Changeset 564
- Timestamp:
- Jun 14, 2010, 5:20:07 PM (13 years ago)
- Location:
- trunk/grails-app
- Files:
-
- 5 edited
-
conf/BootStrap.groovy (modified) (6 diffs)
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domain/dbnp/studycapturing/Event.groovy (modified) (5 diffs)
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domain/dbnp/studycapturing/RelTime.groovy (modified) (1 diff)
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domain/dbnp/studycapturing/Study.groovy (modified) (2 diffs)
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domain/dbnp/studycapturing/TemplateEntity.groovy (modified) (1 diff)
Legend:
- Unmodified
- Added
- Removed
-
trunk/grails-app/conf/BootStrap.groovy
r563 r564 68 68 69 69 // add Terms 70 println ".adding mouse term"70 println ".adding terms" 71 71 def mouseTerm = new Term( 72 72 name: 'Mus musculus', … … 74 74 accession: '10090' 75 75 ).with { if (!validate()) { errors.each { println it} } else save()} 76 println ".adding human term" 76 77 77 def humanTerm = new Term( 78 78 name: 'Homo sapiens', … … 99 99 ).with { if (!validate()) { errors.each { println it} } else save()} 100 100 101 102 101 def bloodTerm = new Term( 103 102 name: 'blood plasma', … … 118 117 ).with { if (!validate()) { errors.each { println it} } else save()} 119 118 120 if (GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT) { 119 120 // Create templates 121 println ".adding templates" 122 123 def genderField = new TemplateField( 124 name: 'Gender',type: TemplateFieldType.STRINGLIST, entity: Subject, 125 listEntries: [new TemplateFieldListItem(name:'Male'),new TemplateFieldListItem(name: 'Female'),new TemplateFieldListItem(name: 'Unknown')]) 126 .with { if (!validate()) { errors.each { println it} } else save()} 127 128 def ageField = new TemplateField( 129 name: 'Age',type: TemplateFieldType.INTEGER,entity: Subject,unit: 'years',comment: 'Either include age at the start of the study or date of birth (if known)') 130 .with { if (!validate()) { errors.each { println it} } else save()} 131 132 def genotypeField = new TemplateField( 133 name: 'Genotype', type: TemplateFieldType.STRING,entity: Subject, 134 comment: 'If present, indicate the genetic variance of the subject (e.g., mutagenized populations,knock-out/in,transgene etc)') 135 .with { if (!validate()) { errors.each { println it} } else save()} 136 137 def genotypeTypeField = new TemplateField( 138 name: 'Genotype type',type: TemplateFieldType.STRINGLIST,entity: Subject, 139 listEntries: [new TemplateFieldListItem(name:'wildtype'), 140 new TemplateFieldListItem(name:'transgenic'), 141 new TemplateFieldListItem(name:'knock-out'), 142 new TemplateFieldListItem(name:'knock-in')], 143 comment: 'If a genotype was specified, please indicate here the type of the genotype') 144 .with { if (!validate()) { errors.each { println it} } else save()} 145 146 def varietyField = new TemplateField( 147 name: 'Variety', type: TemplateFieldType.STRING,entity: Subject, 148 comment: 'taxonomic category consisting of members of a species that differ from others of the same species in minor but heritable characteristics') 149 .with { if (!validate()) { errors.each { println it} } else save()} 150 151 def ecotypeField = new TemplateField( 152 name: 'Ecotype', type: TemplateFieldType.STRING,entity: Subject, 153 comment: 'a type or subspecies of life that is especially well adapted to a certain environment' 154 ) 155 .with { if (!validate()) { errors.each { println it} } else save()} 156 157 158 // Nutritional study template 159 println ".adding academic study template..." 160 def studyTemplate = new Template( 161 name: 'Academic study', 162 entity: dbnp.studycapturing.Study 163 ) 164 .addToFields(new TemplateField(name: 'Description',type: TemplateFieldType.TEXT, entity: Study,comment:'Describe here the type of subjects and the treatment, challenges and sampling.')) 165 .addToFields(new TemplateField(name: 'Objectives',type: TemplateFieldType.TEXT,entity: Study,comment:'Fill out the aim or questions of the study')) 166 .addToFields(new TemplateField(name: 'Consortium',type: TemplateFieldType.STRING,entity: Study,comment:'If the study was performed within a consortium (e.g. NMC, NuGO), you can indicate this here')) 167 .addToFields(new TemplateField(name: 'Cohort name',type: TemplateFieldType.STRING,entity: Study,comment:'If a cohort was used the name or code of the cohort can be define here (define a cohort template)')) 168 .addToFields(new TemplateField(name: 'Lab id',type: TemplateFieldType.STRING,entity: Study,comment:'In which lab was the study performed; indicate the roomnumber.')) 169 .addToFields(new TemplateField(name: 'Institute',type: TemplateFieldType.STRING,entity: Study,comment:'In which institute was the study performed; indicate the full address information (to be replaced by persons-affiliations?)')) 170 .addToFields(new TemplateField(name: 'Study protocol',type: TemplateFieldType.FILE,entity: Study,comment:'Optionally attach a file in which the protocol in the study is described')) 171 .with { if (!validate()) { errors.each { println it} } else save()} 172 173 // Mouse template 174 println ".adding mouse subject template..." 175 def mouseTemplate = new Template( 176 name: 'Mouse', entity: dbnp.studycapturing.Subject) 177 .addToFields(new TemplateField( 178 name: 'Strain', type: TemplateFieldType.ONTOLOGYTERM, ontologies: [nciOntology], entity: Subject, comment: "This is an ontology term, if the right strain is not in the list please add it with 'add more'")) 179 .addToFields(genotypeField) 180 .addToFields(genotypeTypeField) 181 .addToFields(genderField) 182 .addToFields(new TemplateField( 183 name: 'Age', type: TemplateFieldType.INTEGER, entity: Subject, unit: 'weeks', comment: 'Age at start of study')) 184 .addToFields(new TemplateField( 185 name: 'Age type',type: TemplateFieldType.STRINGLIST,entity: Subject, 186 listEntries: [new TemplateFieldListItem(name:'postnatal'),new TemplateFieldListItem(name:'embryonal')])) 187 .addToFields(new TemplateField( 188 name: 'Cage',type: TemplateFieldType.STRING,entity: Subject,comment:'Indicate the cage used for housing (type and/or size)')) 189 .addToFields(new TemplateField( 190 name: '#Mice in cage',type: TemplateFieldType.INTEGER,entity: Subject,comment:'If known, indicate the number of mice per cage')) 191 .addToFields(new TemplateField( 192 name: 'Litter size',type: TemplateFieldType.INTEGER,entity: Subject,comment:'If known, indicate the litter size of the litter from which the subject originates')) 193 .addToFields(new TemplateField( 194 name: 'Weight', type: TemplateFieldType.DOUBLE, unit: 'gram',entity: Subject,comment:'If known indicate the weight of the subject in grams at the start of the study')) 195 .with { if (!validate()) { errors.each { println it} } else save()} 196 197 // Human template 198 println ".adding human subject template..." 