblem_eccentricDb()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_reportProblem_eccentricDb	(	$problems,
		$solutions,
		$options
	)

protected

Reports warnings and potential solutions for the "db" warning type.

Trigger Example: Imagine there is a ID Space defined whose

definition in the YAML is different from in your chado instance

Parameters

array	$problems	An array describing instances with this type of warning with the following format: [Existing db_id]: an array of reports describing how this db differs in your chado instance from what is defined in the YAML. Each report has the following structure: idspace-name: the name of the id space in the YAML which must match the cv in your chado instance. column: the chado column showing a difference property: the yaml property being compared YOURS: the value in your chado instance THEIRS: the value in the YAML
array	$solutions	An array describing possible solutions with the following format: [Existing db_id]: an array of columns in the db table to update. Each entry has the following structure: [column name]: [value in YAML]

Returns: void This function interacts through command-line input/output directly and as such, does not need to return anything to the parent Drush command.

◆ chadoCheckTerms_reportProblem_missingDbYaml()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_reportProblem_missingDbYaml	(	$problems,
		$solutions,
		$options
	)

protected

Reports errors and potential solutions for the "missingDbYaml" error type.

Trigger Example: Imagine there is a term defined whose id is DATUM:12345 but the vocabulary this term is in either

has a number of ID Spaces defined but none of them have the idSpaces[name] of 'DATUM' (case sensitive match required).
does not have any id spaces defined.

Parameters

array	$problems	An array describing instances with this type of error with the following format: [YAML ID Space name]: an array of reports where a term had the ID Space indicated by the key despite that ID Space not being defined in the YAML. Each report has the following structure: missing-db-name: defined-dbs: term: vocab:
array	$solutions	There are currently no easy suggested solutions for this but the parameter is here in case we decide to be more helpful later ;-p

Returns: void This function interacts through command-line input/output directly and as such, does not need to return anything to the parent Drush command.

◆ chadoCheckTerms_reportProblem_obsoleteCv()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_reportProblem_obsoleteCv	(	$problems,
		$solutions,
		$options
	)

protected

Reports errors and potential solutions for the "obsolete_cv" error type.

Trigger Examples: Imagine a term defined with a vocabulary of 'organism_property'

Parameters

array	$problems	An array describing instances with this type of error with the following format: [YAML Term ID]: an array of reports where each report has the following structure: vocab-name: vocab-id: message: will always contain 'Obsolete controlled vocabulary'
array	$solutions	Just a placeholder, will always contain 'Move to local CV'

Returns: void This function interacts through command-line input/output directly and as such, does not need to return anything to the parent Drush command.

◆ chadoCheckTerms_reportProblem_terms()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_reportProblem_terms	(	$problems,
		$solutions,
		$options
	)

protected

Reports errors and potential solutions for the "term" error type.

Trigger Examples: Imagine a term defined with a name of 'Location' and an id of 'NCIT:C25341'

Parameters

array	$problems	An array describing instances with this type of error with the following format: [YAML Term ID]: an array of reports where each report has the following structure: term-name: term-id: category: message: error-column YOURS EXPECTED
array	$solutions	There are currently no easy suggested solutions for this but the parameter is here in case we decide to be more helpful later ;-p

Returns: void This function interacts through command-line input/output directly and as such, does not need to return anything to the parent Drush command.

◆ chadoCheckTerms_reportProblem_yamlDuplication()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_reportProblem_yamlDuplication	(	$problems,
		$solutions,
		$options
	)

protected

Reports errors and potential solutions for the "yamlDuplication" error type.

Trigger Example: the term local:lineage is defined twice in tripal.tripal_content_terms.chado_content_terms.yml

Parameters

array	$problems	An array describing instances with this type of error with the following format: [YAML ID Space name]: an array of reports where a term had the ID Space indicated by the key despite that ID Space not being defined in the YAML. Each report has the following structure: name: id:
array	$solutions	There are currently no easy suggested solutions for this but the parameter is here in case we decide to be more helpful later ;-p

Returns: void This function interacts through command-line input/output directly and as such, does not need to return anything to the parent Drush command.

◆ chadoCheckTerms_reportProblems()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTerms_reportProblems	(	$problems,
		$solutions,
		$summary_rows,
		$options
	)

protected

Reports to user the status of chado as determined by chadoCheckTerms_findProblems.

Parameters

array	$problems	Array containing details for either errors or warnings
array	$solutions	Array containing possible solutions for either errors or warnings
array	$summary_rows	Infomation for the output table
array	$options	Options from drush command line

◆ chadoCheckTermsAreAsExpected()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::chadoCheckTermsAreAsExpected ( $options = ['chado_schema' => NULL, 'auto-expand' => FALSE, 'auto-fix' => FALSE, 'no-fix' => FALSE] )

Checks a given chado install for any inconsistencies between its cvterms and what Tripal expects.

@command tripal-chado:trp-check-terms @aliases trp-check-terms @option chado_schema The name of the chado schema to check. @option auto-expand Indicates that you always want to show specifics of any errors or warnings. @option auto-fix Indicates that you always want us to attempt to fix any issues without the need for us to prompt. @option no-fix Indicates that you do not want us to offer to fix anything. @usage drush trp-check-terms –chado_schema=chado_prod Checks the terms stored in chado_prod.cvterm for consistency.

◆ migrateObsoleteVocabularies()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::migrateObsoleteVocabularies ( array $cv_ids )

protected

Migrates terms in obsolete vocabularies to "local" vocabulary, and then removes the obsolete vocabularies.

Parameters

array $cv_ids An associative array of the obsolete vocabularies, key is pkey_id, value is vocabulary name.

Returns: void

◆ updateChadoTermRecords()

Drupal\tripal_chado\Commands\ChadoCheckTermsAgainstYaml::updateChadoTermRecords	(	string	$table_name,
		string	$pkey,
		array	$records
	)

protected

Updates records in chado based on an array of records.

Parameters

string	$table_name	The name of the chado table to be updated.
string	$pkey	The name of the primary key of the table to be updated.
array	$records	An array of the following format: [primary key of the table]: an array of columns to update where each is of the form: [column]: [value to update it to]

Returns: void

The documentation for this class was generated from the following file:

tripal_chado/src/Commands/ChadoCheckTermsAgainstYaml.php

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

◆ chadoCheckTerms_checkIdSpaces()

◆ chadoCheckTerms_checkTerm()

◆ chadoCheckTerms_checkVocab()

◆ chadoCheckTerms_findCVProblems()

◆ chadoCheckTerms_findProblems()

◆ chadoCheckTerms_printSummaryTable()

◆ chadoCheckTerms_reportProblem_eccentricCv()

◆ chadoCheckTerms_reportProblem_eccentricCVTerm()

◆ chadoCheckTerms_reportProblem_eccentricDb()

◆ chadoCheckTerms_reportProblem_missingDbYaml()

◆ chadoCheckTerms_reportProblem_obsoleteCv()

◆ chadoCheckTerms_reportProblem_terms()

◆ chadoCheckTerms_reportProblem_yamlDuplication()

◆ chadoCheckTerms_reportProblems()

◆ chadoCheckTermsAreAsExpected()

◆ migrateObsoleteVocabularies()

◆ updateChadoTermRecords()