| 1 | * data live in the old mysql database (molgenis14 ) so you need to run the steps of the migration script : https://www.dropbox.com/home/BBmri%20App/migration_issue?select=migration-script.rtf) |
| 2 | * CREATE TABLE !`BiobankSubCategory` ( |
| 3 | |
| 4 | !`id` int(11) NOT NULL, |
| 5 | |
| 6 | PRIMARY KEY (!`id`), |
| 7 | |
| 8 | CONSTRAINT !`biobanksubcategory_ibfk_1` FOREIGN KEY (!`id`) REFERENCES !`OntologyTerm` (!`id`) ON DELETE CASCADE |
| 9 | |
| 10 | ) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci; |
| 11 | |
| 12 | INSERT INTO !BiobankSubCategory (id) |
| 13 | |
| 14 | SELECT id |
| 15 | |
| 16 | FROM !BiobankCategory |
| 17 | |
| 18 | WHERE id NOT IN ("281", "284", "285") ; |
| 19 | |
| 20 | CREATE TABLE !BiobankPersonRole ( |
| 21 | |
| 22 | id INTEGER NOT NULL |
| 23 | |
| 24 | , PRIMARY KEY(id) |
| 25 | |
| 26 | ); |
| 27 | |
| 28 | alter table !OntologyTerm modify column !__Type enum('!OntologyTerm','!PersonRole','Species','!AlternateId','!BiobankCategory','!BiobankTopic','!BiobankDataType', '!BiobankSubCategory','!BiobankPersonRole'); |
| 29 | |
| 30 | ALTER TABLE Biobank DROP FOREIGN KEY biobank_ibfk_5; |
| 31 | |
| 32 | ALTER TABLE !BiobankSubCategory ADD FOREIGN KEY (id) REFERENCES !OntologyTerm (id) ON DELETE CASCADE; |
| 33 | |
| 34 | ALTER TABLE `!BiobankSubCategory` |
| 35 | |
| 36 | ADD CONSTRAINT !`biobank_ibfk_5` |
| 37 | |
| 38 | FOREIGN KEY (!`id`) REFERENCES !OntologyTerm (id) ON DELETE CASCADE; AUTO UPARXEI HDH APO THN DHMIOURGIA TOU) |
| 39 | |
| 40 | ALTER TABLE Biobank ADD FOREIGN KEY (!SubCategory) REFERENCES !BiobankSubCategory (id) ON DELETE RESTRICT; |
| 41 | |
| 42 | ALTER TABLE `Biobank` |
| 43 | |
| 44 | ADD CONSTRAINT !`biobank_ibfk_885` |
| 45 | |
| 46 | FOREIGN KEY (`!SubCategory`) REFERENCES !BiobankSubCategory (id) ON DELETE CASCADE; |
| 47 | |
| 48 | DELETE FROM !BiobankCategory |
| 49 | |
| 50 | WHERE id NOT IN ("281", "284", "285") ; |
| 51 | |
| 52 | ALTER TABLE !BiobankPersonRole ADD FOREIGN KEY (id) REFERENCES !PersonRole (id) ON DELETE CASCADE; |
| 53 | |
| 54 | ALTER TABLE `!BiobankPersonRole` |
| 55 | |
| 56 | ADD CONSTRAINT `!BiobankPersonRole_ibfk_33` |
| 57 | |
| 58 | FOREIGN KEY (`id`) REFERENCES !PersonRole (id) ON DELETE CASCADE; |
| 59 | |
| 60 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='282'; |
| 61 | |
| 62 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='283'; |
| 63 | |
| 64 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='286'; |
| 65 | |
| 66 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='287'; |
| 67 | |
| 68 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='288'; |
| 69 | |
| 70 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='289'; |
| 71 | |
| 72 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='290'; |
| 73 | |
| 74 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='291'; |
| 75 | |
| 76 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='292'; |
| 77 | |
| 78 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='293'; |
| 79 | |
| 80 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='295'; |
| 81 | |
| 82 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='296'; |
| 83 | |
| 84 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='297'; |
| 85 | |
| 86 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='298'; |
| 87 | |
| 88 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='564'; |
| 89 | |
| 90 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='299'; |
| 91 | |
| 92 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='294'; |
| 93 | |
