github.com/Bio-core/jtree@v0.0.0-20190705165106-1d7a7e7d6272/swagger.yaml (about) 1 --- 2 swagger: "2.0" 3 info: 4 description: "Metadata API" 5 version: "0.1.0" 6 title: "Jtree Metadata API" 7 contact: 8 email: "info@distributedgenomics.ca" 9 license: 10 name: "GPL" 11 url: "https://www.gnu.org/licenses/gpl-3.0.en.html" 12 host: "virtserver.swaggerhub.com" 13 basePath: "/Jtree/metadata/0.1.0" 14 schemes: 15 - "http" 16 paths: 17 /patient: 18 post: 19 summary: "adds a patient item" 20 description: "Adds a patient to the system" 21 operationId: "addPatient" 22 consumes: 23 - "application/json" 24 produces: 25 - "application/json" 26 parameters: 27 - in: "body" 28 name: "patient" 29 description: "Patient" 30 required: false 31 schema: 32 $ref: "#/definitions/Patient" 33 responses: 34 201: 35 description: "item created" 36 400: 37 description: "invalid input, object invalid" 38 409: 39 description: "an existing item already exists" 40 41 /sample: 42 post: 43 summary: "adds a sample" 44 description: "Adds a sample to the system" 45 operationId: "addSample" 46 consumes: 47 - "application/json" 48 produces: 49 - "application/json" 50 parameters: 51 - in: "body" 52 name: "sample" 53 description: "Sample" 54 required: false 55 schema: 56 $ref: "#/definitions/Sample" 57 responses: 58 201: 59 description: "item created" 60 400: 61 description: "invalid input, object invalid" 62 409: 63 description: "an existing item already exists" 64 65 /experiment: 66 post: 67 summary: "adds an experiment item" 68 description: "Adds an experiment to the system" 69 operationId: "addExperiment" 70 consumes: 71 - "application/json" 72 produces: 73 - "application/json" 74 parameters: 75 - in: "body" 76 name: "experiment" 77 description: "Experiment" 78 required: false 79 schema: 80 $ref: "#/definitions/Experiment" 81 responses: 82 201: 83 description: "item created" 84 400: 85 description: "invalid input, object invalid" 86 409: 87 description: "an existing item already exists" 88 89 /result: 90 post: 91 summary: "adds a result item" 92 description: "Adds a result to the system" 93 operationId: "addResult" 94 consumes: 95 - "application/json" 96 produces: 97 - "application/json" 98 parameters: 99 - in: "body" 100 name: "result" 101 description: "Result" 102 required: false 103 schema: 104 $ref: "#/definitions/Result" 105 responses: 106 201: 107 description: "item created" 108 400: 109 description: "invalid input, object invalid" 110 409: 111 description: "an existing item already exists" 112 113 /resultdetails: 114 post: 115 summary: "adds a resultdetails item" 116 description: "Adds a resultdetails to the system" 117 operationId: "addResultdetails" 118 consumes: 119 - "application/json" 120 produces: 121 - "application/json" 122 parameters: 123 - in: "body" 124 name: "resultdetails" 125 description: "Resultdetails" 126 required: false 127 schema: 128 $ref: "#/definitions/Resultdetails" 129 responses: 130 201: 131 description: "item created" 132 400: 133 description: "invalid input, object invalid" 134 409: 135 description: "an existing item already exists" 136 137 138 /columns: 139 get: 140 summary: "gets columns" 141 description: "gets column names" 142 operationId: "getSampleColumns" 143 produces: 144 - "application/json" 145 responses: 146 200: 147 description: "columns" 148 schema: 149 type: "array" 150 items: 151 type: "string" 152 400: 153 description: "bad input parameter" 154 155 /query: 156 post: 157 summary: "Query for Sample" 158 operationId: "getSamplesByQuery" 159 consumes: 160 - "application/json" 161 produces: 162 - "application/json" 163 parameters: 164 - in: body 165 name: query 166 required: false 167 schema: 168 $ref: "#/definitions/Query" 169 responses: 170 200: 171 description: "OK" 172 schema: 173 type: "array" 174 items: 175 $ref: "#/definitions/Sample" 176 404: 177 description: "Sample not found" 178 179 /logout: 180 get: 181 summary: "logsout" 182 description: "logs users out" 183 operationId: "logout" 184 produces: 185 - "application/json" 186 responses: 187 200: 188 description: "OK" 189 schema: 190 type: "boolean" 191 404: 192 description: "Sample not found" 193 194 /upload: 195 post: 196 summary: Uploads a file. 197 consumes: 198 - multipart/form-data 199 parameters: 200 - in: formData 201 name: upfile 202 type: file 203 description: The file to upload. 