199 def humanTemplate = new Template( 200 name: 'Human', entity: dbnp.studycapturing.Subject) 201 .addToFields(genderField) 202 .addToFields(ageField) 203 .addToFields(new TemplateField( 204 name: 'DOB',type: TemplateFieldType.DATE,entity: Subject,comment:'Date of birth')) 205 .addToFields(new TemplateField( 206 name: 'Height',type: TemplateFieldType.DOUBLE, entity: Subject, unit: 'm')) 207 .addToFields(new TemplateField( 208 name: 'Weight',type: TemplateFieldType.DOUBLE, entity: Subject, unit: 'kg')) 209 .addToFields(new TemplateField( 210 name: 'BMI',type: TemplateFieldType.DOUBLE, entity: Subject, unit: 'kg/m2',comment:'Body-mass-index')) 211 .addToFields(new TemplateField( 212 name: 'Race',type: TemplateFieldType.STRING,entity: Subject, comment:'If known and of interest the ethnic group can be indicated')) 213 .addToFields(new TemplateField( 214 name: 'Waist circumference',type: TemplateFieldType.FLOAT, unit: 'cm',entity: Subject, comment:'The waist circumference is measured just above the hip bone. Indicate the measure at the start of the study.')) 215 .addToFields(new TemplateField( 216 name: 'Hip circumference',type: TemplateFieldType.FLOAT, unit: 'cm',entity: Subject, comment:'The hip circumference is measured at the level of the two bony prominences front of the hips. Indicate the measure at the start of the study.')) 217 .addToFields(new TemplateField( 218 name: 'Systolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg',entity: Subject, comment:'Indicate the levels at the start of the study in mmHG')) 219 .addToFields(new TemplateField( 220 name: 'Diastolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg',entity: Subject, comment:'Indicate the levels at the start of the study in mmHG')) 221 .addToFields(new TemplateField( 222 name: 'Heart rate',type: TemplateFieldType.FLOAT, unit: 'beats/min',entity: Subject, comment:'Indicate the heart rate at the start of in study in beats per minute')) 223 .addToFields(new TemplateField( 224 name: 'Run-in-food',type: TemplateFieldType.TEXT,entity: Subject, comment:'If defined, give a short description of the food used before the measurements')) 225 .with { if (!validate()) { errors.each { println it} } else save()} 226 227 println ".adding sample remarks field" 228 def sampleRemarksField = new TemplateField( 229 name: 'Remarks', 230 type: TemplateFieldType.TEXT, 231 entity: Sample 232 ) 233 .with { if (!validate()) { errors.each { println it} } else save()} 234 235 println ".adding sample vial textfield" 236 def sampleVialTextField = new TemplateField( 237 name: 'Text on vial', 238 type: TemplateFieldType.STRING, 239 entity: Sample 240 ) 241 .with { if (!validate()) { errors.each { println it} } else save()} 242 243 // Human tissue sample template 244 println ".adding human sample template..." 245 def humanSampleTemplate = new Template( 246 name: 'Human tissue sample', 247 entity: dbnp.studycapturing.Sample 248 ) 249 .addToFields(sampleRemarksField) 250 .addToFields(sampleVialTextField) 251 .addToFields( 252 new TemplateField( 253 name: 'Sample measured weight', 254 unit: 'mg', 255 type: TemplateFieldType.FLOAT, 256 entity: Sample 257 ) 258 ) 259 .with { if (!validate()) { errors.each { println it} } else save()} 260 261 // Human blood sample template 262 println ".adding human sample template..." 263 def humanBloodSampleTemplate = new Template( 264 name: 'Human blood sample', 265 entity: dbnp.studycapturing.Sample 266 ) 267 .addToFields(sampleRemarksField) 268 .addToFields(sampleVialTextField) 269 .addToFields( 270 new TemplateField( 271 name: 'Sample measured volume', 272 unit: 'ml', 273 type: TemplateFieldType.FLOAT, 274 entity: Sample 275 ) 276 ) 277 .with { if (!validate()) { errors.each { println it} } else save()} 278 279 /* 280 def GrowthTreatmentTemplate = new Template( 281 name: 'Growth treatment', 282 entity: dbnp.studycapturing.Event 283 ) 284 .addToFields(sampleDescriptionField) 285 .addToFields(new TemplateField(name: 'position X',type: TemplateFieldType.STRING)) 286 .addToFields(new TemplateField(name: 'position Y',type: TemplateFieldType.STRING)) 287 .addToFields(new TemplateField(name: 'Block',type: TemplateFieldType.STRING)) 288 .addToFields(new TemplateField(name: 'Temparature Day',type: TemplateFieldType.STRING)) 289 .addToFields(new TemplateField(name: 'Temparature Night',type: TemplateFieldType.STRING)) 290 .addToFields(new TemplateField(name: 'Light Intensity',type: TemplateFieldType.STRING)) 291 .addToFields(new TemplateField(name: 'Harvest Delay',type: TemplateFieldType.STRING)) 292 .with { if (!validate()) { errors.each { println it} } else save()} 293 */ 294 295 //Plant template 296 println ".adding geenhouse plant template..." 297 def greenHouseTemplate = new Template( 298 name: 'Plant-green house ', 299 entity: dbnp.studycapturing.Subject 300 ) 301 .addToFields(varietyField) 302 .addToFields(ecotypeField) 303 .addToFields(genotypeField) 304 /* 305 .addToFields(genotypeTypeField) 306 .addToFields( 307 new TemplateField( 308 name: 'Growth location', type: TemplateFieldType.STRINGLIST, 309 listEntries: [ 310 new TemplateFieldListItem(name:'Greenhouse'), 311 new TemplateFieldListItem(name: 'Field') 312 ] 313 ) 314 ) 315 .addToFields( 316 new TemplateField( 317 name: 'Room', type: TemplateFieldType.STRING, 318 comment: 'Chamber number in case of Greenhouse' 319 ) 320 ) 321 */ 322 .addToFields( 323 new TemplateField( 324 name: 'Chamber no.', 325 type: TemplateFieldType.STRING, 326 entity: Subject, 327 comment: 'Chamber number in the Greenhouse' 328 ) 329 ) 330 .addToFields( 331 new TemplateField( 332 name: 'Growth type', 333 entity: Subject, 334 type: TemplateFieldType.STRINGLIST, 335 listEntries: [ 336 new TemplateFieldListItem(name:'Standard'), 337 new TemplateFieldListItem(name: 'Experimental'), 338 new TemplateFieldListItem(name: 'Unknown') 339 ] 340 ) 341 ) 342 .addToFields(new TemplateField( 343 name: 'Growth protocol', entity: Subject, type: TemplateFieldType.TEXT)) 344 .addToFields(new TemplateField( 345 name: 'Position X', entity: Subject, type: TemplateFieldType.FLOAT)) 346 .addToFields(new TemplateField( 347 name: 'Position Y', entity: Subject, type: TemplateFieldType.FLOAT)) 348 .addToFields(new TemplateField( 349 name: 'Block', entity: Subject, type: TemplateFieldType.STRING)) 