Unverified Commit 29e78b71 authored by Marek Szuba's avatar Marek Szuba Committed by GitHub
Browse files

Merge pull request #36 from Ensembl/rel98_testdb

Manually patch the test databases from 90 to 98 [release/98]
parents 791ebe25 f2c97b6a
1 \N schema_version 90 1 \N schema_version 98
2 1 assembly.default NCBI34 2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606 3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens 26 1 species.classification Homo sapiens
...@@ -89,3 +89,24 @@ ...@@ -89,3 +89,24 @@
156 \N patch patch_89_90_a.sql|schema_version 156 \N patch patch_89_90_a.sql|schema_version
157 \N patch patch_89_90_b.sql|remove_status 157 \N patch patch_89_90_b.sql|remove_status
158 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive 158 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
159 \N patch patch_90_91_a.sql|schema_version
160 \N patch patch_90_91_b.sql|align_type
161 \N patch patch_90_91_c.sql|protein_align_type
162 \N patch patch_90_91_d.sql|remove_external_data
163 \N patch patch_91_92_a.sql|schema_version
164 \N patch patch_91_92_b.sql|add_cigar_line_align_type
165 \N patch patch_92_93_a.sql|schema_version
166 \N patch patch_92_93_b.sql|biotype_table
167 \N patch patch_92_93_c.sql|collate_index_interpro
168 \N patch patch_93_94_a.sql|schema_version
169 \N patch patch_93_94_b.sql|nullable_ox_analysis
170 \N patch patch_93_94_c.sql|default_aln_type
171 \N patch patch_94_95_a.sql|schema_version
172 \N patch patch_94_95_b.sql|vertebrate_division_rename
173 \N patch patch_95_96_a.sql|schema_version
174 \N patch patch_96_97_a.sql|schema_version
175 \N patch patch_96_97_b.sql|biotype_so_term
176 \N patch patch_96_97_c.sql|rnaproduct_tables
177 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
178 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
179 \N patch patch_97_98_a.sql|schema_version
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238775 21723 Translation 158511 119 0 238775 21723 Translation 158511 119 \N
238776 21723 Translation 158512 119 0 238776 21723 Translation 158512 119 \N
238777 21723 Translation 120579 119 0 238777 21723 Translation 120579 119 \N
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238779 21723 Translation 158514 119 0 238779 21723 Translation 158514 119 \N
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238782 21723 Translation 158517 119 0 238782 21723 Translation 158517 119 \N
238783 21723 Translation 158518 119 0 238783 21723 Translation 158518 119 \N
238784 21723 Translation 158519 119 0 238784 21723 Translation 158519 119 \N
238785 21723 Translation 158520 119 0 238785 21723 Translation 158520 119 \N
238786 21723 Translation 158521 119 0 238786 21723 Translation 158521 119 \N
238787 21723 Translation 158522 119 0 238787 21723 Translation 158522 119 \N
238788 21723 Translation 158523 119 0 238788 21723 Translation 158523 119 \N
