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
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
......@@ -89,3 +89,24 @@
156 \N patch patch_89_90_a.sql|schema_version
157 \N patch patch_89_90_b.sql|remove_status
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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500 21735 Translation 332 119 \N
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502 21735 Translation 334 119 \N
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41169 21729 Translation 28813 119 \N
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41183 21729 Translation 20 119 \N
42617 21730 Translation 29946 119 \N
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42619 21730 Translation 29948 119 \N
49607 21732 Translation 34890 119 \N
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49609 21732 Translation 34892 119 \N
49727 21721 Translation 34984 119 \N
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52553 21724 Translation 37039 119 \N
52554 21724 Translation 37040 119 \N
54721 21729 Translation 38683 119 \N
54722 21729 Translation 38684 119 \N
56601 21719 Translation 40088 119 \N
56602 21719 Translation 40089 119 \N
56603 21719 Translation 40090 119 \N
72763 21721 Translation 51533 119 \N
72764 21721 Translation 51534 119 \N
72765 21721 Translation 51535 119 \N
76579 21732 Translation 53919 119 \N
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76581 21732 Translation 53921 119 \N
83261 21726 Translation 58594 119 \N
83262 21726 Translation 58595 119 \N
83263 21726 Translation 58596 119 \N
83264 21726 Translation 58597 119 \N
83265 21726 Translation 58598 119 \N
83266 21726 Translation 28816 119 \N
83267 21726 Translation 58599 119 \N
83268 21726 Translation 139 119 \N
83269 21726 Translation 141 119 \N
83270 21726 Translation 143 119 \N
104881 21737 Translation 72100 119 \N
104882 21737 Translation 72101 119 \N
130254 21734 Translation 89323 119 \N
130255 21734 Translation 89324 119 \N
130256 21734 Translation 89325 119 \N
130257 21733 Translation 89326 119 \N
130258 21733 Translation 89324 119 \N
130259 21733 Translation 89327 119 \N
142713 21738 Translation 97756 119 \N
142714 21738 Translation 97757 119 \N
142715 21738 Translation 97758 119 \N
142716 21738 Translation 97759 119 \N
149839 21722 Translation 102408 119 \N
149840 21722 Translation 102409 119 \N
149841 21722 Translation 102410 119 \N
149842 21722 Translation 34986 119 \N
149843 21722 Translation 994 119 \N
149844 21720 Translation 102411 119 \N
149845 21720 Translation 102409 119 \N
149846 21720 Translation 102412 119 \N
149847 21720 Translation 102413 119 \N
149848 21719 Translation 102414 119 \N
149849 21719 Translation 102409 119 \N
149850 21719 Translation 102415 119 \N
151214 21738 Translation 103295 119 \N
151215 21738 Translation 103296 119 \N
151216 21738 Translation 103297 119 \N
151217 21738 Translation 15954 119 \N
151218 21738 Translation 103298 119 \N
151219 21738 Translation 2617 119 \N
151220 21738 Translation 18952 119 \N
151221 21738 Translation 50 119 \N
151222 21738 Translation 891 119 \N
151223 21738 Translation 51 119 \N
151224 21738 Translation 269 119 \N
179285 21724 Translation 120576 119 \N
179286 21724 Translation 120577 119 \N
179287 21724 Translation 120578 119 \N
179288 21724 Translation 120579 119 \N
179289 21724 Translation 120580 119 \N
179290 21724 Translation 120581 119 \N
179291 21724 Translation 120582 119 \N
179292 21724 Translation 120583 119 \N
179293 21724 Translation 120584 119 \N
179294 21724 Translation 1166 119 \N
179295 21724 Translation 793 119 \N
179296 21724 Translation 438 119 \N
190803 21731 Translation 128324 119 \N
190804 21731 Translation 128325 119 \N
190805 21731 Translation 128326 119 \N
191214 21728 Translation 128591 119 \N
191215 21728 Translation 128592 119 \N
191216 21728 Translation 128593 119 \N
191217 21728 Translation 28816 119 \N
191218 21728 Translation 128594 119 \N
191219 21728 Translation 128595 119 \N
191220 21728 Translation 128596 119 \N
191221 21728 Translation 128597 119 \N
191222 21728 Translation 54393 119 \N