350 .addToFields(new TemplateField( 351 name: 'Temperature at day', entity: Subject, type: TemplateFieldType.FLOAT)) 352 .addToFields(new TemplateField( 353 name: 'Temperature at night', entity: Subject, type: TemplateFieldType.FLOAT)) 354 .addToFields(new TemplateField( 355 name: 'Photo period', entity: Subject, type: TemplateFieldType.STRING)) 356 .addToFields(new TemplateField( 357 name: 'Light intensity', entity: Subject, type: TemplateFieldType.STRING)) 358 .addToFields(new TemplateField( 359 name: 'Start date', entity: Subject, type: TemplateFieldType.DATE)) 360 .addToFields(new TemplateField( 361 name: 'Harvest date', entity: Subject, type: TemplateFieldType.DATE)) 362 .addToFields(new TemplateField( 363 name: 'Harvest delay', entity: Subject, type: TemplateFieldType.TEXT)) 364 .addToFields(new TemplateField( 365 name: 'Additional info', entity: Subject, type: TemplateFieldType.TEXT)) 366 .with { if (!validate()) { errors.each { println it} } else save()} 367 368 println ".adding open-field plant template..." 369 def FieldTemplate = new Template( 370 name: 'Plant-open field', 371 entity: dbnp.studycapturing.Subject 372 ) 373 .addToFields(varietyField) 374 .addToFields(ecotypeField) 375 .addToFields(genotypeField) 376 .addToFields(new TemplateField( 377 name: 'Start date', entity: Subject, type: TemplateFieldType.DATE)) 378 .addToFields(new TemplateField( 379 name: 'Harvest date', entity: Subject, type: TemplateFieldType.DATE)) 380 .addToFields(new TemplateField( 381 name: 'Growth type', entity: Subject, type: TemplateFieldType.STRINGLIST, 382 listEntries: [new TemplateFieldListItem(name:'Standard'),new TemplateFieldListItem(name: 'Experimental')])) 383 .addToFields(new TemplateField( 384 name: 'Growth protocol', entity: Subject, type: TemplateFieldType.TEXT)) 385 .addToFields(new TemplateField( 386 name: 'Harvest delay', entity: Subject, type: TemplateFieldType.TEXT)) 387 .with { if (!validate()) { errors.each { println it} } else save()} 388 389 //Plant template 390 println ".adding chamber plant template..." 391 def chamberTemplate = new Template( 392 name: 'Plant-chamber', 393 entity: dbnp.studycapturing.Subject 394 ) 395 .addToFields(varietyField) 396 .addToFields(ecotypeField) 397 .addToFields(genotypeField) 398 /* 399 .addToFields(genotypeTypeField) 400 .addToFields( 401 new TemplateField( 402 name: 'Growth location', 403 type: TemplateFieldType.STRINGLIST, 404 listEntries: [ 405 new TemplateFieldListItem(name:'Greenhouse'), 406 new TemplateFieldListItem(name: 'Field') 407 ] 408 ) 409 ) 410 */ 411 .addToFields(new TemplateField( 412 name: 'Room', type: TemplateFieldType.STRING, entity: Subject, 413 comment: 'room number')) 414 .addToFields(new TemplateField( 415 name: 'Chamber no.', type: TemplateFieldType.STRING, entity: Subject, 416 comment: 'Chamber number')) 417 .addToFields(new TemplateField( 418 name: 'Block', type: TemplateFieldType.STRING, entity: Subject)) 419 .addToFields(new TemplateField( 420 name: 'Position X', type: TemplateFieldType.FLOAT, entity: Subject)) 421 .addToFields(new TemplateField( 422 name: 'Position Y', type: TemplateFieldType.FLOAT, entity: Subject)) 423 .addToFields(new TemplateField( 424 name: 'Temperature at day', type: TemplateFieldType.FLOAT, entity: Subject)) 425 .addToFields(new TemplateField( 426 name: 'Temperature at night', type: TemplateFieldType.FLOAT, entity: Subject)) 427 .addToFields(new TemplateField( 428 name: 'Photo period', type: TemplateFieldType.STRING, entity: Subject)) 429 .addToFields(new TemplateField( 430 name: 'Light intensity', type: TemplateFieldType.STRING, entity: Subject)) 431 .addToFields(new TemplateField( 432 name: 'Start date', type: TemplateFieldType.DATE, entity: Subject)) 433 .addToFields(new TemplateField( 434 name: 'Harvest date', type: TemplateFieldType.DATE, entity: Subject)) 435 .addToFields(new TemplateField( 436 name: 'Growth type', type: TemplateFieldType.STRINGLIST, entity: Subject, 437 listEntries: [new TemplateFieldListItem(name:'Standard'),new TemplateFieldListItem(name: 'Experimental')])) 438 .addToFields(new TemplateField( 439 name: 'Growth protocol', type: TemplateFieldType.TEXT, entity: Subject)) 440 .addToFields(new TemplateField( 441 name: 'Harvest delay', type: TemplateFieldType.TEXT, entity: Subject)) 442 .with { if (!validate()) { errors.each { println it} } else save()} 443 444 println ".adding plant sample template..." 445 def plantSampleTemplate = new Template( 446 name: 'Plant sample', 447 entity: dbnp.studycapturing.Sample 448 ) 449 .addToFields(sampleRemarksField) 450 .addToFields(sampleVialTextField) 451 .with { if (!validate()) { errors.each { println it} } else save()} 452 453 println ".adding material prep template" 454 def materialPrepTemplate = new Template( 455 name: 'Plant-material preparation', 456 description: 'material preparation', 457 entity: dbnp.studycapturing.Event 458 ) 459 .addToFields(new TemplateField( 460 name: 'Tissue', 461 type: TemplateFieldType.STRING, 462 entity: Event, 463 comment: 'organ/ fraction of culture/ plant part') 464 ) 465 .addToFields( 466 new TemplateField( 467 name: 'Grinding', 468 type: TemplateFieldType.STRINGLIST, 469 entity: Event, 470 listEntries: [ 471 new TemplateFieldListItem(name:'yes'), 472 new TemplateFieldListItem(name: 'no'), 473 new TemplateFieldListItem(name: 'unknown') 474 ] 475 ) 476 ) 477 .addToFields( 478 new TemplateField( 479 name: 'Storage location', 480 type: TemplateFieldType.STRING, 481 entity: Event 482 ) 483 ) 484 .addToFields( 485 new TemplateField( 486 name: 'protocol reference', 487 type: TemplateFieldType.STRING, 488 entity: Event 489 ) 490 ) 491 .with { if (!validate()) { errors.each { println it} } else save()} 492 493 def protocolField = new TemplateField( 494 name: 'Protocol', 495 type: TemplateFieldType.FILE, 496 entity: Event, 497 comment: 'You can upload a protocol here which describes the procedure which was used when carrying out the event' 498 ) 499 .with { if (!validate()) { errors.each { println it} } else save()} 500 501 // diet treatment template 502 println ".adding diet treatement template" 503 def dietTreatmentTemplate = new Template( 504 name: 'Diet treatment', 505 entity: dbnp.studycapturing.Event 506 ) 507 .addToFields( 508 new TemplateField( 509 name: 'Diet', 510 type: TemplateFieldType.STRINGLIST, 511 entity: Event, 512 listEntries: [ 513 new TemplateFieldListItem(name:'low fat'), 514 new TemplateFieldListItem(name: 'high fat') 515 ] 516 ) 517 ) 518 .addToFields(protocolField) 519 .with { if (!validate()) { errors.each { println it} } else save()} 520 521 // boost