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ensembl-gh-mirror
ensembl-io
Commits
43251e25
Commit
43251e25
authored
Feb 14, 2019
by
Tiago Grego
Browse files
patched core test schema to version 97
parent
f2339548
Changes
9
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9 changed files
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51 additions
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11 deletions
+51
-11
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+4
-1
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+2
-1
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+4
-1
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+2
-1
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+4
-1
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+2
-1
modules/t/test-genome-DBs/homo_sapiens/variation/failed_description.txt
...-genome-DBs/homo_sapiens/variation/failed_description.txt
+2
-0
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
+9
-1
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
+22
-4
No files found.
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @
43251e25
1 \N schema_version 9
5
1 \N schema_version 9
7
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
...
...
@@ -102,3 +102,6 @@
169 \N patch patch_93_94_c.sql|default_aln_type
170 \N patch patch_94_95_a.sql|schema_version
171 \N patch patch_94_95_b.sql|vertebrate_division_rename
172 \N patch patch_95_96_a.sql|schema_version
173 \N patch patch_96_97_a.sql|schema_version
174 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
View file @
43251e25
...
...
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description`
text
,
`biotype_group`
enum
(
'coding'
,
'pseudogene'
,
'snoncoding'
,
'lnoncoding'
,
'mnoncoding'
,
'LRG'
,
'undefined'
,
'no_group'
)
DEFAULT
NULL
,
`so_acc`
varchar
(
64
)
DEFAULT
NULL
,
`so_term`
varchar
(
1023
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`biotype_id`
),
UNIQUE
KEY
`name_type_idx`
(
`name`
,
`object_type`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
66
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY
KEY
(
`meta_id`
),
UNIQUE
KEY
`species_key_value_idx`
(
`species_id`
,
`meta_key`
,
`meta_value`
),
KEY
`species_value_idx`
(
`species_id`
,
`meta_value`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
17
2
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
17
5
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
View file @
43251e25
1 \N schema_version 9
5
1 \N schema_version 9
7
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
...
...
@@ -102,3 +102,6 @@
151 \N patch patch_93_94_c.sql|default_aln_type
152 \N patch patch_94_95_a.sql|schema_version
153 \N patch patch_94_95_b.sql|vertebrate_division_rename
154 \N patch patch_95_96_a.sql|schema_version
155 \N patch patch_96_97_a.sql|schema_version
156 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
View file @
43251e25
...
...
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description`
text
,
`biotype_group`
enum
(
'coding'
,
'pseudogene'
,
'snoncoding'
,
'lnoncoding'
,
'mnoncoding'
,
'LRG'
,
'undefined'
,
'no_group'
)
DEFAULT
NULL
,
`so_acc`
varchar
(
64
)
DEFAULT
NULL
,
`so_term`
varchar
(
1023
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`biotype_id`
),
UNIQUE
KEY
`name_type_idx`
(
`name`
,
`object_type`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY
KEY
(
`meta_id`
),
UNIQUE
KEY
`species_key_value_idx`
(
`species_id`
,
`meta_key`
,
`meta_value`
),
KEY
`species_value_idx`
(
`species_id`
,
`meta_value`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
15
4
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
15
7
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
View file @
43251e25
1 \N schema_version 9
5
1 \N schema_version 9
7
2014 1 species.classification Haplorrhini
40 1 assembly.default GRCh37
41 1 assembly.date 2009-02
...
...
@@ -107,3 +107,6 @@
2114 \N patch patch_93_94_c.sql|default_aln_type
2115 \N patch patch_94_95_a.sql|schema_version
2116 \N patch patch_94_95_b.sql|vertebrate_division_rename
2117 \N patch patch_95_96_a.sql|schema_version
2118 \N patch patch_96_97_a.sql|schema_version
2119 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
View file @
43251e25
...
...
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description`
text
,
`biotype_group`
enum
(
'coding'
,
'pseudogene'
,
'snoncoding'
,
'lnoncoding'
,
'mnoncoding'
,
'LRG'
,
'undefined'
,
'no_group'
)
DEFAULT
NULL
,
`so_acc`
varchar
(
64
)
DEFAULT
NULL
,
`so_term`
varchar
(
1023
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`biotype_id`
),
UNIQUE
KEY
`name_type_idx`
(
`name`
,
`object_type`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY
KEY
(
`meta_id`
),
UNIQUE
KEY
`species_key_value_idx`
(
`species_id`
,
`meta_key`
,
`meta_value`
),
KEY
`species_value_idx`
(
`species_id`
,
`meta_value`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
21
17
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
21
20
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
modules/t/test-genome-DBs/homo_sapiens/variation/failed_description.txt
View file @
43251e25
...
...
@@ -17,3 +17,5 @@
18 Supporting evidence can not be re-mapped to the current assembly
19 Variant maps to more than one genomic location
20 Variant at first base in sequence
21 Reference allele does not match the bases at this genome location
22 Alleles cannot be resolved
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
View file @
43251e25
1 \N schema_type variation
2 \N schema_version 9
3
2 \N schema_version 9
6
3 \N patch patch_84_85_a.sql|schema version
4 \N patch patch_84_85_b.sql|create sample_synonym
5 \N patch patch_84_85_c.sql|drop column moltype from variation_synonym
...