191223 21728 Translation 612 119 \N
191224 21728 Translation 1284 119 \N
191225 21728 Translation 128347 119 \N
191226 21728 Translation 673 119 \N
191227 21728 Translation 19243 119 \N
191240 21725 Translation 128605 119 \N
191241 21725 Translation 28816 119 \N
191242 21725 Translation 128606 119 \N
191243 21725 Translation 128607 119 \N
191244 21725 Translation 315 119 \N
191245 21725 Translation 3908 119 \N
191246 21725 Translation 143 119 \N
229061 21717 Translation 152191 119 \N
229062 21717 Translation 102409 119 \N
229063 21717 Translation 152192 119 \N
229064 21717 Translation 6990 119 \N
229065 21717 Translation 614 119 \N
229073 21716 Translation 152200 119 \N
229074 21716 Translation 102409 119 \N
229075 21716 Translation 152201 119 \N
229076 21716 Translation 152202 119 \N
229077 21716 Translation 6990 119 \N
229078 21716 Translation 614 119 \N
229273 21732 Translation 152329 119 \N
229274 21732 Translation 89324 119 \N
229275 21732 Translation 152330 119 \N
238768 21723 Translation 158504 119 \N
238769 21723 Translation 158505 119 \N
238770 21723 Translation 158506 119 \N
238771 21723 Translation 158507 119 \N
238772 21723 Translation 158508 119 \N
238773 21723 Translation 158509 119 \N
238774 21723 Translation 158510 119 \N
238775 21723 Translation 158511 119 \N
238776 21723 Translation 158512 119 \N
238777 21723 Translation 120579 119 \N
238778 21723 Translation 158513 119 \N
238779 21723 Translation 158514 119 \N
238780 21723 Translation 158515 119 \N
238781 21723 Translation 158516 119 \N
238782 21723 Translation 158517 119 \N
238783 21723 Translation 158518 119 \N
238784 21723 Translation 158519 119 \N
238785 21723 Translation 158520 119 \N
238786 21723 Translation 158521 119 \N
238787 21723 Translation 158522 119 \N
238788 21723 Translation 158523 119 \N
238789 21723 Translation 158524 119 \N
238790 21723 Translation 158525 119 \N
238791 21723 Translation 257 119 \N
238792 21723 Translation 258 119 \N
238793 21723 Translation 259 119 \N
238794 21723 Translation 612 119 \N
238795 21723 Translation 260 119 \N
238796 21723 Translation 994 119 \N
238797 21723 Translation 5371 119 \N
251369 21723 Translation 166799 119 \N
251370 21723 Translation 166800 119 \N
253531 21736 Translation 168321 119 \N
253532 21736 Translation 168322 119 \N
253533 21736 Translation 168323 119 \N
253534 21736 Translation 168324 119 \N
253682 21727 Translation 168444 119 \N
253683 21727 Translation 168445 119 \N
253684 21727 Translation 168446 119 \N
4 31033 takifugu_rubripes FUGU4 2007-11-Ensembl 0 1 \N \N \N \N 24 \N
27 51511 ciona_savignyi CSAV2.0 2006-04-Ensembl 0 1 \N \N \N \N 39 \N
31 9544 macaca_mulatta MMUL_1 2006-01-Ensembl 1 1 \N \N \N \N 40 \N
4 31033 takifugu_rubripes FUGU4 2007-11-Ensembl 0 0 \N \N \N \N 24 \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 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
37 8090 oryzias_latipes MEDAKA1 2006-05-Ensembl 1 1 \N \N \N \N 41 \N
43 9258 ornithorhynchus_anatinus OANA5 2007-01-Ensembl 1 1 \N \N \N \N 42 \N
46 13616 monodelphis_domestica BROADO5 2007-02-Ensembl 1 1 \N \N \N \N 44 \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 0 \N \N \N \N 42 \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
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
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
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
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
79 9813 procavia_capensis proCap1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
80 9739 tursiops_truncatus turTru1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
......@@ -26,44 +26,44 @@
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115 61853 nomascus_leucogenys Nleu1.0 2010-10-Ensembl 0 1 \N \N \N \N 62 \N
116 8364 xenopus_tropicalis JGI_4.2 2010-09-Ensembl 0 1 \N \N \N \N 62 \N
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121 9305 sarcophilus_harrisii DEVIL7.0 2011-03-Ensembl 0 1 \N \N \N \N 64 \N
122 9913 bos_taurus UMD3.1 2011-04-Ensembl 1 1 \N \N \N \N 64 \N
115 61853 nomascus_leucogenys Nleu1.0 2010-10-Ensembl 0 0 \N \N \N \N 62 \N
