tripal / chado_search

Mainlab Chado Search: enabling advanced search function for a Tripal/Chado database

Mainab Chado Search

Mainlab Chado Search has been moved to GitLab. Please visit GitLab at the following URL for the latest code:

https://gitlab.com/mainlabwsu/chado_search

chado_search's Issues

relation "feature" does not exist

hi, @chunhuaicheng

i need to populate the chado_search_gene_search MV when i use chado_search, but i show 0 row after executing the drush trp-run-jobs --username=admin --root=/var/www/html command. So i execute the MV query below

SELECT
F.feature_id,
F.name AS feature_name,
F.uniquename AS feature_uniquename,
F.seqlen AS feature_seqlen,
(SELECT genus || ' ' || species FROM organism WHERE organism_id = F.organism_id) AS organism,
(SELECT genus FROM organism WHERE organism_id = F.organism_id),
(SELECT species FROM organism WHERE organism_id = F.organism_id),
(SELECT common_name FROM organism WHERE organism_id = F.organism_id) AS organism_common_name,
(SELECT name FROM cvterm WHERE cvterm_id = F.type_id) AS feature_type,
LOC.srcfeature_id,
LOC.name AS landmark,
(fmin + 1) AS fmin,
fmax,
LOC.name || ':' || (fmin + 1) || '..' || fmax AS location,
A.name AS analysis,
-- Blast Best Hit
(SELECT string_agg(distinct
(SELECT array_to_string(regexp_matches(value, '<Hit_def>(.+?)</Hit_def>'), '')
FROM analysisfeatureprop AFP2 WHERE AFP2.analysisfeatureprop_id = AFP.analysisfeatureprop_id)
, '. ')
FROM analysisfeatureprop AFP
INNER JOIN analysisfeature AF2 ON AF2.analysisfeature_id = AFP.analysisfeature_id
WHERE
type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'analysis_blast_output_iteration_hits')
AND
AF2.feature_id = F.feature_id
) AS blast_value,
-- KEGG
(SELECT string_agg(distinct
(SELECT trim(regexp_replace(value, '<.+>', ''))
FROM analysisfeatureprop AFP2 WHERE AFP2.analysisfeatureprop_id = AFP.analysisfeatureprop_id)
, '. ')
FROM analysisfeatureprop AFP
INNER JOIN analysisfeature AF2 ON AF2.analysisfeature_id = AFP.analysisfeature_id
WHERE
type_id IN (SELECT cvterm_id FROM cvterm WHERE cv_id = (SELECT cv_id FROM cv WHERE name = 'KEGG_ORTHOLOGY' or name = 'KEGG_PATHWAYS'))
AND
AF2.feature_id = F.feature_id
) AS kegg_value,
-- Interpro
(
SELECT string_agg(distinct value, '. ')
FROM (
SELECT
AF2.feature_id,
array_to_string (regexp_matches(value, 'name="(.+?)"', 'g'), '') AS value
FROM analysisfeatureprop AFP2
INNER JOIN analysisfeature AF2 ON AF2.analysisfeature_id = AFP2.analysisfeature_id
WHERE AFP2.type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'analysis_interpro_xmloutput_hit')
AND AF2.feature_id = F.feature_id
) INTERPRO GROUP BY feature_id
) AS interpro_value,
-- GO term
(
SELECT string_agg(distinct name, '. ')
FROM (
SELECT feature_id,
V.name
FROM feature_cvterm FC
INNER JOIN cvterm V ON V.cvterm_id = FC.cvterm_id
WHERE FC.feature_id = F.feature_id
AND cv_id IN (SELECT cv_id FROM cv WHERE name IN ('biological_process', 'cellular_component', 'molecular_function'))
) GOTERM GROUP BY feature_id
) AS go_term,
-- Genbank Keywords
(
SELECT string_agg(value, '. ')
FROM featureprop
WHERE type_id IN
(SELECT cvterm_id
FROM cvterm
WHERE cv_id =
(SELECT cv_id
FROM cv
WHERE name = 'tripal_genbank_parser')
AND name IN ('genbank_note','genbank_gene','product','function','genbank_detail','genbank_description'))
AND feature_id = F.feature_id
GROUP BY feature_id
) AS gb_keyword
-- Base Table
FROM feature F
INNER JOIN analysisfeature AF ON AF.feature_id = F.feature_id
INNER JOIN analysis A ON A.analysis_id = AF.analysis_id
-- Genome Location
LEFT JOIN
((SELECT
GENE.feature_id,
LMARK.srcfeature_id,
LMARK.fmin,
LMARK.fmax,
LMARK.name
FROM Feature GENE
INNER JOIN featureloc GMATLOC ON GMATLOC.srcfeature_id = GENE.feature_id
INNER JOIN (
SELECT
LMATLOC.feature_id,
LMATLOC.srcfeature_id,
LMATLOC.fmin,
LMATLOC.fmax,
CHR.name
FROM Feature CHR
INNER JOIN featureloc LMATLOC ON LMATLOC.srcfeature_id = CHR.feature_id
WHERE (SELECT type_id FROM feature F WHERE F.feature_id = LMATLOC.feature_id) = (SELECT cvterm_id FROM cvterm WHERE name = 'match' AND cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence'))
AND CHR.type_id IN (SELECT cvterm_id FROM cvterm WHERE name IN ('chromosome', 'supercontig') AND cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence'))
) LMARK ON LMARK.feature_id = GMATLOC.feature_id
WHERE GENE.type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'gene' AND cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence')))
UNION
(SELECT FL.feature_id, srcfeature_id, fmin, fmax, F.name FROM featureloc FL
INNER JOIN feature F ON F.feature_id = FL.srcfeature_id
WHERE F.type_id IN (SELECT cvterm_id FROM cvterm WHERE name IN ('chromosome', 'supercontig') AND cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence'))
)
) LOC ON LOC.feature_id = AF.feature_id
WHERE
(
-- Restrict the sequence type to gene/mRNA/contig for Unigene/RefTrans
(F.type_id IN (SELECT cvterm_id FROM cvterm WHERE name IN ('contig', 'gene', 'mRNA') AND cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence'))) AND
(A.analysis_id IN (SELECT analysis_id FROM analysisprop WHERE type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'Analysis Type') AND value IN ('reftrans', 'unigene', 'bulk_data', 'ncbi_data', 'transcriptome', 'other_transcripts')))
OR
-- Restrict the sequence type to gene/mRNA for whole genome assembly
(F.type_id IN (SELECT cvterm_id FROM cvterm WHERE name IN ('gene', 'mRNA') AND cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence'))) AND
(A.analysis_id IN (SELECT analysis_id FROM analysisprop WHERE type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'Analysis Type') AND value = 'whole_genome'))
)