treatment template 522 println ".adding boost treatment template" 523 def boostTreatmentTemplate = new Template( 524 name: 'Compound challenge', 525 entity: dbnp.studycapturing.Event 526 ) 527 .addToFields( 528 new TemplateField( 529 name: 'Compound', 530 type: TemplateFieldType.ONTOLOGYTERM, 531 entity: Event, 532 ontologies: [chebiOntology] 533 ) 534 ) 535 .addToFields( 536 new TemplateField( 537 name: 'Control', 538 type: TemplateFieldType.BOOLEAN, 539 entity: Event 540 ) 541 ) 542 .addToFields(protocolField) 543 .with { if (!validate()) { errors.each { println it} } else save()} 544 545 // fasting treatment template 546 println ".adding fasting treatment template" 547 def fastingTreatment = new Template( 548 name: 'Fasting treatment', 549 description: 'Fasting for a specific amount of time', 550 entity: dbnp.studycapturing.Event 551 ) 552 .addToFields( 553 new TemplateField( 554 name: 'Fasting period', 555 type: TemplateFieldType.RELTIME, 556 entity: Event 557 ) 558 ) 559 .with { if (!validate()) { errors.each { println it} } else save()} 560 561 // SamplingEvent templates 562 println ".adding sampling protocol template field" 563 def samplingProtocolField = new TemplateField( 564 name: 'Sample Protocol', 565 entity: SamplingEvent, 566 type: TemplateFieldType.FILE, 567 comment: 'You can upload a protocol here which describes the procedure which was used when carrying out the sampling event' 568 ) 569 .with { if (!validate()) { errors.each { println it} } else save()} 570 571 // liver sampling event template 572 println ".adding liver sampling event template" 573 def liverSamplingEventTemplate = new Template( 574 name: 'Liver extraction', 575 description: 'Liver sampling for transcriptomics arrays', 576 entity: dbnp.studycapturing.SamplingEvent 577 ) 578 .addToFields(samplingProtocolField) 579 .addToFields( 580 new TemplateField( 581 name: 'Sample weight', 582 unit: 'mg', 583 entity: SamplingEvent, 584 type: TemplateFieldType.FLOAT 585 ) 586 ) 587 .with { if (!validate()) { errors.each { println it} } else save()} 588 589 // blood sampling 590 println ".adding blood sampling event template" 591 def bloodSamplingEventTemplate = new Template( 592 name: 'Blood extraction', 593 description: 'Blood extraction targeted at lipid assays', 594 entity: dbnp.studycapturing.SamplingEvent 595 ) 596 .addToFields(samplingProtocolField) 597 .addToFields( 598 new TemplateField( 599 name: 'Sample volume', 600 entity: SamplingEvent, 601 unit: 'ml', 602 type: TemplateFieldType.FLOAT 603 ) 604 ) 605 .with { if (!validate()) { errors.each { println it} } else save()} 606 607 // plant sample extraction event template 608 println ".adding plant sample extraction event template" 609 def plantSamplingExtractEventTemplate = new Template( 610 name: 'Plant sample extraction', 611 description: 'sample extraction', 612 entity: dbnp.studycapturing.SamplingEvent, 613 sampleTemplates: [plantSampleTemplate] 614 ) 615 .addToFields(samplingProtocolField) 616 .addToFields( 617 new TemplateField( 618 name: 'Sample weight', 619 unit: 'ul', 620 entity: SamplingEvent, 621 type: TemplateFieldType.FLOAT 622 ) 623 ) 624 .addToFields( 625 new TemplateField( 626 name: 'Sample when measured', 627 type: TemplateFieldType.STRINGLIST, 628 entity: SamplingEvent, 629 listEntries: [ 630 new TemplateFieldListItem(name:'Dried'), 631 new TemplateFieldListItem(name: 'Fresh'), 632 new TemplateFieldListItem(name: 'Unknown') 633 ] 634 ) 635 ) 636 .with { if (!validate()) { errors.each { println it} } else save()} 637 638 // plant sampling event template 639 println ".adding plant sampling event template" 640 def plantSamplingEventTemplate = new Template( 641 name: 'Plant-sample ', 642 description: 'plant sample ', 643 entity: dbnp.studycapturing.SamplingEvent, 644 sampleTemplates: [plantSampleTemplate] 645 ) 646 //.addToFields(samplingProtocolField) 647 .addToFields( 648 new TemplateField( 649 name: 'material', 650 comment: 'physical charecteristic. e.g, grounded powder of tomato seed or liquid', 651 entity: SamplingEvent, 652 type: TemplateFieldType.STRING 653 ) 654 ) 655 .addToFields( 656 new TemplateField( 657 name: 'Description', 658 type: TemplateFieldType.STRING, 659 entity: SamplingEvent 660 ) 661 ) 662 .addToFields( 663 new TemplateField( 664 name: 'extracted material', 665 comment: 'substance to be extracted. e.g., lipids, volatiles, primary metabolites etc', 666 type: TemplateFieldType.STRING, 667 entity: SamplingEvent 668 ) 669 ) 670 .addToFields( 671 new TemplateField( 672 name: 'Text on vial', 673 entity: SamplingEvent, 674 type: TemplateFieldType.STRING 675 ) 676 ) 677 .with { if (!validate()) { errors.each { println it} } else save()} 678 679 // Add example studies 680 if (grails.util.GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT) { 121 681 122 682 // Create a few persons, roles and Affiliations … … 186 746 ) 187 747 .save(); 188 } 189 190 // Create templates 191 192 def genderField = new TemplateField( 193 name: 'Gender',type: TemplateFieldType.STRINGLIST, entity: Subject, 194 listEntries: [new TemplateFieldListItem(name:'Male'),new TemplateFieldListItem(name: 'Female'),new TemplateFieldListItem(name: 'Unknown')]) 195 .with { if (!validate()) { errors.each { println it} } else save()} 196 197 def ageField = new TemplateField( 198 name: 'Age',type: TemplateFieldType.INTEGER,entity: Subject,unit: 'years',comment: 'Either include age at the start of the study or date of birth (if known)') 199 .with { if (!validate()) { errors.each { println it} } else save()} 200 201 def genotypeField = new TemplateField( 202 name: 'Genotype', type: TemplateFieldType.STRING,entity: Subject, 203 comment: 'If present, indicate the genetic variance of the subject (e.g., mutagenized populations,knock-out/in,transgene etc)') 204 .with { if (!validate()) { errors.each { println it} } else save()} 205 206 def genotypeTypeField = new TemplateField( 207 name: 'Genotype type',type: TemplateFieldType.STRINGLIST,entity: Subject, 208 listEntries: [new TemplateFieldListItem(name:'wildtype'), 209 new TemplateFieldListItem(name:'transgenic'), 210 new TemplateFieldListItem(name:'knock-out'), 211 new TemplateFieldListItem(name:'knock-in')], 212 comment: 'If a genotype was specified, please indicate here the type of the genotype') 213 .with { if (!validate()) { errors.each { println it} } else save()} 214 215 def varietyField = new TemplateField( 216 name: 'Variety', type: TemplateFieldType.STRING,entity: Subject, 217 comment: 'taxonomic category consisting of members of a species that differ from others of the same species in minor but heritable characteristics') 218 .with { if (!validate()) { errors.each { println it} } else save()} 219 220 def ecotypeField = new TemplateField( 221 name: 'Ecotype', type: TemplateFieldType.STRING,entity: Subject, 222 comment: 'a type or subspecies of life that is especially well adapted to a certain environment' 223 ) 224 .with { if (!validate()) { errors.each { println it} } else save()} 225 226 227 // Nutritional study template 228 println ".adding academic study template..." 