116 8364 xenopus_tropicalis JGI_4.2 2010-09-Ensembl 0 0 \N \N \N \N 62 \N
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118 59463 myotis_lucifugus Myoluc2.0 2010-12-Ensembl 0 0 \N \N \N \N 63 \N
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121 9305 sarcophilus_harrisii DEVIL7.0 2011-03-Ensembl 0 0 \N \N \N \N 64 \N
122 9913 bos_taurus UMD3.1 2011-04-Ensembl 1 0 \N \N \N \N 64 \N
123 9595 gorilla_gorilla gorGor3.1 2009-08-Ensembl 1 0 \N \N \N \N 64 \N
124 30611 otolemur_garnettii OtoGar3 2011-06-Ensembl 0 1 \N \N \N \N 65 \N
125 9598 pan_troglodytes CHIMP2.1.4 2011-05-Ensembl 1 1 \N \N \N \N 65 \N
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125 9598 pan_troglodytes CHIMP2.1.4 2011-05-Ensembl 1 0 \N \N \N \N 65 \N
126 8049 gadus_morhua gadMor1 2010-01-Ensembl 0 0 \N \N \N \N 65 \N
127 4932 saccharomyces_cerevisiae R64-1-1 2011-09-SGD 1 1 \N \N \N \N 65 \N
128 7719 ciona_intestinalis KH 2011-08-Ensembl 1 1 \N \N \N \N 66 \N
129 7897 latimeria_chalumnae LatCha1 2011-09-Ensembl 0 1 \N \N \N \N 66 \N
130 8128 oreochromis_niloticus Orenil1.0 2011-05-Ensembl 0 1 \N \N \N \N 67 \N
131 43179 ictidomys_tridecemlineatus spetri2 2011-12-Ensembl 0 1 \N \N \N \N 67 \N
132 9823 sus_scrofa Sscrofa10.2 2011-09-Ensembl 1 1 \N \N \N \N 67 \N
129 7897 latimeria_chalumnae LatCha1 2011-09-Ensembl 0 0 \N \N \N \N 66 \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 0 \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
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
137 8083 xiphophorus_maculatus Xipmac4.4.2 2012-01-Ensembl 0 1 \N \N \N \N 69 \N
138 9669 mustela_putorius_furo MusPutFur1.0 2012-04-Ensembl 0 1 \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
142 9031 gallus_gallus Galgal4 2011-12-Ensembl 1 1 \N \N \N \N 71 \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 0 \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 0 \N \N \N \N 70 \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
144 8839 anas_platyrhynchos BGI_duck_1.0 2009-09-Ensembl 0 1 \N \N \N \N 73 \N
145 59894 ficedula_albicollis FicAlb_1.4 2012-05-Ensembl 0 1 \N \N \N \N 73 \N
146 7994 astyanax_mexicanus AstMex102 2013-04-Ensembl 0 1 \N \N \N \N 74 \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 0 \N \N \N \N 73 \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
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
150 9606 homo_sapiens NCBI33 2014-01-Ensembl 1 1 \N \N \N \N 76 \N
151 9555 papio_anubis PapAnu2.0 2013-01-Ensembl 1 1 \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
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 0 \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 0 \N \N \N \N 76 \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
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
3 \N patch patch_84_85_a.sql|schema_version
4 \N patch patch_84_85_b.sql|gene_tree_root_attr
......@@ -35,3 +35,21 @@
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
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
201 ENSEMBL_ORTHOLOGUES Homology.homology
202 ENSEMBL_PARALOGUES Homology.homology
402 NC_TREES NCTree.nc_tree_node
101 SYNTENY SyntenyRegion.synteny
16 LASTZ_NET GenomicAlignBlock.pairwise_alignment
401 PROTEIN_TREES ProteinTree.protein_tree_node protein-trees
201 ENSEMBL_ORTHOLOGUES Homology.homology orthologues
202 ENSEMBL_PARALOGUES Homology.homology paralogues
402 NC_TREES NCTree.nc_tree_node ncRNA-trees
101 SYNTENY SyntenyRegion.synteny synteny
16 LASTZ_NET GenomicAlignBlock.pairwise_alignment LastZ
......@@ -24,8 +24,8 @@ CREATE TABLE `conservation_score` (
`genomic_align_block_id` bigint(20) unsigned NOT NULL,
`window_size` smallint(5) unsigned NOT NULL,
`position` int(10) unsigned NOT NULL,
`expected_score` blob,
`diff_score` blob,
`expected_score` blob DEFAULT NULL,
`diff_score` blob DEFAULT NULL,
KEY `genomic_align_block_id` (`genomic_align_block_id`,`window_size`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=15000000 AVG_ROW_LENGTH=841;
......@@ -36,34 +36,32 @@ CREATE TABLE `constrained_element` (
`dnafrag_end` int(12) unsigned NOT NULL,