204 responses: 205 200: 206 description: "OK" 207 schema: 208 type: "boolean" 209 404: 210 description: "File not found" 211 409: 212 description: "an existing item already exists" 213 214 definitions: 215 Patient: 216 type: "object" 217 properties: 218 patient_id: 219 type: "string" 220 x-nullable: true 221 x-go-custom-tag: "db:\"patient_id\"" 222 sample_id: 223 type: "string" 224 x-nullable: true 225 x-go-custom-tag: "db:\"sample_id\"" 226 first_name: 227 type: "string" 228 x-nullable: true 229 x-go-custom-tag: "db:\"first_name\"" 230 last_name: 231 type: "string" 232 x-nullable: true 233 x-go-custom-tag: "db:\"last_name\"" 234 initials: 235 type: "string" 236 x-nullable: true 237 x-go-custom-tag: "db:\"initials\"" 238 gender: 239 type: "string" 240 x-nullable: true 241 x-go-custom-tag: "db:\"gender\"" 242 mrn: 243 type: "string" 244 x-nullable: true 245 x-go-custom-tag: "db:\"mrn\"" 246 dob: 247 type: "string" 248 x-nullable: true 249 x-go-custom-tag: "db:\"dob\"" 250 on_hcn: 251 type: "string" 252 x-nullable: true 253 x-go-custom-tag: "db:\"on_hcn\"" 254 clinical_history: 255 type: "string" 256 x-nullable: true 257 x-go-custom-tag: "db:\"clinical_history\"" 258 patient_type: 259 type: "string" 260 x-nullable: true 261 x-go-custom-tag: "db:\"patient_type\"" 262 se_num: 263 type: "string" 264 x-nullable: true 265 x-go-custom-tag: "db:\"se_num\"" 266 date_received: 267 type: "string" 268 x-nullable: true 269 x-go-custom-tag: "db:\"date_received\"" 270 referring_physican: 271 type: "string" 272 x-nullable: true 273 x-go-custom-tag: "db:\"referring_physican\"" 274 date_reported: 275 type: "string" 276 x-nullable: true 277 x-go-custom-tag: "db:\"date_reported\"" 278 surgical_date: 279 type: "string" 280 x-nullable: true 281 x-go-custom-tag: "db:\"surgical_date\"" 282 Sample: 283 type: "object" 284 properties: 285 sample_id: 286 type: "string" 287 x-nullable: true 288 x-go-custom-tag: "db:\"sample_id\"" 289 facility: 290 type: "string" 291 x-nullable: true 292 x-go-custom-tag: "db:\"facility\"" 293 test_requested: 294 type: "string" 295 x-nullable: true 296 x-go-custom-tag: "db:\"test_requested\"" 297 se_num: 298 type: "string" 299 x-nullable: true 300 x-go-custom-tag: "db:\"se_num\"" 301 date_collected: 302 type: "string" 303 x-nullable: true 304 x-go-custom-tag: "db:\"date_collected\"" 305 date_received: 306 type: "string" 307 x-nullable: true 308 x-go-custom-tag: "db:\"date_received\"" 309 sample_type: 310 type: "string" 311 x-nullable: true 312 x-go-custom-tag: "db:\"sample_type\"" 313 material_received: 314 type: "string" 315 x-nullable: true 316 x-go-custom-tag: "db:\"material_received\"" 317 material_received_num: 318 type: "string" 319 x-nullable: true 320 x-go-custom-tag: "db:\"material_received_num\"" 321 material_received_other: 322 type: "string" 323 x-nullable: true 324 x-go-custom-tag: "db:\"material_received_other\"" 325 volume_of_blood_marrow: 326 type: "number" 327 format: "float" 328 x-nullable: true 329 x-go-custom-tag: "db:\"volume_of_blood_marrow\"" 330 surgical_num: 331 type: "string" 332 x-nullable: true 333 x-go-custom-tag: "db:\"surgical_num\"" 334 tumor_site: 335 type: "string" 336 x-nullable: true 337 x-go-custom-tag: "db:\"tumor_site\"" 338 historical_diagnosis: 339 type: "string" 340 x-nullable: true 341 x-go-custom-tag: "db:\"historical_diagnosis\"" 342 tumor_percnt_of_total: 343 type: "number" 344 format: "float" 345 x-nullable: true 346 x-go-custom-tag: "db:\"tumor_percnt_of_total\"" 347 tumor_percnt_of_circled: 348 type: "number" 349 format: "float" 350 x-nullable: true 351 x-go-custom-tag: "db:\"tumor_percnt_of_circled\"" 352 reviewed_by: 353 type: "string" 354 x-nullable: true 355 x-go-custom-tag: "db:\"reviewed_by\"" 356 h_e_slide_location: 357 type: "string" 358 x-nullable: true 359 x-go-custom-tag: "db:\"h_e_slide_location\"" 360 non_uhn_id: 361 type: "string" 362 x-nullable: true 363 x-go-custom-tag: "db:\"non_uhn_id\"" 364 name_of_requestor: 365 type: "string" 366 x-nullable: true 367 x-go-custom-tag: "db:\"name_of_requestor\"" 368 dna_concentration: 369 type: "number" 370 format: "float" 371 