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ensembl-gh-mirror
ensembl-test
Commits
a305d5ad
Commit
a305d5ad
authored
Feb 03, 2021
by
Tamara El Naboulsi
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Changes for 105 version bump
parent
90d0843b
Pipeline
#127690
passed with stage
in 3 minutes and 50 seconds
Changes
6
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1
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6 changed files
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55 additions
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43 deletions
+55
-43
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+2
-1
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+1
-1
modules/t/test-genome-DBs/multi/compara/meta.txt
modules/t/test-genome-DBs/multi/compara/meta.txt
+4
-1
modules/t/test-genome-DBs/multi/compara/table.sql
modules/t/test-genome-DBs/multi/compara/table.sql
+45
-38
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
+2
-1
modules/t/test-genome-DBs/mus_musculus/core/table.sql
modules/t/test-genome-DBs/mus_musculus/core/table.sql
+1
-1
No files found.
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @
a305d5ad
1 \N schema_version 10
4
1 \N schema_version 10
5
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
...
...
@@ -119,3 +119,4 @@
193 \N patch patch_101_102_a.sql|schema_version
194 \N patch patch_102_103_a.sql|schema_version
195 \N patch patch_103_104_a.sql|schema_version
196 \N patch patch_104_105_a.sql|schema_version
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
View file @
a305d5ad
...
...
@@ -490,7 +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
=
19
6
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
19
7
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
modules/t/test-genome-DBs/multi/compara/meta.txt
View file @
a305d5ad
8
5 \N schema_version 104
8
9 \N schema_version 105
2 \N schema_type compara
3 \N patch patch_84_85_a.sql|schema_version
4 \N patch patch_84_85_b.sql|gene_tree_root_attr
...
...
@@ -67,3 +67,6 @@
82 \N patch patch_101_102_c.sql|stn_node_id_bigint
84 \N patch patch_102_103_a.sql|schema_version
86 \N patch patch_103_104_a.sql|schema_version
87 \N patch patch_103_104_b.sql|dnafrag_alt_region
88 \N patch patch_103_104_c.sql|fix_int_types
90 \N patch patch_104_105_a.sql|schema_version
modules/t/test-genome-DBs/multi/compara/table.sql
View file @
a305d5ad
...
...
@@ -14,7 +14,7 @@ CREATE TABLE `CAFE_gene_family` (
CREATE
TABLE
`CAFE_species_gene`
(
`cafe_gene_family_id`
int
(
10
)
unsigned
NOT
NULL
,
`node_id`
bigint
(
20
)
unsigned
NOT
NULL
,
`n_members`
int
(
4
)
unsigned
NOT
NULL
,
`n_members`
int
(
10
)
unsigned
NOT
NULL
,
`pvalue`
double
(
5
,
4
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`cafe_gene_family_id`
,
`node_id`
),
KEY
`node_id`
(
`node_id`
)
...
...
@@ -32,9 +32,9 @@ CREATE TABLE `conservation_score` (
CREATE
TABLE
`constrained_element`
(
`constrained_element_id`
bigint
(
20
)
unsigned
NOT
NULL
,
`dnafrag_id`
bigint
(
20
)
unsigned
NOT
NULL
,
`dnafrag_start`
int
(
1
2
)
unsigned
NOT
NULL
,
`dnafrag_end`
int
(
1
2
)
unsigned
NOT
NULL
,
`dnafrag_strand`
int
(
2
)
NOT
NULL
,
`dnafrag_start`
int
(
1
0
)
unsigned
NOT
NULL
,
`dnafrag_end`
int
(
1
0
)
unsigned
NOT
NULL
,
`dnafrag_strand`
tinyint
(
4
)
NOT
NULL
,
`method_link_species_set_id`
int
(
10
)
unsigned
NOT
NULL
,
`p_value`
double
NOT
NULL
DEFAULT
'0'
,
`score`
double
NOT
NULL
DEFAULT
'0'
,
...
...