229 def studyTemplate = new Template( 230 name: 'Academic study', 231 entity: dbnp.studycapturing.Study 232 ) 233 .addToFields(new TemplateField(name: 'Description',type: TemplateFieldType.TEXT, entity: Study,comment:'Describe here the type of subjects and the treatment, challenges and sampling.')) 234 /* 235 .addToFields(new TemplateField( 236 name: 'Study code', 237 type: TemplateFieldType.STRING, 238 entity: Study, 239 preferredIdentifier:true, 240 comment: 'Fill out the code by which many people will recognize your study') 241 ) 242 */ 243 .addToFields(new TemplateField(name: 'Objectives',type: TemplateFieldType.TEXT,entity: Study,comment:'Fill out the aim or questions of the study')) 244 .addToFields(new TemplateField(name: 'Consortium',type: TemplateFieldType.STRING,entity: Study,comment:'If the study was performed within a consortium (e.g. NMC, NuGO), you can indicate this here')) 245 .addToFields(new TemplateField(name: 'Cohort name',type: TemplateFieldType.STRING,entity: Study,comment:'If a cohort was used the name or code of the cohort can be define here (define a cohort template)')) 246 .addToFields(new TemplateField(name: 'Lab id',type: TemplateFieldType.STRING,entity: Study,comment:'In which lab was the study performed; indicate the roomnumber.')) 247 .addToFields(new TemplateField(name: 'Institute',type: TemplateFieldType.STRING,entity: Study,comment:'In which institute was the study performed; indicate the full address information (to be replaced by persons-affiliations?)')) 248 .addToFields(new TemplateField(name: 'Study protocol',type: TemplateFieldType.FILE,entity: Study,comment:'Optionally attach a file in which the protocol in the study is described')) 249 .with { if (!validate()) { errors.each { println it} } else save()} 250 251 // Mouse template 252 println ".adding mouse subject template..." 253 def mouseTemplate = new Template( 254 name: 'Mouse', entity: dbnp.studycapturing.Subject) 255 .addToFields(new TemplateField( 256 name: 'Strain', type: TemplateFieldType.ONTOLOGYTERM, ontologies: [nciOntology], entity: Subject, comment: "This is an ontology term, if the right strain is not in the list please add it with 'add more'")) 257 .addToFields(genotypeField) 258 .addToFields(genotypeTypeField) 259 .addToFields(genderField) 260 .addToFields(new TemplateField( 261 name: 'Age', type: TemplateFieldType.INTEGER, entity: Subject, unit: 'weeks', comment: 'Age at start of study')) 262 .addToFields(new TemplateField( 263 name: 'Age type',type: TemplateFieldType.STRINGLIST,entity: Subject, 264 listEntries: [new TemplateFieldListItem(name:'postnatal'),new TemplateFieldListItem(name:'embryonal')])) 265 .addToFields(new TemplateField( 266 name: 'Cage',type: TemplateFieldType.STRING,entity: Subject,comment:'Indicate the cage used for housing (type and/or size)')) 267 .addToFields(new TemplateField( 268 name: '#Mice in cage',type: TemplateFieldType.INTEGER,entity: Subject,comment:'If known, indicate the number of mice per cage')) 269 .addToFields(new TemplateField( 270 name: 'Litter size',type: TemplateFieldType.INTEGER,entity: Subject,comment:'If known, indicate the litter size of the litter from which the subject originates')) 271 .addToFields(new TemplateField( 272 name: 'Weight', type: TemplateFieldType.DOUBLE, unit: 'gram',entity: Subject,comment:'If known indicate the weight of the subject in grams at the start of the study')) 273 .with { if (!validate()) { errors.each { println it} } else save()} 274 275 // Human template 276 println ".adding human subject template..." 277 def humanTemplate = new Template( 278 name: 'Human', entity: dbnp.studycapturing.Subject) 279 .addToFields(genderField) 280 .addToFields(ageField) 281 .addToFields(new TemplateField( 282 name: 'DOB',type: TemplateFieldType.DATE,entity: Subject,comment:'Date of birth')) 283 .addToFields(new TemplateField( 284 name: 'Height',type: TemplateFieldType.DOUBLE, entity: Subject, unit: 'm')) 285 .addToFields(new TemplateField( 286 name: 'Weight',type: TemplateFieldType.DOUBLE, entity: Subject, unit: 'kg')) 287 .addToFields(new TemplateField( 288 name: 'BMI',type: TemplateFieldType.DOUBLE, entity: Subject, unit: 'kg/m2',comment:'Body-mass-index')) 289 .addToFields(new TemplateField( 290 name: 'Race',type: TemplateFieldType.STRING,entity: Subject, comment:'If known and of interest the ethnic group can be indicated')) 291 .addToFields(new TemplateField( 292 name: 'Waist circumference',type: TemplateFieldType.FLOAT, unit: 'cm',entity: Subject, comment:'The waist circumference is measured just above the hip bone. Indicate the measure at the start of the study.')) 293 .addToFields(new TemplateField( 294 name: 'Hip circumference',type: TemplateFieldType.FLOAT, unit: 'cm',entity: Subject, comment:'The hip circumference is measured at the level of the two bony prominences front of the hips. Indicate the measure at the start of the study.')) 295 .addToFields(new TemplateField( 296 name: 'Systolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg',entity: Subject, comment:'Indicate the levels at the start of the study in mmHG')) 297 .addToFields(new TemplateField( 298 name: 'Diastolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg',entity: Subject, comment:'Indicate the levels at the start of the study in mmHG')) 299 .addToFields(new TemplateField( 300 name: 'Heart rate',type: TemplateFieldType.FLOAT, unit: 'beats/min',entity: Subject, comment:'Indicate the heart rate at the start of in study in beats per minute')) 301 .addToFields(new TemplateField( 302 name: 'Run-in-food',type: TemplateFieldType.TEXT,entity: Subject, comment:'If defined, give a short description of the food used before the measurements')) 303 .with { if (!validate()) { errors.each { println it} } else save()} 304 305 println ".adding sample remarks field" 306 def sampleRemarksField = new TemplateField( 307 name: 'Remarks', 308 type: TemplateFieldType.TEXT, 309 entity: Sample 310 ) 311 .with { if (!validate()) { errors.each { println it} } else save()} 312 313 println ".adding sample vial textfield" 314 def sampleVialTextField = new TemplateField( 315 name: 'Text on vial', 316 type: TemplateFieldType.STRING, 317 entity: Sample 318 ) 319 .with { if (!validate()) { errors.each { println it} } else save()} 320 321 // Human tissue sample template 322 println ".adding human sample template..." 