238789 21723 Translation 158524 119 0 238789 21723 Translation 158524 119 \N
238790 21723 Translation 158525 119 0 238790 21723 Translation 158525 119 \N
238791 21723 Translation 257 119 0 238791 21723 Translation 257 119 \N
238792 21723 Translation 258 119 0 238792 21723 Translation 258 119 \N
238793 21723 Translation 259 119 0 238793 21723 Translation 259 119 \N
238794 21723 Translation 612 119 0 238794 21723 Translation 612 119 \N
238795 21723 Translation 260 119 0 238795 21723 Translation 260 119 \N
238796 21723 Translation 994 119 0 238796 21723 Translation 994 119 \N
238797 21723 Translation 5371 119 0 238797 21723 Translation 5371 119 \N
251369 21723 Translation 166799 119 0 251369 21723 Translation 166799 119 \N
251370 21723 Translation 166800 119 0 251370 21723 Translation 166800 119 \N
253531 21736 Translation 168321 119 0 253531 21736 Translation 168321 119 \N
253532 21736 Translation 168322 119 0 253532 21736 Translation 168322 119 \N
253533 21736 Translation 168323 119 0 253533 21736 Translation 168323 119 \N
253534 21736 Translation 168324 119 0 253534 21736 Translation 168324 119 \N
253682 21727 Translation 168444 119 0 253682 21727 Translation 168444 119 \N
253683 21727 Translation 168445 119 0 253683 21727 Translation 168445 119 \N
253684 21727 Translation 168446 119 0 253684 21727 Translation 168446 119 \N
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27 51511 ciona_savignyi CSAV2.0 2006-04-Ensembl 0 1 \N \N \N \N 39 \N 27 51511 ciona_savignyi CSAV2.0 2006-04-Ensembl 0 0 \N \N \N \N 39 \N
31 9544 macaca_mulatta MMUL_1 2006-01-Ensembl 1 1 \N \N \N \N 40 \N 31 9544 macaca_mulatta MMUL_1 2006-01-Ensembl 1 0 \N \N \N \N 40 \N
33 9371 echinops_telfairi TENREC 2006-01-Ensembl 0 0 \N \N \N \N 40 \N 33 9371 echinops_telfairi TENREC 2006-01-Ensembl 0 0 \N \N \N \N 40 \N
36 69293 gasterosteus_aculeatus BROADS1 2006-06-Ensembl 1 1 \N \N \N \N 40 \N 36 69293 gasterosteus_aculeatus BROADS1 2006-06-Ensembl 1 1 \N \N \N \N 40 \N
37 8090 oryzias_latipes MEDAKA1 2006-05-Ensembl 1 1 \N \N \N \N 41 \N 37 8090 oryzias_latipes MEDAKA1 2006-05-Ensembl 1 0 \N \N \N \N 41 \N
43 9258 ornithorhynchus_anatinus OANA5 2007-01-Ensembl 1 1 \N \N \N \N 42 \N 43 9258 ornithorhynchus_anatinus OANA5 2007-01-Ensembl 1 0 \N \N \N \N 42 \N
46 13616 monodelphis_domestica BROADO5 2007-02-Ensembl 1 1 \N \N \N \N 44 \N 46 13616 monodelphis_domestica BROADO5 2007-02-Ensembl 1 0 \N \N \N \N 44 \N
48 37347 tupaia_belangeri TREESHREW 2006-10-Ensembl 0 0 \N \N \N \N 43 \N 48 37347 tupaia_belangeri TREESHREW 2006-10-Ensembl 0 0 \N \N \N \N 43 \N
49 9365 erinaceus_europaeus HEDGEHOG 2006-10-Ensembl 0 0 \N \N \N \N 43 \N 49 9365 erinaceus_europaeus HEDGEHOG 2006-10-Ensembl 0 0 \N \N \N \N 43 \N
55 42254 sorex_araneus COMMON_SHREW1 2007-04-Ensembl 0 0 \N \N \N \N 45 \N 55 42254 sorex_araneus COMMON_SHREW1 2007-04-Ensembl 0 0 \N \N \N \N 45 \N