| 94 | select * from !OntologyTerm where name="Software Engineer"; |
| 95 | |
| 96 | delete from !OntologyTerm where id=561; |
| 97 | |
| 98 | select * from !BiobankPersonRole; |
| 99 | |
| 100 | insert into !BiobankPersonRole values(561); |
| 101 | |
| 102 | select * from !OntologyTerm where name="coordinator"; |
| 103 | |
| 104 | delete from !OntologyTerm where id=593; |
| 105 | |
| 106 | select * from !BiobankPersonRole; |
| 107 | |
| 108 | insert into !BiobankPersonRole values(277); |
| 109 | |
| 110 | select * from !OntologyTerm where name="postdoc"; |
| 111 | |
| 112 | delete from !OntologyTerm where id=594; |
| 113 | |
| 114 | select * from !BiobankPersonRole; |
| 115 | |
| 116 | insert into !BiobankPersonRole values(278); |
| 117 | |
| 118 | select * from !OntologyTerm where name="administrator"; |
| 119 | |
| 120 | delete from !OntologyTerm where id=595; |
| 121 | |
| 122 | select * from !BiobankPersonRole; |
| 123 | |
| 124 | insert into !BiobankPersonRole values(279); |
| 125 | |
| 126 | select * from !OntologyTerm where name="IT responsible"; |
| 127 | |
| 128 | delete from !OntologyTerm where id=596; |
| 129 | |
| 130 | select * from !BiobankPersonRole; |
| 131 | |
| 132 | insert into !BiobankPersonRole values(280); |
| 133 | |
| 134 | |
| 135 | |
| 136 | COMMIT; |
| 137 | |
| 138 | ====================================================================================== |
| 139 | |
| 140 | !SubCategory |
| 141 | |
| 142 | biobank_ibfk_1 |
| 143 | |
| 144 | CONSTRAINT !`biobank_ibfk_5` FOREIGN KEY (!`SubCategory`) REFERENCES !`BiobankSubCategory` (!`id`) |
| 145 | |
| 146 | CONSTRAINT !`biobank_ibfk_5` FOREIGN KEY (!`SubCategory`) REFERENCES !`BiobankSubCategory` (!`id`), |
| 147 | |
| 148 | =============================WITH COMMENTS =========================================== |
| 149 | |
| 150 | CREATE TABLE !`BiobankSubCategory` ( |
| 151 | |
| 152 | !`id` int(11) NOT NULL, |
| 153 | |
| 154 | PRIMARY KEY (!`id`), |
| 155 | |
| 156 | CONSTRAINT !`biobanksubcategory_ibfk_1` FOREIGN KEY (!`id`) REFERENCES !`OntologyTerm` (!`id`) ON DELETE CASCADE |
| 157 | |
| 158 | ) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci; |
| 159 | |
| 160 | /* move data from !BiobankCategory to !BiobankSubCategory table */ |
| 161 | |
| 162 | INSERT INTO !BiobankSubCategory (id) |
| 163 | |
| 164 | SELECT id |
| 165 | |
| 166 | FROM !BiobankCategory |
| 167 | |
| 168 | WHERE id NOT IN ("281", "284", "285") ; |
| 169 | |
| 170 | /*WHERE name NOT IN ("A. Core Biobanks, DNA available", "B: Supporting biobanks, DNA not yet available" ,"C: Biobanken in opbouw") ;* - IF NEEDED CORRECT THE IDs/ |
| 171 | |
| 172 | /* alter constraints */ |
| 173 | |
| 174 | ALTER TABLE Biobank DROP FOREIGN KEY biobank_ibfk_5; |
| 175 | |
| 176 | ALTER TABLE !BiobankSubCategory ADD FOREIGN KEY (id) REFERENCES !OntologyTerm (id) ON DELETE CASCADE; |
| 177 | |
| 178 | NOT OK : ERROR 1050 (42S01): Table './bbmri/!BiobankSubCategory' already exists |
| 179 | |
| 180 | THEN USE : |
| 181 | |
| 182 | ALTER TABLE `!BiobankSubCategory` |
| 183 | |
| 184 | ADD CONSTRAINT !`id` |
| 185 | |
| 186 | FOREIGN KEY (!`id`) REFERENCES !OntologyTerm (id) ON DELETE CASCADE; |
| 187 | |
| 188 | ALTER TABLE Biobank ADD FOREIGN KEY (!SubCategory) REFERENCES !BiobankSubCategory (id) ON DELETE RESTRICT; |
| 189 | |
| 190 | NOT OK : ERROR 1050 (42S01): Table './bbmri/Biobank' already exists |
| 191 | |
| 192 | THEN USE : |
| 193 | |
| 194 | ALTER TABLE `Biobank` |
| 195 | |
| 196 | ADD CONSTRAINT `!SubCategory` |
| 197 | |
