From acfa9c97c272266baed25fafa63e89b5491e7993 Mon Sep 17 00:00:00 2001 From: danielp Date: Tue, 15 Oct 2024 15:59:50 +0100 Subject: [PATCH] Fixed test. Again --- src/tests/databases/core_8/meta.txt | 3 +- src/tests/databases/core_9/attrib_type.txt | 3 - src/tests/databases/core_9/coord_system.txt | 1 - src/tests/databases/core_9/meta.txt | 26 ------ src/tests/databases/core_9/seq_region.txt | 3 - .../databases/core_9/seq_region_attrib.txt | 8 -- .../databases/core_9/seq_region_synonym.txt | 3 - src/tests/databases/core_9/table.sql | 86 ------------------- 8 files changed, 2 insertions(+), 131 deletions(-) delete mode 100644 src/tests/databases/core_9/attrib_type.txt delete mode 100644 src/tests/databases/core_9/coord_system.txt delete mode 100644 src/tests/databases/core_9/meta.txt delete mode 100644 src/tests/databases/core_9/seq_region.txt delete mode 100644 src/tests/databases/core_9/seq_region_attrib.txt delete mode 100644 src/tests/databases/core_9/seq_region_synonym.txt delete mode 100644 src/tests/databases/core_9/table.sql diff --git a/src/tests/databases/core_8/meta.txt b/src/tests/databases/core_8/meta.txt index e157a3d9..725a1ac8 100644 --- a/src/tests/databases/core_8/meta.txt +++ b/src/tests/databases/core_8/meta.txt @@ -4,6 +4,7 @@ 11 1 assembly.ucsc_alias SCARY 15 1 gencode.version 999 16 1 genebuild.last_geneset_update 01 +3 1 organism.biosample_id SAMN04256190 3 1 organism.common_name Caenorhabditis elegans (PRJNA13758) 7 1 organism.division Ensembl_TEST 6 1 organism.production_name Caenorhabditis_elegans @@ -14,7 +15,7 @@ 2 1 organism.taxonomy_id 6239 10 1 organism.type monsters 5 1 organism.url Jabbe -17 1 genebuild.version ENS01 +17 1 genebuild.version EXT01 18 1 genebuild.sample_gene ENSAMXG00005000318 19 1 genebuild.sample_location KB871578.1:9766653-9817473 20 1 strain.type test diff --git a/src/tests/databases/core_9/attrib_type.txt b/src/tests/databases/core_9/attrib_type.txt deleted file mode 100644 index 59c569dd..00000000 --- a/src/tests/databases/core_9/attrib_type.txt +++ /dev/null @@ -1,3 +0,0 @@ -6 toplevel Top Level Top Level Non-Redundant Sequence Region -547 sequence_location sequence_location To identify sequence locations / cellular compartments that DNA sequence comes from.Values are supposed to be SO compliant (children of the plastid_sequence SO:0000740 and nuclear_sequence SO:0000738 ): "apicoplast_chromosome", "chloroplast_chromosome", "chromoplast_chromosome", "cyanelle_chromosome", "leucoplast_chromosome", "macronuclear_chromosome", "micronuclear_chromosome", "mitochondrial_chromosome", "nuclear_chromosome". -316 circular_seq Circular sequence Circular chromosome or plasmid molecule \ No newline at end of file diff --git a/src/tests/databases/core_9/coord_system.txt b/src/tests/databases/core_9/coord_system.txt deleted file mode 100644 index 51314bf1..00000000 --- a/src/tests/databases/core_9/coord_system.txt +++ /dev/null @@ -1 +0,0 @@ -1 1 primary_assembly test 1 default_version,sequence_level diff --git a/src/tests/databases/core_9/meta.txt b/src/tests/databases/core_9/meta.txt deleted file mode 100644 index 9bb50da0..00000000 --- a/src/tests/databases/core_9/meta.txt +++ /dev/null @@ -1,26 +0,0 @@ -12 1 assembly.accession test1 -14 1 assembly.default jaber01 -13 1 assembly.name jaber01 -11 1 assembly.ucsc_alias SCARY -15 1 gencode.version 999 -16 1 genebuild.last_geneset_update 01 -3 1 organism.common_name Caenorhabditis elegans (PRJNA13758) -7 1 organism.division Ensembl_TEST -6 1 organism.production_name Caenorhabditis_elegans -4 1 organism.scientific_name Caenorhabditis elegans -1 1 organism.species_taxonomy_id 6239 -8 1 organism.strain N2 -9 1 organism.strain_group testing -2 1 organism.taxonomy_id 6239 -10 1 organism.type monsters -5 1 organism.url Jabbe -17 1 genebuild.version ENS01 -18 1 