@@ -51,11 +51,18 @@ CREATE TABLE `dnafrag` (
`coord_system_name`
varchar
(
40
)
NOT
NULL
DEFAULT
''
,
`cellular_component`
enum
(
'NUC'
,
'MT'
,
'PT'
,
'OTHER'
)
NOT
NULL
DEFAULT
'NUC'
,
`is_reference`
tinyint
(
1
)
NOT
NULL
DEFAULT
'1'
,
`codon_table_id`
tinyint
(
2
)
unsigned
NOT
NULL
DEFAULT
'1'
,
`codon_table_id`
tinyint
(
3
)
unsigned
NOT
NULL
DEFAULT
'1'
,
PRIMARY
KEY
(
`dnafrag_id`
),
UNIQUE
KEY
`name`
(
`genome_db_id`
,
`name`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
14026981
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`dnafrag_alt_region`
(
`dnafrag_id`
bigint
(
20
)
unsigned
NOT
NULL
,
`dnafrag_start`
int
(
10
)
unsigned
NOT
NULL
,
`dnafrag_end`
int
(
10
)
unsigned
NOT
NULL
,
PRIMARY
KEY
(
`dnafrag_id`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`dnafrag_region`
(
`synteny_region_id`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`dnafrag_id`
bigint
(
20
)
unsigned
NOT
NULL
DEFAULT
'0'
,
...
...
@@ -69,10 +76,10 @@ CREATE TABLE `dnafrag_region` (
CREATE
TABLE
`exon_boundaries`
(
`gene_member_id`
int
(
10
)
unsigned
NOT
NULL
,
`seq_member_id`
int
(
10
)
unsigned
NOT
NULL
,
`dnafrag_start`
int
(
1
1
)
NOT
NULL
,
`dnafrag_end`
int
(
1
1
)
NOT
NULL
,
`dnafrag_start`
int
(
1
0
)
unsigned
NOT
NULL
,
`dnafrag_end`
int
(
1
0
)
unsigned
NOT
NULL
,
`sequence_length`
int
(
10
)
unsigned
NOT
NULL
,
`left_over`
tinyint
(
1
)
NOT
NULL
DEFAULT
'0'
,
`left_over`
tinyint
(
3
)
unsigned
NOT
NULL
DEFAULT
'0'
,
KEY
`seq_member_id`
(
`seq_member_id`
),
KEY
`gene_member_id`
(
`gene_member_id`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -117,7 +124,7 @@ CREATE TABLE `gene_align` (
`gene_align_id`
int
(
10
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
`seq_type`
varchar
(
40
)
DEFAULT
NULL
,
`aln_method`
varchar
(
40
)
NOT
NULL
DEFAULT
''
,
`aln_length`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`aln_length`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
PRIMARY
KEY
(
`gene_align_id`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
100000189
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -132,7 +139,7 @@ CREATE TABLE `gene_align_member` (
CREATE
TABLE
`gene_member`
(
`gene_member_id`
int
(
10
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
`stable_id`
varchar
(
128
)
NOT
NULL
,
`version`
int
(
10
)
DEFAULT
'0'
,
`version`
int
(
10
)
unsigned
DEFAULT
'0'
,
`source_name`
enum
(
'ENSEMBLGENE'
,
'EXTERNALGENE'
)
NOT
NULL
,
`taxon_id`
int
(
10
)
unsigned
NOT
NULL
,
`genome_db_id`
int
(
10
)
unsigned
DEFAULT
NULL
,
...
...
@@ -140,8 +147,8 @@ CREATE TABLE `gene_member` (
`canonical_member_id`
int
(
10
)
unsigned
DEFAULT
NULL
,
`description`
text
,
`dnafrag_id`
bigint
(
20
)
unsigned
DEFAULT
NULL
,
`dnafrag_start`
int
(
10
)
DEFAULT
NULL
,
`dnafrag_end`
int
(
10
)
DEFAULT
NULL
,
`dnafrag_start`
int
(
10
)
unsigned
DEFAULT
NULL
,
`dnafrag_end`
int
(
10
)
unsigned
DEFAULT
NULL
,
`dnafrag_strand`
tinyint
(
4
)
DEFAULT
NULL
,
`display_label`
varchar
(
128
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`gene_member_id`
),
...
...
@@ -184,8 +191,8 @@ CREATE TABLE `gene_tree_node` (
`node_id`
int
(
10
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
`parent_id`
int
(
10
)
unsigned
DEFAULT
NULL
,
`root_id`
int
(
10
)
unsigned
DEFAULT
NULL
,
`left_index`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`right_index`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`left_index`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`right_index`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`distance_to_parent`
double
NOT
NULL
DEFAULT
'1'
,
`seq_member_id`
int
(
10
)
unsigned
DEFAULT
NULL
,
PRIMARY
KEY
(
`node_id`
),
...
...
