Changeset 16138
- Timestamp:
- 09/07/08 14:10:45 (1 month ago)
- Files:
-
- trunk/bio/sources/affy-probes/.project (modified) (1 diff)
- trunk/bio/sources/bdgp-insitu/bdgp-insitu_additions.xml (modified) (2 diffs)
- trunk/bio/sources/bdgp-insitu/main/src/org/intermine/bio/dataconversion/BDGPInsituConverter.java (modified) (1 diff)
- trunk/bio/sources/fly-fish/.classpath (modified) (1 diff)
- trunk/bio/sources/fly-fish/main/src/org/intermine/bio/dataconversion/FlyFishConverter.java (modified) (2 diffs)
- trunk/bio/sources/fly-fish/test/resources/FlyFishTestItems.xml (modified) (20 diffs)
Legend:
- Unmodified
- Added
- Removed
- Modified
- Copied
- Moved
trunk/bio/sources/affy-probes/.project
r11333 r16138 1 1 <?xml version="1.0" encoding="UTF-8"?> 2 2 <projectDescription> 3 <name>bio-source s-affy-probes</name>3 <name>bio-source-affy-probes</name> 4 4 <comment></comment> 5 5 <projects> trunk/bio/sources/bdgp-insitu/bdgp-insitu_additions.xml
r15878 r16138 10 10 <reference name="publication" referenced-type="org.flymine.model.genomic.Publication"/> 11 11 <reference name="dataSet" referenced-type="org.flymine.model.genomic.DataSet"/> 12 <reference name="source" referenced-type="org.flymine.model.genomic.DataSource"/> 13 <reference name="gene" referenced-type="org.flymine.model.genomic.Gene" reverse-reference="mRNAExpressionResults"/> 12 <reference name="gene" referenced-type="org.flymine.model.genomic.Gene" reverse-reference="mRNAExpressionResults"/> 14 13 <collection name="images" referenced-type="org.flymine.model.genomic.Image"/> 15 14 <collection name="stages" referenced-type="org.flymine.model.genomic.Stage"/> … … 20 19 </class> 21 20 <class name="org.flymine.model.genomic.Image" is-interface="true"> 22 <attribute name="url" type="java.lang.String"/> 21 <attribute name="url" type="java.lang.String"/> 23 22 </class> 24 23 <class name="org.flymine.model.genomic.Stage" is-interface="true"> 25 24 <attribute name="name" type="java.lang.String"/> 26 25 </class> 27 26 28 27 </classes> trunk/bio/sources/bdgp-insitu/main/src/org/intermine/bio/dataconversion/BDGPInsituConverter.java
r16117 r16138 233 233 } else if (terms.containsKey(name)) { 234 234 return terms.get(name); 235 } else {236 237 238 239 240 241 242 } 235 } 236 Item termItem = createItem("MRNAExpressionTerm"); 237 termItem.setAttribute("name", name); 238 termItem.setAttribute("type", "ImaGO"); 239 store(termItem); 240 terms.put(name, termItem); 241 return termItem; 242 243 243 } 244 244 trunk/bio/sources/fly-fish/.classpath
r9860 r16138 11 11 <classpathentry combineaccessrules="false" kind="src" path="/intermine-integrate-test"/> 12 12 <classpathentry combineaccessrules="false" kind="src" path="/bio-postprocess-main"/> 13 <classpathentry kind="lib" path="test/resources"/> 13 14 <classpathentry kind="output" path="bin"/> 14 15 </classpath> trunk/bio/sources/fly-fish/main/src/org/intermine/bio/dataconversion/FlyFishConverter.java
r15808 r16138 194 194 if (termItems.containsKey(expression)) { 195 195 return termItems.get(expression); 196 } else {197 198 199 200 201 202 203 } 196 } 197 Item term = createItem("MRNAExpressionTerm"); 198 term.setAttribute("name", expression); 199 term.setAttribute("type", "fly-FISH"); 200 store(term); 201 termItems.put(expression, term); 202 return term; 203 204 204 } 205 205 … … 216 216 if (geneItems.containsKey(primaryIdentifier)) { 217 217 return geneItems.get(primaryIdentifier); 218 } else {219 220 221 222 223 224 225 } 218 } 219 Item gene = createItem("Gene"); 220 gene.setAttribute("primaryIdentifier", primaryIdentifier); 221 gene.setReference("organism", orgDrosophila); 222 geneItems.put(primaryIdentifier, gene); 223 store(gene); 224 return gene; 225 226 226 } 227 227 trunk/bio/sources/fly-fish/test/resources/FlyFishTestItems.xml
r15894 r16138 17 17 <attribute name="stageRange" value="stage 6-7 (fly-FISH)"/> 18 18 <reference name="dataSet" ref_id="1_1"/> 19 <reference name="source" ref_id="0_1"/>20 19 <reference name="gene" ref_id="5_4"/> 21 20 <reference name="publication" ref_id="3_1"/> … … 30 29 <attribute name="stageRange" value="stage 6-7 (fly-FISH)"/> 31 30 <reference name="dataSet" ref_id="1_1"/> 32 <reference name="source" ref_id="0_1"/>33 31 <reference name="gene" ref_id="5_2"/> 34 32 <reference name="publication" ref_id="3_1"/> … … 50 48 <attribute name="stageRange" value="stage 8-9 (fly-FISH)"/> 51 49 <reference name="dataSet" ref_id="1_1"/> 52 <reference name="source" ref_id="0_1"/>53 50 <reference name="gene" ref_id="5_3"/> 