323 def humanSampleTemplate = new Template( 324 name: 'Human tissue sample', 325 entity: dbnp.studycapturing.Sample 326 ) 327 .addToFields(sampleRemarksField) 328 .addToFields(sampleVialTextField) 329 .addToFields( 330 new TemplateField( 331 name: 'Sample measured weight', 332 unit: 'mg', 333 type: TemplateFieldType.FLOAT, 334 entity: Sample 335 ) 336 ) 337 .with { if (!validate()) { errors.each { println it} } else save()} 338 339 // Human blood sample template 340 println ".adding human sample template..." 341 def humanBloodSampleTemplate = new Template( 342 name: 'Human blood sample', 343 entity: dbnp.studycapturing.Sample 344 ) 345 .addToFields(sampleRemarksField) 346 .addToFields(sampleVialTextField) 347 .addToFields( 348 new TemplateField( 349 name: 'Sample measured volume', 350 unit: 'ml', 351 type: TemplateFieldType.FLOAT, 352 entity: Sample 353 ) 354 ) 355 .with { if (!validate()) { errors.each { println it} } else save()} 356 357 /* 358 def GrowthTreatmentTemplate = new Template( 359 name: 'Growth treatment', 360 entity: dbnp.studycapturing.Event 361 ) 362 .addToFields(sampleDescriptionField) 363 .addToFields(new TemplateField(name: 'position X',type: TemplateFieldType.STRING)) 364 .addToFields(new TemplateField(name: 'position Y',type: TemplateFieldType.STRING)) 365 .addToFields(new TemplateField(name: 'Block',type: TemplateFieldType.STRING)) 366 .addToFields(new TemplateField(name: 'Temparature Day',type: TemplateFieldType.STRING)) 367 .addToFields(new TemplateField(name: 'Temparature Night',type: TemplateFieldType.STRING)) 368 .addToFields(new TemplateField(name: 'Light Intensity',type: TemplateFieldType.STRING)) 369 .addToFields(new TemplateField(name: 'Harvest Delay',type: TemplateFieldType.STRING)) 370 .with { if (!validate()) { errors.each { println it} } else save()} 371 */ 372 373 //Plant template 374 println ".adding geenhouse plant template..." 375 def greenHouseTemplate = new Template( 376 name: 'Plant-green house ', 377 entity: dbnp.studycapturing.Subject 378 ) 379 .addToFields(varietyField) 380 .addToFields(ecotypeField) 381 .addToFields(genotypeField) 382 /* 383 .addToFields(genotypeTypeField) 384 .addToFields( 385 new TemplateField( 386 name: 'Growth location', type: TemplateFieldType.STRINGLIST, 387 listEntries: [ 388 new TemplateFieldListItem(name:'Greenhouse'), 389 new TemplateFieldListItem(name: 'Field') 390 ] 391 ) 392 ) 393 .addToFields( 394 new TemplateField( 395 name: 'Room', type: TemplateFieldType.STRING, 396 comment: 'Chamber number in case of Greenhouse' 397 ) 398 ) 399 */ 400 .addToFields( 401 new TemplateField( 402 name: 'Chamber no.', 403 type: TemplateFieldType.STRING, 404 entity: Subject, 405 comment: 'Chamber number in the Greenhouse' 406 ) 407 ) 408 .addToFields( 409 new TemplateField( 410 name: 'Growth type', 411 entity: Subject, 412 type: TemplateFieldType.STRINGLIST, 413 listEntries: [ 414 new TemplateFieldListItem(name:'Standard'), 415 new TemplateFieldListItem(name: 'Experimental'), 416 new TemplateFieldListItem(name: 'Unknown') 417 ] 418 ) 419 ) 420 .addToFields(new TemplateField( 421 name: 'Growth protocol', entity: Subject, type: TemplateFieldType.TEXT)) 422 .addToFields(new TemplateField( 423 name: 'Position X', entity: Subject, type: TemplateFieldType.FLOAT)) 424 .addToFields(new TemplateField( 425 name: 'Position Y', entity: Subject, type: TemplateFieldType.FLOAT)) 426 .addToFields(new TemplateField( 427 name: 'Block', entity: Subject, type: TemplateFieldType.STRING)) 428 .addToFields(new TemplateField( 429 name: 'Temperature at day', entity: Subject, type: TemplateFieldType.FLOAT)) 430 .addToFields(new TemplateField( 431 name: 'Temperature at night', entity: Subject, type: TemplateFieldType.FLOAT)) 432 .addToFields(new TemplateField( 433 name: 'Photo period', entity: Subject, type: TemplateFieldType.STRING)) 434 .addToFields(new TemplateField( 435 name: 'Light intensity', entity: Subject, type: TemplateFieldType.STRING)) 436 .addToFields(new TemplateField( 437 name: 'Start date', entity: Subject, type: TemplateFieldType.DATE)) 438 .addToFields(new TemplateField( 439 name: 'Harvest date', entity: Subject, type: TemplateFieldType.DATE)) 440 .addToFields(new TemplateField( 441 name: 'Harvest delay', entity: Subject, type: TemplateFieldType.TEXT)) 442 .addToFields(new TemplateField( 443 name: 'Additional info', entity: Subject, type: TemplateFieldType.TEXT)) 444 .with { if (!validate()) { errors.each { println it} } else save()} 445 446 println ".adding open-field plant template..." 447 def FieldTemplate = new Template( 448 name: 'Plant-open field', 449 entity: dbnp.studycapturing.Subject 450 ) 451 .addToFields(varietyField) 452 .addToFields(ecotypeField) 453 .addToFields(genotypeField) 454 .addToFields(new TemplateField( 455 name: 'Start date', entity: Subject, type: TemplateFieldType.DATE)) 456 .addToFields(new TemplateField( 457 name: 'Harvest date', entity: Subject, type: TemplateFieldType.DATE)) 458 .addToFields(new TemplateField( 459 name: 'Growth type', entity: Subject, type: TemplateFieldType.STRINGLIST, 460 listEntries: [new TemplateFieldListItem(name:'Standard'),new TemplateFieldListItem(name: 'Experimental')])) 461 .addToFields(new TemplateField( 462 name: 'Growth protocol', entity: Subject, type: TemplateFieldType.TEXT)) 463 .addToFields(new TemplateField( 464 name: 'Harvest delay', entity: Subject, type: TemplateFieldType.TEXT)) 465 .with { if (!validate()) { errors.each { println it} } else save()} 466 467 //Plant template 468 println ".adding chamber plant template..." 