58 30608 microcebus_murinus micMur1 2007-07-Ensembl 0 0 \N \N \N \N 48 \N 58 30608 microcebus_murinus micMur1 2007-07-Ensembl 0 0 \N \N \N \N 48 \N
60 9601 pongo_abelii PPYG2 2007-10-Ensembl 1 1 \N \N \N \N 49 \N 60 9601 pongo_abelii PPYG2 2007-10-Ensembl 1 1 \N \N \N \N 49 \N
61 9796 equus_caballus EquCab2 2007-09-Ensembl 1 1 \N \N \N \N 49 \N 61 9796 equus_caballus EquCab2 2007-09-Ensembl 1 0 \N \N \N \N 49 \N
65 99883 tetraodon_nigroviridis TETRAODON8 2007-11-Ensembl 1 1 \N \N \N \N 50 \N 65 99883 tetraodon_nigroviridis TETRAODON8 2007-11-Ensembl 1 1 \N \N \N \N 50 \N
67 9978 ochotona_princeps pika 2008-01-Ensembl 0 0 \N \N \N \N 50 \N 67 9978 ochotona_princeps pika 2008-01-Ensembl 0 0 \N \N \N \N 50 \N
69 10141 cavia_porcellus cavPor3 2008-03-Ensembl 0 1 \N \N \N \N 51 \N 69 10141 cavia_porcellus cavPor3 2008-03-Ensembl 0 0 \N \N \N \N 51 \N
78 9358 choloepus_hoffmanni choHof1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N 78 9358 choloepus_hoffmanni choHof1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
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...@@ -26,44 +26,44 @@ ...@@ -26,44 +26,44 @@
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111 28377 anolis_carolinensis AnoCar2.0 2010-09-Ensembl 1 1 \N \N \N \N 61 \N 111 28377 anolis_carolinensis AnoCar2.0 2010-09-Ensembl 1 1 \N \N \N \N 61 \N
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128 7719 ciona_intestinalis KH 2011-08-Ensembl 1 1 \N \N \N \N 66 \N 128 7719 ciona_intestinalis KH 2011-08-Ensembl 1 1 \N \N \N \N 66 \N
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130 8128 oreochromis_niloticus Orenil1.0 2011-05-Ensembl 0 1 \N \N \N \N 67 \N 130 8128 oreochromis_niloticus Orenil1.0 2011-05-Ensembl 0 0 \N \N \N \N 67 \N
131 43179 ictidomys_tridecemlineatus spetri2 2011-12-Ensembl 0 1 \N \N \N \N 67 \N 131 43179 ictidomys_tridecemlineatus spetri2 2011-12-Ensembl 0 0 \N \N \N \N 67 \N
132 9823 sus_scrofa Sscrofa10.2 2011-09-Ensembl 1 1 \N \N \N \N 67 \N 132 9823 sus_scrofa Sscrofa10.2 2011-09-Ensembl 1 0 \N \N \N \N 67 \N
134 10090 mus_musculus GRCm38 2012-01-Ensembl 1 1 \N \N \N \N 68 \N 134 10090 mus_musculus GRCm38 2012-01-Ensembl 1 1 \N \N \N \N 68 \N
135 9615 canis_familiaris CanFam3.1 2011-11-Ensembl 1 1 \N \N \N \N 68 \N 135 9615 canis_familiaris CanFam3.1 2011-11-Ensembl 1 1 \N \N \N \N 68 \N
136 13735 pelodiscus_sinensis PelSin_1.0 2011-11-Ensembl 0 1 \N \N \N \N 68 \N 136 13735 pelodiscus_sinensis PelSin_1.0 2011-11-Ensembl 0 0 \N \N \N \N 68 \N
137 8083 xiphophorus_maculatus Xipmac4.4.2 2012-01-Ensembl 0 1 \N \N \N \N 69 \N 137 8083 xiphophorus_maculatus Xipmac4.4.2 2012-01-Ensembl 0 0 \N \N \N \N 69 \N
138 9669 mustela_putorius_furo MusPutFur1.0 2012-04-Ensembl 0 1 \N \N \N \N 69 \N 138 9669 mustela_putorius_furo MusPutFur1.0 2012-04-Ensembl 0 0 \N \N \N \N 69 \N
139 9685 felis_catus Felis_catus_6.2 2011-12-Ensembl 1 1 \N \N \N \N 70 \N 139 9685 felis_catus Felis_catus_6.2 2011-12-Ensembl 1 0 \N \N \N \N 70 \N