and throw an exception [42P01] ERROR: relation "feature" does not exist, i don't kown where the feature get from.

Error messages about cottongen.settings.txt

Dear all, I installed chado_search by using process below.

git clone https://gitlab.com/mainlabwsu/chado_search.git cp cottongen.settings.txt settings.conf drush pm-enable chado_search

However, when I entered search page (http://localhost/find/qualitative_traits), error message was shown below.

Unable to create SelectFilter form element. Please check your settings. SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "chado_search_qualitative_traits" does not exist LINE 1: ...lic, chado; SELECT distinct trait_descriptor FROM chado_sear... ^ Unable to bind DynamicSelectFilter form element. Please check your SQL statement in the AJAX callback. SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "chado_search_qualitative_traits" does not exist LINE 1: ..., public, chado; SELECT distinct trait_value FROM chado_sear... ^ Unable to create SelectFilter form element. Please check your settings. SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "chado_search_qualitative_traits" does not exist LINE 1: ...lic, chado; SELECT distinct trait_descriptor FROM chado_sear... ^ Unable to bind DynamicSelectFilter form element. Please check your SQL statement in the AJAX callback. SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "chado_search_qualitative_traits" does not exist LINE 1: ..., public, chado; SELECT distinct trait_value FROM chado_sear... ^ Unable to create SelectFilter form element. Please check your settings. SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "chado_search_qualitative_traits" does not exist LINE 1: ...lic, chado; SELECT distinct trait_descriptor FROM chado_sear... ^ Unable to bind DynamicSelectFilter form element. Please check your SQL statement in the AJAX callback. SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "chado_search_qualitative_traits" does not exist LINE 1: ..., public, chado; SELECT distinct trait_value FROM chado_sear... ^

Is there any to solve this error?

Best,

:( there is one column not in table

the column "landmark" not in the chado_search_gene_search table

How to show the data for the chado_search?

How can i fill the data to the select tag, and i had click the Populate button in the MViews configuration page?

is any guide to show the usage of chado_search?

throw the phpexception, any ways to solve it?

PDOException: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "chado.chado_search_sequence_search" does not exist LINE 1: SELECT distinct organism FROM chado.chado_search_sequence_se... ^: SELECT distinct organism FROM chado.chado_search_sequence_search ORDER BY organism; Array ( ) in chado_query() (line 1538 of /var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).