...
@@ -31,3 +31,11 @@
31 \N patch patch_92_93_a.sql|schema version
32 \N patch patch_92_93_b.sql|Extend phenotype_ontology_accession mapped_by_attrib predefined set
33 \N patch patch_92_93_c.sql|Add new evidence attribs to the variation and variation_feature tables
34 \N patch patch_93_94_a.sql|schema version
35 \N patch patch_94_95_a.sql|schema version
36 \N patch patch_94_95_b.sql|create table to store allele synonyms
37 \N patch patch_95_96_a.sql|schema version
38 \N patch patch_95_96_b.sql|modify index on variation_synonym
39 \N patch patch_95_96_c.sql|add new entries to the failed_description table
40 \N patch patch_95_96_d.sql|create table to store failed variation features
41 \N patch patch_95_96_e.sql|Rename motif_name to binding_matrix_stable_id.
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
View file @
43251e25
...
...
@@ -20,6 +20,16 @@ CREATE TABLE `allele_code` (
UNIQUE
KEY
`allele_idx`
(
`allele`
(
1000
))
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`allele_synonym`
(
`allele_synonym_id`
int
(
10
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
`variation_id`
int
(
10
)
unsigned
NOT
NULL
,
`hgvs_genomic`
varchar
(
600
)
NOT
NULL
,
`name`
varchar
(
255
)
NOT
NULL
,
PRIMARY
KEY
(
`allele_synonym_id`
),
UNIQUE
KEY
`variation_name_idx`
(
`variation_id`
,
`name`
),
KEY
`name_idx`
(
`name`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`associate_study`
(
`study1_id`
int
(
10
)
unsigned
NOT
NULL
,
`study2_id`
int
(
10
)
unsigned
NOT
NULL
,
...
...
@@ -103,7 +113,7 @@ CREATE TABLE `failed_description` (
`failed_description_id`
int
(
10
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
`description`
text
NOT
NULL
,
PRIMARY
KEY
(
`failed_description_id`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
2
1
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
2
3
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`failed_structural_variation`
(
`failed_structural_variation_id`
int
(
11
)
NOT
NULL
AUTO_INCREMENT
,
...
...
@@ -121,6 +131,14 @@ CREATE TABLE `failed_variation` (
UNIQUE
KEY
`variation_idx`
(
`variation_id`
,
`failed_description_id`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`failed_variation_feature`
(
`failed_variation_feature_id`
int
(
11
)
NOT
NULL
AUTO_INCREMENT
,
`variation_feature_id`
int
(
10
)
unsigned
NOT
NULL
,
`failed_description_id`
int
(
10
)
unsigned
NOT
NULL
,
PRIMARY
KEY
(
`failed_variation_feature_id`
),
UNIQUE
KEY
`variation_feature_idx`
(
`variation_feature_id`
,
`failed_description_id`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`genotype_code`
(
`genotype_code_id`
int
(
11
)
unsigned
NOT
NULL
,
`allele_code_id`
int
(
11
)
unsigned
NOT
NULL
,
...
...
@@ -168,7 +186,7 @@ CREATE TABLE `meta` (
PRIMARY
KEY
(
`meta_id`
),
UNIQUE
KEY
`species_key_value_idx`
(
`species_id`
,
`meta_key`
,
`meta_value`
),
KEY
`species_value_idx`
(
`species_id`
,
`meta_value`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
3
4
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
4
2
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
NOT
NULL
,
...
...
@@ -185,7 +203,7 @@ CREATE TABLE `motif_feature_variation` (
`allele_string`
text
,
`somatic`
tinyint
(
1
)
NOT
NULL
DEFAULT
'0'
,
`consequence_types`
set
(
'TF_binding_site_variant'
,
'TFBS_ablation'
,
'TFBS_fusion'
,
'TFBS_amplification'
,
'TFBS_translocation'
)
DEFAULT
NULL
,
`
motif_name
`
varchar
(
60
)
DEFAULT
NULL
,
`
binding_matrix_stable_id
`
varchar
(
60
)
DEFAULT
NULL
,
`motif_start`
int
(
11
)
unsigned
DEFAULT
NULL
,
`motif_end`
int
(
11
)
unsigned
DEFAULT
NULL
,
`motif_score_delta`
float
DEFAULT
NULL
,
...
...
@@ -665,7 +683,7 @@ CREATE TABLE `variation_synonym` (
`source_id`
int
(
10
)
unsigned
NOT
NULL
,
`name`
varchar
(
255
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`variation_synonym_id`
),
UNIQUE
KEY
`name`
(
`name`
,
`source_id`
),
UNIQUE
KEY
`name
_idx
`
(
`name`
,
`source_id`
,
`variation_id`
),
KEY
`variation_idx`
(
`variation_id`
),
KEY
`subsnp_idx`
(
`subsnp_id`
),
KEY
`source_idx`
(
`source_id`
)
...
...
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