142 9031 gallus_gallus Galgal4 2011-12-Ensembl 1 1 \N \N \N \N 71 \N 142 9031 gallus_gallus Galgal4 2011-12-Ensembl 1 0 \N \N \N \N 71 \N
143 6239 caenorhabditis_elegans WBcel235 2014-09-WormBase 1 1 \N \N \N \N 71 \N 143 6239 caenorhabditis_elegans WBcel235 2014-09-WormBase 1 1 \N \N \N \N 71 \N
144 8839 anas_platyrhynchos BGI_duck_1.0 2009-09-Ensembl 0 1 \N \N \N \N 73 \N 144 8839 anas_platyrhynchos BGI_duck_1.0 2009-09-Ensembl 0 0 \N \N \N \N 73 \N
145 59894 ficedula_albicollis FicAlb_1.4 2012-05-Ensembl 0 1 \N \N \N \N 73 \N 145 59894 ficedula_albicollis FicAlb_1.4 2012-05-Ensembl 0 0 \N \N \N \N 73 \N
146 7994 astyanax_mexicanus AstMex102 2013-04-Ensembl 0 1 \N \N \N \N 74 \N 146 7994 astyanax_mexicanus AstMex102 2013-04-Ensembl 0 0 \N \N \N \N 74 \N
147 9940 ovis_aries Oar_v3.1 2012-12-Ensembl 1 1 \N \N \N \N 74 \N 147 9940 ovis_aries Oar_v3.1 2012-12-Ensembl 1 1 \N \N \N \N 74 \N
148 7918 lepisosteus_oculatus LepOcu1 2012-01-Ensembl 1 1 \N \N \N \N 74 \N 148 7918 lepisosteus_oculatus LepOcu1 2012-01-Ensembl 1 1 \N \N \N \N 74 \N
149 9361 dasypus_novemcinctus Dasnov3.0 2013-06-Ensembl 0 1 \N \N \N \N 74 \N 149 9361 dasypus_novemcinctus Dasnov3.0 2013-06-Ensembl 0 0 \N \N \N \N 74 \N
150 9606 homo_sapiens NCBI33 2014-01-Ensembl 1 1 \N \N \N \N 76 \N 150 9606 homo_sapiens NCBI33 2014-01-Ensembl 1 0 \N \N \N \N 76 \N
151 9555 papio_anubis PapAnu2.0 2013-01-Ensembl 1 1 \N \N \N \N 76 \N 151 9555 papio_anubis PapAnu2.0 2013-01-Ensembl 1 0 \N \N \N \N 76 \N
152 48698 poecilia_formosa PoeFor_5.1.2 2013-11-Ensembl 0 1 \N \N \N \N 76 \N 152 48698 poecilia_formosa PoeFor_5.1.2 2013-11-Ensembl 0 0 \N \N \N \N 76 \N
153 60711 chlorocebus_sabaeus ChlSab1.1 2014-03-Ensembl 1 1 \N \N \N \N 77 \N 153 60711 chlorocebus_sabaeus ChlSab1.1 2014-03-Ensembl 1 1 \N \N \N \N 77 \N
154 7955 danio_rerio GRCz10 2014-09-Ensembl 1 1 \N \N \N \N 80 \N 154 7955 danio_rerio GRCz10 2014-09-Ensembl 1 0 \N \N \N \N 80 \N
155 10116 rattus_norvegicus Rnor_6.0 2014-09-Ensembl 1 1 \N \N \N \N 80 \N 155 10116 rattus_norvegicus Rnor_6.0 2014-09-Ensembl 1 1 \N \N \N \N 80 \N
156 7227 drosophila_melanogaster BDGP6 2014-05-FlyBase 1 1 \N \N \N \N 79 \N 156 7227 drosophila_melanogaster BDGP6 2014-05-FlyBase 1 1 \N \N \N \N 79 \N
36 \N schema_version 90 66 \N schema_version 98
2 \N schema_type compara 2 \N schema_type compara
3 \N patch patch_84_85_a.sql|schema_version 3 \N patch patch_84_85_a.sql|schema_version
4 \N patch patch_84_85_b.sql|gene_tree_root_attr 4 \N patch patch_84_85_b.sql|gene_tree_root_attr
...@@ -35,3 +35,21 @@ ...@@ -35,3 +35,21 @@
40 \N patch patch_89_90_d.sql|genomic_align_tree_left_node_id_null 40 \N patch patch_89_90_d.sql|genomic_align_tree_left_node_id_null
41 \N patch patch_89_90_e.sql|seq_member_projection 41 \N patch patch_89_90_e.sql|seq_member_projection