genebuild.sample_gene ENSAMXG00005000318 -19 1 genebuild.sample_location KB871578.1:9766653-9817473 -20 1 strain.type test -23 1 genome.genome_uuid a733550b-93e7-11ec-a39d-005056b38ce3 -24 1 genebuild.havana_datafreeze_date test2 -25 1 assembly.stats.total_genome_length 546 -26 1 genebuild.start_date 2023-07-Ensembl -27 \N schema_version 110 -28 1 genebuild.last_geneset_update 2023-01 diff --git a/src/tests/databases/core_9/seq_region.txt b/src/tests/databases/core_9/seq_region.txt deleted file mode 100644 index d79f754f..00000000 --- a/src/tests/databases/core_9/seq_region.txt +++ /dev/null @@ -1,3 +0,0 @@ -1 TEST1_seq_BAD 1 666666 -2 TEST2_seqB 1 666 -3 TEST3_seqC 1 1666666 diff --git a/src/tests/databases/core_9/seq_region_attrib.txt b/src/tests/databases/core_9/seq_region_attrib.txt deleted file mode 100644 index aad2591e..00000000 --- a/src/tests/databases/core_9/seq_region_attrib.txt +++ /dev/null @@ -1,8 +0,0 @@ -1 6 1 -2 6 1 -3 6 1 -1 547 nuclear_chromosome -2 547 nuclear_chromosome -3 547 mitochondrial_chromosome -1 316 1 -2 316 0 \ No newline at end of file diff --git a/src/tests/databases/core_9/seq_region_synonym.txt b/src/tests/databases/core_9/seq_region_synonym.txt deleted file mode 100644 index de43d915..00000000 --- a/src/tests/databases/core_9/seq_region_synonym.txt +++ /dev/null @@ -1,3 +0,0 @@ -1 1 TEST1_seq 50710 -2 2 TEST2_seq 50710 -3 3 TEST3_seq 50710 diff --git a/src/tests/databases/core_9/table.sql b/src/tests/databases/core_9/table.sql deleted file mode 100644 index 953da984..00000000 --- a/src/tests/databases/core_9/table.sql +++ /dev/null @@ -1,86 +0,0 @@ -CREATE TABLE coord_system -( - coord_system_id int unsigned auto_increment - primary key, - species_id int unsigned default 1 not null, - name varchar(40) not null, - version varchar(255) null, - `rank` int not null, - attrib set ('default_version', 'sequence_level') null, - constraint name_idx - unique (name, version, species_id), - constraint rank_idx - unique (`rank`, species_id) -); - -CREATE INDEX species_idx - on coord_system (species_id); - -CREATE TABLE meta -( - meta_id int auto_increment - primary key, - species_id int unsigned default 1 null, - meta_key varchar(40) not null, - meta_value varchar(255) not null, - constraint species_key_value_idx - unique (species_id, meta_key, meta_value) -); - -CREATE INDEX species_value_idx - on meta (species_id, meta_value); - -CREATE TABLE seq_region -( - seq_region_id int unsigned auto_increment - primary key, - name varchar(255) not null, - coord_system_id int unsigned not null, - length int unsigned not null, - constraint name_cs_idx - unique (name, coord_system_id) -); - -CREATE INDEX cs_idx - on seq_region (coord_system_id); - -CREATE TABLE seq_region_attrib -( - seq_region_id int unsigned default 0 not null, - attrib_type_id smallint unsigned default 0 not null, - value text not null, - constraint region_attribx - unique (seq_region_id, attrib_type_id, value(500)) -); - -CREATE INDEX seq_region_idx - on seq_region_attrib (seq_region_id); - -CREATE INDEX type_val_idx - on seq_region_attrib (attrib_type_id, value(40)); - -CREATE INDEX val_only_idx - on seq_region_attrib (value(40)); - -CREATE TABLE seq_region_synonym -( - seq_region_synonym_id int unsigned auto_increment - primary key, - seq_region_id int unsigned not null, - synonym varchar(250) not null, - external_db_id int unsigned null, - constraint syn_idx - unique (synonym, seq_region_id) -); - -CREATE INDEX seq_region_idx - on seq_region_synonym (seq_region_id); - -CREATE TABLE `attrib_type` ( - `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, - `code` varchar(20) NOT NULL DEFAULT '', - `name` varchar(255) NOT NULL DEFAULT '', - `description` text, - PRIMARY KEY (`attrib_type_id`), - UNIQUE KEY `code_idx` (`code`) -); \ No newline at end of file