469 def chamberTemplate = new Template( 470 name: 'Plant-chamber', 471 entity: dbnp.studycapturing.Subject 472 ) 473 .addToFields(varietyField) 474 .addToFields(ecotypeField) 475 .addToFields(genotypeField) 476 /* 477 .addToFields(genotypeTypeField) 478 .addToFields( 479 new TemplateField( 480 name: 'Growth location', 481 type: TemplateFieldType.STRINGLIST, 482 listEntries: [ 483 new TemplateFieldListItem(name:'Greenhouse'), 484 new TemplateFieldListItem(name: 'Field') 485 ] 486 ) 487 ) 488 */ 489 .addToFields(new TemplateField( 490 name: 'Room', type: TemplateFieldType.STRING, entity: Subject, 491 comment: 'room number')) 492 .addToFields(new TemplateField( 493 name: 'Chamber no.', type: TemplateFieldType.STRING, entity: Subject, 494 comment: 'Chamber number')) 495 .addToFields(new TemplateField( 496 name: 'Block', type: TemplateFieldType.STRING, entity: Subject)) 497 .addToFields(new TemplateField( 498 name: 'Position X', type: TemplateFieldType.FLOAT, entity: Subject)) 499 .addToFields(new TemplateField( 500 name: 'Position Y', type: TemplateFieldType.FLOAT, entity: Subject)) 501 .addToFields(new TemplateField( 502 name: 'Temperature at day', type: TemplateFieldType.FLOAT, entity: Subject)) 503 .addToFields(new TemplateField( 504 name: 'Temperature at night', type: TemplateFieldType.FLOAT, entity: Subject)) 505 .addToFields(new TemplateField( 506 name: 'Photo period', type: TemplateFieldType.STRING, entity: Subject)) 507 .addToFields(new TemplateField( 508 name: 'Light intensity', type: TemplateFieldType.STRING, entity: Subject)) 509 .addToFields(new TemplateField( 510 name: 'Start date', type: TemplateFieldType.DATE, entity: Subject)) 511 .addToFields(new TemplateField( 512 name: 'Harvest date', type: TemplateFieldType.DATE, entity: Subject)) 513 .addToFields(new TemplateField( 514 name: 'Growth type', type: TemplateFieldType.STRINGLIST, entity: Subject, 515 listEntries: [new TemplateFieldListItem(name:'Standard'),new TemplateFieldListItem(name: 'Experimental')])) 516 .addToFields(new TemplateField( 517 name: 'Growth protocol', type: TemplateFieldType.TEXT, entity: Subject)) 518 .addToFields(new TemplateField( 519 name: 'Harvest delay', type: TemplateFieldType.TEXT, entity: Subject)) 520 .with { if (!validate()) { errors.each { println it} } else save()} 521 522 println ".adding plant sample template..." 523 def plantSampleTemplate = new Template( 524 name: 'Plant sample', 525 entity: dbnp.studycapturing.Sample 526 ) 527 .addToFields(sampleRemarksField) 528 .addToFields(sampleVialTextField) 529 .with { if (!validate()) { errors.each { println it} } else save()} 530 531 println ".adding material prep template" 532 def materialPrepTemplate = new Template( 533 name: 'Plant-material preparation', 534 description: 'material preparation', 535 entity: dbnp.studycapturing.Event 536 ) 537 .addToFields(new TemplateField( 538 name: 'Tissue', 539 type: TemplateFieldType.STRING, 540 entity: Event, 541 comment: 'organ/ fraction of culture/ plant part') 542 ) 543 .addToFields( 544 new TemplateField( 545 name: 'Grinding', 546 type: TemplateFieldType.STRINGLIST, 547 entity: Event, 548 listEntries: [ 549 new TemplateFieldListItem(name:'yes'), 550 new TemplateFieldListItem(name: 'no'), 551 new TemplateFieldListItem(name: 'unknown') 552 ] 553 ) 554 ) 555 .addToFields( 556 new TemplateField( 557 name: 'Storage location', 558 type: TemplateFieldType.STRING, 559 entity: Event 560 ) 561 ) 562 .addToFields( 563 new TemplateField( 564 name: 'protocol reference', 565 type: TemplateFieldType.STRING, 566 entity: Event 567 ) 568 ) 569 .with { if (!validate()) { errors.each { println it} } else save()} 570 571 def protocolField = new TemplateField( 572 name: 'Protocol', 573 type: TemplateFieldType.FILE, 574 entity: Event, 575 comment: 'You can upload a protocol here which describes the procedure which was used when carrying out the event' 576 ) 577 .with { if (!validate()) { errors.each { println it} } else save()} 578 579 // diet treatment template 580 println ".adding diet treatement template" 581 def dietTreatmentTemplate = new Template( 582 name: 'Diet treatment', 583 entity: dbnp.studycapturing.Event 584 ) 585 .addToFields( 586 new TemplateField( 587 name: 'Diet', 588 type: TemplateFieldType.STRINGLIST, 589 entity: Event, 590 listEntries: [ 591 new TemplateFieldListItem(name:'low fat'), 592 new TemplateFieldListItem(name: 'high fat') 593 ] 594 ) 595 ) 596 .addToFields(protocolField) 597 .with { if (!validate()) { errors.each { println it} } else save()} 598 599 // boost treatment template 600 println ".adding boost treatment template" 601 def boostTreatmentTemplate = new Template( 602 name: 'Compound challenge', 603 entity: dbnp.studycapturing.Event 604 ) 605 .addToFields( 606 new TemplateField( 607 name: 'Compound', 608 type: TemplateFieldType.ONTOLOGYTERM, 609 entity: Event, 610 ontologies: [chebiOntology] 611 ) 612 ) 613 .addToFields( 614 new TemplateField( 615 name: 'Control', 616 type: TemplateFieldType.BOOLEAN, 617 entity: Event 618 ) 619 ) 620 .addToFields(protocolField) 621 .with { if (!validate()) { errors.each { println it} } else save()} 622 623 // fasting treatment template 624 println ".adding fasting treatment template" 625 def fastingTreatment = new Template( 626 name: 'Fasting treatment', 627 description: 'Fasting for a specific amount of time', 628 entity: dbnp.studycapturing.Event 629 ) 630 .addToFields( 631 new TemplateField( 632 name: 'Fasting period', 633 type: TemplateFieldType.RELTIME, 634 entity: Event 635 ) 636 ) 637 .with { if (!validate()) { errors.each { println it} } else save()} 638 639 // SamplingEvent templates 640 println ".adding sampling protocol template field" 641 def samplingProtocolField = new TemplateField( 642 name: 'Sample Protocol', 643 entity: SamplingEvent, 644 type: TemplateFieldType.FILE, 645 comment: 'You can upload a protocol here which describes the procedure which was used when carrying out the sampling event' 646 ) 647 .with { if (!validate()) { errors.each { println it} } else save()} 648 649 // liver sampling event template 650 println ".adding liver sampling event template" 651 def liverSamplingEventTemplate = new Template( 652 name: 'Liver extraction', 653 description: 'Liver sampling for transcriptomics arrays', 654 entity: dbnp.studycapturing.SamplingEvent 655 ) 656 .addToFields(samplingProtocolField) 657 .addToFields( 658 new TemplateField( 659 name: 'Sample weight', 660 unit: 'mg', 661 entity: SamplingEvent, 662 type: TemplateFieldType.FLOAT 663 ) 664 ) 665 .with { if (!validate()) { errors.each { println it} } else save()} 666 667 // blood sampling 668 println ".adding blood sampling event template" 669 def bloodSamplingEventTemplate = new Template( 670 name: 'Blood extraction', 671 description: 'Blood extraction targeted at lipid assays', 672 entity: dbnp.studycapturing.SamplingEvent 673 ) 674 .addToFields(samplingProtocolField) 675 .addToFields( 676 new TemplateField( 677 name: 'Sample volume', 678 entity: SamplingEvent, 679 unit: 'ml', 680 type: TemplateFieldType.FLOAT 681 ) 682 ) 683 .with { if (!validate()) { errors.each { println it} } else save()} 684 685 // plant sample extraction event template 686 println ".adding plant sample extraction event template" 687 def plantSamplingExtractEventTemplate = new Template( 688 name: 'Plant sample extraction', 689 description: 'sample extraction', 690 entity: dbnp.studycapturing.SamplingEvent, 691 sampleTemplates: [plantSampleTemplate] 692 ) 693 .addToFields(samplingProtocolField) 694 .addToFields( 695 new TemplateField( 696 name: 'Sample weight', 697 unit: 'ul', 698 entity: SamplingEvent, 699 type: TemplateFieldType.FLOAT 700 ) 701 ) 702 .addToFields( 703 new TemplateField( 704 name: 'Sample when measured', 705 type: TemplateFieldType.STRINGLIST, 706 entity: SamplingEvent, 707 listEntries: [ 708 new TemplateFieldListItem(name:'Dried'), 709 new TemplateFieldListItem(name: 'Fresh'), 710 new TemplateFieldListItem(name: 'Unknown') 711 ] 712 ) 713 ) 714 .with { if (!validate()) { errors.each { println it} } else save()} 715 716 // plant sampling event template 717 println ".adding plant sampling event template" 718 def plantSamplingEventTemplate = new Template( 719 name: 'Plant-sample ', 720 description: 'plant sample ', 721 entity: dbnp.studycapturing.SamplingEvent, 722 sampleTemplates: [plantSampleTemplate] 723 ) 724 //.addToFields(samplingProtocolField) 725 .addToFields( 726 new TemplateField( 727 name: 'material', 728 comment: 'physical charecteristic. e.g, grounded powder of tomato seed or liquid', 729 entity: SamplingEvent, 730 type: TemplateFieldType.STRING 731 ) 732 ) 733 .addToFields( 734 new TemplateField( 735 name: 'Description', 736 type: TemplateFieldType.STRING, 737 entity: SamplingEvent 738 ) 739 ) 740 .addToFields( 741 new TemplateField( 742 name: 'extracted material', 743 comment: 'substance to be extracted. e.g., lipids, volatiles, primary metabolites etc', 744 type: TemplateFieldType.STRING, 745 entity: SamplingEvent 746 ) 747 ) 748 .addToFields( 749 new TemplateField( 750 name: 'Text on vial', 751 entity: SamplingEvent, 752 type: TemplateFieldType.STRING 753 ) 754 ) 755 .with { if (!validate()) { errors.each { println it} } else save()} 756 757 // Add example studies 758 if (grails.util.GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT) { 748 749 // Add example mouse study 759 750 println ".adding NuGO PPS3 leptin example study..." 760 751 def mouseStudy = new Study( … … 962 953 .save() 963 954 955 // Add example human study 964 956 println ".adding NuGO PPSH example study..." 965 957 -
trunk/grails-app/domain/dbnp/studycapturing/Event.groovy
r541 r564 45 45 static List<TemplateField> giveDomainFields() { return Event.domainFields } 46 46 47 // TODO: Kees start documenting your code48 47 static final List<TemplateField> domainFields = [ 49 48 new TemplateField( 50 49 name: 'startTime', 51 type: TemplateFieldType.RELTIME), 50 type: TemplateFieldType.RELTIME, 51 comment: "Please enter the start time as a relative time from study start date. "+RelTime.getHelpText()), 52 52 new TemplateField( 53 53 name: 'endTime', 54 type: TemplateFieldType.RELTIME) 54 type: TemplateFieldType.RELTIME, 55 comment: "Please enter the end time as a relative time from study start date. "+RelTime.getHelpText()) 55 56 ] 56 57 58 // TODO: Jahn, could you indicate in a comment why these different duration functions exist? 57 59 def getDuration() { 58 60 return new RelTime(startTime, endTime); … … 67 69 } 68 70 69 // TODO: Kees start documenting your code70 71 def getPrettyDuration() { 71 72 getPrettyDuration(getDuration()) 72 73 } 73 74 74 // TODO: Kees start documenting your code75 75 def getDurationString() { 76 76 def d = getDuration() … … 78 78 } 79 79 80 // TODO: Kees start documenting your code81 80 def getShortDuration() { 82 81 def d = getDuration() … … 84 83 } 85 84 86 // TODO: Kees start documenting your code 85 /** 86 * Return whether this is SamplingEvent 87 * @return boolean 88 */ 87 89 def isSamplingEvent() { 88 90 return (this instanceof SamplingEvent) 89 91 } 90 92 91 // TODO: Kees start documenting your code92 93 def belongsToGroup(Set<EventGroup> groups) { 93 94 def eventFound = false; … … 102 103 } 103 104 104 // TODO: Kees start documenting your code105 105 def String toString() { 106 106 return fieldExists('Description') ? getFieldValue('Description') : "" -
trunk/grails-app/domain/dbnp/studycapturing/RelTime.groovy
r540 r564 167 167 } 168 168 169 170 171 /** 172 * Return a sentence that may be used in interfaces to give the user an instruction on how to enter RelTimes in string format 173 */ 174 public static final String getHelpText() { 175 return "Use the first letter of weeks/days/hours/minutes/seconds, e.g. '1w 2d' for 1 week + 2 days or '10m30s for 10 minutes and 30 seconds."; 176 } 177 169 178 /** 170 179 * Parses a string into a RelTime long -
trunk/grails-app/domain/dbnp/studycapturing/Study.groovy
r554 r564 17 17 Date lastUpdated 18 18 Date startDate 19 20 21 /** 22 * return the domain fields for this domain class 23 * @return List 24 */ 25 static List<TemplateField> giveDomainFields() { return Study.domainFields } 26 27 static final List<TemplateField> domainFields = [ 28 new TemplateField( 29 name: 'title', 30 type: TemplateFieldType.STRING), 31 new TemplateField( 32 name: 'code', 33 type: TemplateFieldType.STRING, 34 preferredIdentifier:true, 35 comment: 'Fill out the code by which many people will recognize your study'), 36 new TemplateField( 37 name: 'startDate', 38 type: TemplateFieldType.DATE, 39 comment: 'Fill out the official start date or date of first action') 40 ] 19 List subjects 20 List events 21 List samplingEvents 22 List eventGroups 23 List samples 24 List assays 41 25 42 26 static hasMany = [ … … 63 47 autoTimestamp true 64 48 } 49 50 /** 51 * return the domain fields for this domain class 52 * @return List 53 */ 54 static List<TemplateField> giveDomainFields() { return Study.domainFields } 55 56 static final List<TemplateField> domainFields = [ 57 new TemplateField( 58 name: 'title', 59 type: TemplateFieldType.STRING), 60 new TemplateField( 61 name: 'code', 62 type: TemplateFieldType.STRING, 63 preferredIdentifier:true, 64 comment: 'Fill out the code by which many people will recognize your study'), 65 new TemplateField( 66 name: 'startDate', 67 type: TemplateFieldType.DATE, 68 comment: 'Fill out the official start date or date of first action') 69 ] 65 70 66 71 /** -
trunk/grails-app/domain/dbnp/studycapturing/TemplateEntity.groovy
r561 r564 420 420 // Convenience setter for boolean fields 421 421 if( field.type == TemplateFieldType.BOOLEAN && value && value.class == String ) { 422 if (value.equals("true") ) {422 if (value.equals("true") || value.equals("on")) { 423 423 value = true 424 424 } 425 else if (value.equals("false") ) {425 else if (value.equals("false") || value.equals("off")) { 426 426 value = false 427 427 }
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