42 \N patch patch_89_90_f.sql|gene_member_missing_biotype_groups 42 \N patch patch_89_90_f.sql|gene_member_missing_biotype_groups
44 \N patch patch_90_91_a.sql|schema_version
45 \N patch patch_90_91_b.sql|gene_member_qc.seq_member_id.unsigned.foreign_key
46 \N patch patch_90_91_c.sql|gene_member.biotype_group-index
48 \N patch patch_91_92_a.sql|schema_version
49 \N patch patch_91_92_b.sql|mapping_session_new_type_hmm
50 \N patch patch_91_92_c.sql|gene_tree_root_tag_255
52 \N patch patch_92_93_a.sql|schema_version
54 \N patch patch_93_94_a.sql|schema_version
55 \N patch patch_93_94_b.sql|homology_description_not_null
56 \N patch patch_93_94_c.sql|method_link_display_name
58 \N patch patch_94_95_a.sql|schema_version
59 \N patch patch_94_95_b.sql|remove_unused_indices
60 \N patch patch_94_95_c.sql|genome_db_is_good_for_alignment
61 \N patch patch_94_95_d.sql|node_type_within_species_speciation
63 \N patch patch_95_96_a.sql|schema_version
65 \N patch patch_96_97_a.sql|schema_version
67 \N patch patch_97_98_a.sql|schema_version
68 \N patch patch_97_98_b.sql|division_name
401 PROTEIN_TREES ProteinTree.protein_tree_node 401 PROTEIN_TREES ProteinTree.protein_tree_node protein-trees
201 ENSEMBL_ORTHOLOGUES Homology.homology 201 ENSEMBL_ORTHOLOGUES Homology.homology orthologues
202 ENSEMBL_PARALOGUES Homology.homology 202 ENSEMBL_PARALOGUES Homology.homology paralogues
402 NC_TREES NCTree.nc_tree_node 402 NC_TREES NCTree.nc_tree_node ncRNA-trees
101 SYNTENY SyntenyRegion.synteny 101 SYNTENY SyntenyRegion.synteny synteny
16 LASTZ_NET GenomicAlignBlock.pairwise_alignment 16 LASTZ_NET GenomicAlignBlock.pairwise_alignment LastZ
...@@ -24,8 +24,8 @@ CREATE TABLE `conservation_score` ( ...@@ -24,8 +24,8 @@ CREATE TABLE `conservation_score` (
`genomic_align_block_id` bigint(20) unsigned NOT NULL, `genomic_align_block_id` bigint(20) unsigned NOT NULL,
`window_size` smallint(5) unsigned NOT NULL, `window_size` smallint(5) unsigned NOT NULL,
`position` int(10) unsigned NOT NULL, `position` int(10) unsigned NOT NULL,
`expected_score` blob, `expected_score` blob DEFAULT NULL,
`diff_score` blob, `diff_score` blob DEFAULT NULL,
KEY `genomic_align_block_id` (`genomic_align_block_id`,`window_size`) KEY `genomic_align_block_id` (`genomic_align_block_id`,`window_size`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=15000000 AVG_ROW_LENGTH=841; ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=15000000 AVG_ROW_LENGTH=841;
...@@ -36,34 +36,32 @@ CREATE TABLE `constrained_element` ( ...@@ -36,34 +36,32 @@ CREATE TABLE `constrained_element` (
`dnafrag_end` int(12) unsigned NOT NULL, `dnafrag_end` int(12) unsigned NOT NULL,
`dnafrag_strand` int(2) NOT NULL, `dnafrag_strand` int(2) NOT NULL,
`method_link_species_set_id` int(10) unsigned NOT NULL, `method_link_species_set_id` int(10) unsigned NOT NULL,
`p_value` double NOT NULL DEFAULT '0', `p_value` double NOT NULL DEFAULT 0,
`score` double NOT NULL DEFAULT '0',