54 51 <reference name="publication" ref_id="3_1"/> … … 60 57 <attribute name="stageRange" value="stage 6-7 (fly-FISH)"/> 61 58 <reference name="dataSet" ref_id="1_1"/> 62 <reference name="source" ref_id="0_1"/>63 59 <reference name="gene" ref_id="5_3"/> 64 60 <reference name="publication" ref_id="3_1"/> … … 70 66 <attribute name="stageRange" value="stage 1-3 (fly-FISH)"/> 71 67 <reference name="dataSet" ref_id="1_1"/> 72 <reference name="source" ref_id="0_1"/>73 68 <reference name="gene" ref_id="5_4"/> 74 69 <reference name="publication" ref_id="3_1"/> … … 117 112 <attribute name="stageRange" value="stage 1-3 (fly-FISH)"/> 118 113 <reference name="dataSet" ref_id="1_1"/> 119 <reference name="source" ref_id="0_1"/>120 114 <reference name="gene" ref_id="5_1"/> 121 115 <reference name="publication" ref_id="3_1"/> … … 127 121 <attribute name="stageRange" value="stage 1-3 (fly-FISH)"/> 128 122 <reference name="dataSet" ref_id="1_1"/> 129 <reference name="source" ref_id="0_1"/>130 123 <reference name="gene" ref_id="5_4"/> 131 124 <reference name="publication" ref_id="3_1"/> … … 147 140 <attribute name="stageRange" value="stage 6-7 (fly-FISH)"/> 148 141 <reference name="dataSet" ref_id="1_1"/> 149 <reference name="source" ref_id="0_1"/>150 142 <reference name="gene" ref_id="5_1"/> 151 143 <reference name="publication" ref_id="3_1"/> … … 171 163 <attribute name="stageRange" value="stage 8-9 (fly-FISH)"/> 172 164 <reference name="dataSet" ref_id="1_1"/> 173 <reference name="source" ref_id="0_1"/>174 165 <reference name="gene" ref_id="5_2"/> 175 166 <reference name="publication" ref_id="3_1"/> … … 181 172 <attribute name="stageRange" value="stage 4-5 (fly-FISH)"/> 182 173 <reference name="dataSet" ref_id="1_1"/> 183 <reference name="source" ref_id="0_1"/>184 174 <reference name="gene" ref_id="5_2"/> 185 175 <reference name="publication" ref_id="3_1"/> … … 198 188 <attribute name="stageRange" value="stage 4-5 (fly-FISH)"/> 199 189 <reference name="dataSet" ref_id="1_1"/> 200 <reference name="source" ref_id="0_1"/>201 190 <reference name="gene" ref_id="5_4"/> 202 191 <reference name="publication" ref_id="3_1"/> … … 215 204 <attribute name="stageRange" value="stage 1-3 (fly-FISH)"/> 216 205 <reference name="dataSet" ref_id="1_1"/> 217 <reference name="source" ref_id="0_1"/>218 206 <reference name="gene" ref_id="5_2"/> 219 207 <reference name="publication" ref_id="3_1"/> … … 233 221 <attribute name="stageRange" value="stage 1-3 (fly-FISH)"/> 234 222 <reference name="dataSet" ref_id="1_1"/> 235 <reference name="source" ref_id="0_1"/>236 223 <reference name="gene" ref_id="5_3"/> 237 224 <reference name="publication" ref_id="3_1"/> … … 253 240 <attribute name="stageRange" value="stage 8-9 (fly-FISH)"/> 254 241 <reference name="dataSet" ref_id="1_1"/> 255 <reference name="source" ref_id="0_1"/>256 242 <reference name="gene" ref_id="5_1"/> 257 243 <reference name="publication" ref_id="3_1"/> … … 267 253 <attribute name="stageRange" value="stage 6-7 (fly-FISH)"/> 268 254 <reference name="dataSet" ref_id="1_1"/> 269 <reference name="source" ref_id="0_1"/>270 255 <reference name="gene" ref_id="5_4"/> 271 256 <reference name="publication" ref_id="3_1"/> … … 277 262 <attribute name="stageRange" value="stage 8-9 (fly-FISH)"/> 278 263 <reference name="dataSet" ref_id="1_1"/> 279 <reference name="source" ref_id="0_1"/>280 264 <reference name="gene" ref_id="5_4"/> 281 265 <reference name="publication" ref_id="3_1"/> … … 287 271 <attribute name="stageRange" value="stage 4-5 (fly-FISH)"/> 288 272 <reference name="dataSet" ref_id="1_1"/> 289 <reference name="source" ref_id="0_1"/>290 273 <reference name="gene" ref_id="5_1"/> 291 274 <reference name="publication" ref_id="3_1"/> … … 311 294 <attribute name="stageRange" value="stage 4-5 (fly-FISH)"/> 312 295 <reference name="dataSet" ref_id="1_1"/> 313 <reference name="source" ref_id="0_1"/>314 296 <reference name="gene" ref_id="5_4"/> 315 297 <reference name="publication" ref_id="3_1"/> … … 321 303 <attribute name="stageRange" value="stage 4-5 (fly-FISH)"/> 322 304 <reference name="dataSet" ref_id="1_1"/> 323 <reference name="source" ref_id="0_1"/>324 305 <reference name="gene" ref_id="5_3"/> 325 306 <reference name="publication" ref_id="3_1"/> … … 338 319 <attribute name="stageRange" value="stage 8-9 (fly-FISH)"/> 339 320 <reference name="dataSet" ref_id="1_1"/> 340 <reference name="source" ref_id="0_1"/>341 321 <reference name="gene" ref_id="5_4"/> 342 322 <reference name="publication" ref_id="3_1"/>