@@ -299,11 +306,11 @@ CREATE TABLE `genomic_align` (
`genomic_align_block_id`
bigint
(
20
)
unsigned
NOT
NULL
,
`method_link_species_set_id`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`dnafrag_id`
bigint
(
20
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`dnafrag_start`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`dnafrag_end`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`dnafrag_start`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`dnafrag_end`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`dnafrag_strand`
tinyint
(
4
)
NOT
NULL
DEFAULT
'0'
,
`cigar_line`
mediumtext
NOT
NULL
,
`visible`
tinyint
(
2
)
unsigned
NOT
NULL
DEFAULT
'1'
,
`visible`
tinyint
(
3
)
unsigned
NOT
NULL
DEFAULT
'1'
,
`node_id`
bigint
(
20
)
unsigned
DEFAULT
NULL
,
PRIMARY
KEY
(
`genomic_align_id`
),
KEY
`genomic_align_block_id`
(
`genomic_align_block_id`
),
...
...
@@ -317,10 +324,10 @@ CREATE TABLE `genomic_align_block` (
`method_link_species_set_id`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`score`
double
DEFAULT
NULL
,
`perc_id`
tinyint
(
3
)
unsigned
DEFAULT
NULL
,
`length`
int
(
10
)
NOT
NULL
,
`length`
int
(
10
)
unsigned
NOT
NULL
,
`group_id`
bigint
(
20
)
unsigned
DEFAULT
NULL
,
`level_id`
tinyint
(
2
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`direction`
tinyint
(
1
)
unsigned
DEFAULT
NULL
,
`level_id`
tinyint
(
3
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`direction`
tinyint
(
3
)
unsigned
DEFAULT
NULL
,
PRIMARY
KEY
(
`genomic_align_block_id`
),
KEY
`method_link_species_set_id`
(
`method_link_species_set_id`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
6770001148336
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -329,8 +336,8 @@ CREATE TABLE `genomic_align_tree` (
`node_id`
bigint
(
20
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
`parent_id`
bigint
(
20
)
unsigned
DEFAULT
NULL
,
`root_id`
bigint
(
20
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`left_index`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`right_index`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`left_index`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`right_index`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`left_node_id`
bigint
(
20
)
unsigned
DEFAULT
NULL
,
`right_node_id`
bigint
(
20
)
unsigned
DEFAULT
NULL
,
`distance_to_parent`
double
NOT
NULL
DEFAULT
'1'
,
...
...
@@ -429,7 +436,7 @@ CREATE TABLE `meta` (
PRIMARY
KEY
(
`meta_id`
),
UNIQUE
KEY
`species_key_value_idx`
(
`species_id`
,
`meta_key`
,
`meta_value`
(
255
)),
KEY
`species_value_idx`
(
`species_id`
,
`meta_value`
(
255
))
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
87
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
91
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`method_link`
(
`method_link_id`
int
(
10
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
...
...
@@ -504,7 +511,7 @@ CREATE TABLE `ncbi_taxa_node` (
CREATE
TABLE
`other_member_sequence`
(
`seq_member_id`
int
(
10
)
unsigned
NOT
NULL
,
`seq_type`
varchar
(
40
)
NOT
NULL
,
`length`
int
(
10
)
NOT
NULL
,
`length`
int
(
10
)
unsigned
NOT
NULL
,
`sequence`
mediumtext
NOT
NULL
,
PRIMARY
KEY
(
`seq_member_id`
,
`seq_type`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
MAX_ROWS
=
10000000
AVG_ROW_LENGTH
=
60000
;
...
...
@@ -515,18 +522,18 @@ CREATE TABLE `peptide_align_feature` (
`hmember_id`
int
(
10
)
unsigned
NOT
NULL
,
`qgenome_db_id`
int
(
10
)
unsigned
DEFAULT
NULL
,
`hgenome_db_id`
int
(
10
)
unsigned
DEFAULT
NULL
,
`qstart`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`qend`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`qstart`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`qend`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`hstart`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`hend`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`score`
double
(
16
,
4
)
NOT
NULL
DEFAULT
'0.0000'
,
`evalue`
double
NOT
NULL
,
`align_length`
int
(
10
)
NOT
NULL
,
`identical_matches`
int
(
10
)
NOT
NULL
,
`perc_ident`
int
(
10
)
NOT
NULL
,
`positive_matches`
int
(
10
)
NOT
NULL
,
`perc_pos`
int
(
10
)
NOT
NULL
,
`hit_rank`
int
(
10
)
NOT
NULL
,
`align_length`
int
(
10
)
unsigned
NOT
NULL
,
`identical_matches`
int
(
10
)
unsigned
NOT
NULL
,
`perc_ident`
tinyint
(
3
)
unsigned
NOT
NULL
,
`positive_matches`
int
(
10
)
unsigned
NOT
NULL
,
`perc_pos`
tinyint
(
3
)
unsigned
NOT
NULL
,
`hit_rank`
smallint
(
5
)
unsigned
NOT
NULL
,
`cigar_line`
mediumtext
,
PRIMARY
KEY
(
`peptide_align_feature_id`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
MAX_ROWS
=
100000000
AVG_ROW_LENGTH
=
133
;
...