| 198 | FOREIGN KEY (`!SubCategory`) REFERENCES !BiobankSubCategory (id) ON DELETE CASCADE; |
| 199 | |
| 200 | /* delete moved data from !BiobankCategory */ |
| 201 | |
| 202 | DELETE FROM !BiobankCategory |
| 203 | |
| 204 | WHERE id NOT IN ("281", "284", "285") ; |
| 205 | |
| 206 | /*IF NEEDED CORRECT THE IDs |
| 207 | |
| 208 | WHERE name IN ("A. Core Biobanks, DNA available", "B: Supporting biobanks, DNA not yet available" ,"C: Biobanken in opbouw") ; |
| 209 | |
| 210 | */ |
| 211 | |
| 212 | CREATE TABLE !BiobankPersonRole ( |
| 213 | |
| 214 | id INTEGER NOT NULL |
| 215 | |
| 216 | , PRIMARY KEY(id) |
| 217 | |
| 218 | ); |
| 219 | |
| 220 | ALTER TABLE !BiobankPersonRole ADD FOREIGN KEY (id) REFERENCES !PersonRole (id) ON DELETE CASCADE; |
| 221 | |
| 222 | alter table !OntologyTerm modify column !__Type enum('!OntologyTerm','!PersonRole','Species','!AlternateId','!BiobankCategory','!BiobankTopic','!BiobankDataType', '!BiobankSubCategory','!BiobankPersonRole'); |
| 223 | |
| 224 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='282'; |
| 225 | |
| 226 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='283'; |
| 227 | |
| 228 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='286'; |
| 229 | |
| 230 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='287'; |
| 231 | |
| 232 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='288'; |
| 233 | |
| 234 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='289'; |
| 235 | |
| 236 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='290'; |
| 237 | |
| 238 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='291'; |
| 239 | |
| 240 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='292'; |
| 241 | |
| 242 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='293'; |
| 243 | |
| 244 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='295'; |
| 245 | |
| 246 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='296'; |
| 247 | |
| 248 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='297'; |
| 249 | |
| 250 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='298'; |
| 251 | |
| 252 | UPDATE !OntologyTerm SET !__Type="!BiobankSubCategory" WHERE id='564'; |
| 253 | |
| 254 | /*below we resolve the problem of duplicate entries in ontology term for !PersonRole*/ |
| 255 | |
| 256 | select * from !OntologyTerm where name="Software Engineer"; |
| 257 | |
| 258 | delete from !OntologyTerm where id=561; |
| 259 | |
| 260 | select * from !BiobankPersonRole; |
| 261 | |
| 262 | insert into !BiobankPersonRole values(561); |
| 263 | |
| 264 | select * from !OntologyTerm where name="coordinator"; |
| 265 | |
| 266 | delete from !OntologyTerm where id=593; |
| 267 | |
| 268 | select * from !BiobankPersonRole; |
| 269 | |
| 270 | insert into !BiobankPersonRole values(277); |
| 271 | |
| 272 | select * from !OntologyTerm where name="postdoc"; |
| 273 | |
| 274 | delete from !OntologyTerm where id=594; |
| 275 | |
| 276 | select * from !BiobankPersonRole; |
| 277 | |
| 278 | insert into !BiobankPersonRole values(278); |
| 279 | |
| 280 | select * from !OntologyTerm where name="administrator"; |
| 281 | |
| 282 | delete from !OntologyTerm where id=595; |
| 283 | |
| 284 | select * from !BiobankPersonRole; |
| 285 | |
| 286 | insert into !BiobankPersonRole values(279); |
| 287 | |
| 288 | select * from !OntologyTerm where name="IT responsible"; |
| 289 | |
| 290 | delete from !OntologyTerm where id=596; |
| 291 | |
| 292 | select * from !BiobankPersonRole; |
| 293 | |
| 294 | insert into !BiobankPersonRole values(280); |
| 295 | |
| 296 | |
| 297 | |
| 298 | COMMIT; |