...
@@ -534,7 +541,7 @@ CREATE TABLE `peptide_align_feature` (
CREATE
TABLE
`seq_member`
(
`seq_member_id`
int
(
10
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
`stable_id`
varchar
(
128
)
NOT
NULL
,
`version`
int
(
10
)
DEFAULT
'0'
,
`version`
int
(
10
)
unsigned
DEFAULT
'0'
,
`source_name`
enum
(
'ENSEMBLPEP'
,
'ENSEMBLTRANS'
,
'Uniprot/SPTREMBL'
,
'Uniprot/SWISSPROT'
,
'EXTERNALPEP'
,
'EXTERNALTRANS'
,
'EXTERNALCDS'
)
NOT
NULL
,
`taxon_id`
int
(
10
)
unsigned
NOT
NULL
,
`genome_db_id`
int
(
10
)
unsigned
DEFAULT
NULL
,
...
...
@@ -544,8 +551,8 @@ CREATE TABLE `seq_member` (
`has_translation_edits`
tinyint
(
1
)
NOT
NULL
DEFAULT
'0'
,
`description`
text
,
`dnafrag_id`
bigint
(
20
)
unsigned
DEFAULT
NULL
,
`dnafrag_start`
int
(
10
)
DEFAULT
NULL
,
`dnafrag_end`
int
(
10
)
DEFAULT
NULL
,
`dnafrag_start`
int
(
10
)
unsigned
DEFAULT
NULL
,
`dnafrag_end`
int
(
10
)
unsigned
DEFAULT
NULL
,
`dnafrag_strand`
tinyint
(
4
)
DEFAULT
NULL
,
`display_label`
varchar
(
128
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`seq_member_id`
),
...
...
@@ -577,7 +584,7 @@ CREATE TABLE `seq_member_projection_stable_id` (
CREATE
TABLE
`sequence`
(
`sequence_id`
int
(
10
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
`length`
int
(
10
)
NOT
NULL
,
`length`
int
(
10
)
unsigned
NOT
NULL
,
`md5sum`
char
(
32
)
NOT
NULL
,
`sequence`
longtext
NOT
NULL
,
PRIMARY
KEY
(
`sequence_id`
),
...
...
@@ -612,8 +619,8 @@ CREATE TABLE `species_tree_node` (
`node_id`
bigint
(
20
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
`parent_id`
bigint
(
20
)
unsigned
DEFAULT
NULL
,
`root_id`
bigint
(
20
)
unsigned
DEFAULT
NULL
,
`left_index`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`right_index`
int
(
10
)
NOT
NULL
DEFAULT
'0'
,
`left_index`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`right_index`
int
(
10
)
unsigned
NOT
NULL
DEFAULT
'0'
,
`distance_to_parent`
double
DEFAULT
'1'
,
`taxon_id`
int
(
10
)
unsigned
DEFAULT
NULL
,
`genome_db_id`
int
(
10
)
unsigned
DEFAULT
NULL
,
...
...
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
View file @
a305d5ad
1 \N schema_type core
2 \N schema_version 10
4
2 \N schema_version 10
5
3 \N patch patch_65_66_a.sql|schema_version
4 \N patch patch_65_66_b.sql|fix_external_db_id
5 \N patch patch_65_66_c.sql|reorder_unmapped_obj_index
...
...
@@ -197,3 +197,4 @@
1709 \N patch patch_101_102_a.sql|schema_version
1710 \N patch patch_102_103_a.sql|schema_version
1711 \N patch patch_103_104_a.sql|schema_version
1712 \N patch patch_104_105_a.sql|schema_version
modules/t/test-genome-DBs/mus_musculus/core/table.sql
View file @
a305d5ad
...
...
@@ -490,7 +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
=
171
2
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
171
3
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
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