x-nullable: true 372 x-go-custom-tag: "db:\"dna_concentration\"" 373 dna_volume: 374 type: "number" 375 format: "float" 376 x-nullable: true 377 x-go-custom-tag: "db:\"dna_volume\"" 378 dna_location: 379 type: "string" 380 x-nullable: true 381 x-go-custom-tag: "db:\"dna_location\"" 382 rna_concentration: 383 type: "number" 384 format: "float" 385 x-nullable: true 386 x-go-custom-tag: "db:\"rna_concentration\"" 387 rna_volume: 388 type: "number" 389 format: "float" 390 x-nullable: true 391 x-go-custom-tag: "db:\"rna_volume\"" 392 rna_location: 393 type: "string" 394 x-nullable: true 395 x-go-custom-tag: "db:\"rna_location\"" 396 wbc_location: 397 type: "string" 398 x-nullable: true 399 x-go-custom-tag: "db:\"wbc_location\"" 400 plasma_location: 401 type: "string" 402 x-nullable: true 403 x-go-custom-tag: "db:\"plasma_location\"" 404 cf_plasma_location: 405 type: "string" 406 x-nullable: true 407 x-go-custom-tag: "db:\"cf_plasma_location\"" 408 pb_bm_location: 409 type: "string" 410 x-nullable: true 411 x-go-custom-tag: "db:\"pb_bm_location\"" 412 rna_lysate_location: 413 type: "string" 414 x-nullable: true 415 x-go-custom-tag: "db:\"rna_lysate_location\"" 416 sample_size: 417 type: "string" 418 x-nullable: true 419 x-go-custom-tag: "db:\"sample_size\"" 420 study_id: 421 type: "string" 422 x-nullable: true 423 x-go-custom-tag: "db:\"study_id\"" 424 sample_name: 425 type: "string" 426 x-nullable: true 427 x-go-custom-tag: "db:\"sample_name\"" 428 date_submitted: 429 type: "string" 430 x-nullable: true 431 x-go-custom-tag: "db:\"date_submitted\"" 432 container_type: 433 type: "string" 434 x-nullable: true 435 x-go-custom-tag: "db:\"container_type\"" 436 container_name: 437 type: "string" 438 x-nullable: true 439 x-go-custom-tag: "db:\"container_name\"" 440 container_id: 441 type: "string" 442 x-nullable: true 443 x-go-custom-tag: "db:\"container_id\"" 444 container_well: 445 type: "string" 446 x-nullable: true 447 x-go-custom-tag: "db:\"container_well\"" 448 copath_num: 449 type: "string" 450 x-nullable: true 451 x-go-custom-tag: "db:\"copath_num\"" 452 other_identifier: 453 type: "string" 454 x-nullable: true 455 x-go-custom-tag: "db:\"other_identifier\"" 456 has_sample_files: 457 type: "boolean" 458 x-nullable: true 459 x-go-custom-tag: "db:\"has_sample_files\"" 460 dna_sample_barcode: 461 type: "string" 462 x-nullable: true 463 x-go-custom-tag: "db:\"dna_sample_barcode\"" 464 dna_extraction_date: 465 type: "string" 466 x-nullable: true 467 x-go-custom-tag: "db:\"dna_extraction_date\"" 468 dna_quality: 469 type: "string" 470 x-nullable: true 471 x-go-custom-tag: "db:\"dna_quality\"" 472 ffpe_qc_date: 473 type: "string" 474 x-nullable: true 475 x-go-custom-tag: "db:\"ffpe_qc_date\"" 476 delta_ct_Value: 477 type: "number" 478 format: "float" 479 x-nullable: true 480 x-go-custom-tag: "db:\"delta_ct_Value\"" 481 comments: 482 type: "string" 483 x-nullable: true 484 x-go-custom-tag: "db:\"comments\"" 485 rnase_p_date: 486 type: "string" 487 x-nullable: true 488 x-go-custom-tag: "db:\"rnase_p_date\"" 489 dna_quality_by_rnase_p: 490 type: "number" 491 format: "float" 492 x-nullable: true 493 x-go-custom-tag: "db:\"dna_quality_by_rnase_p\"" 494 rna_quality: 495 type: "number" 496 format: "float" 497 x-nullable: true 498 x-go-custom-tag: "db:\"rna_quality\"" 499 rna_extraction_date: 500 type: "string" 501 x-nullable: true 502 x-go-custom-tag: "db:\"rna_extraction_date\"" 503 Query: 504 type: "object" 505 properties: 506 selected_condition: 507 type: "array" 508 items: 509 type: "array" 510 items: 511 type: "string" 512 selected_tables: 513 type: "array" 514 items: 515 type: "string" 516 selected_fields: 517 type: "array" 518 items: 519 type: "string" 520 Experiment: 521 type: "object" 522 properties: 523 chip_cartridge_barcode: 524 type: "string" 525 x-nullable: true 526 x-go-custom-tag: "db:\"chip_cartridge_barcode\"" 527 complete_date: 528 type: "string" 529 x-nullable: true 530 x-go-custom-tag: "db:\"complete_date\"" 531 experiment_id: 532 type: "string" 533 x-nullable: true 534 x-go-custom-tag: "db:\"experiment_id\"" 535 has_project_files: 536 type: "boolean" 537 x-nullable: true 538 x-go-custom-tag: "db:\"has_project_files\"" 539 opened_date: 540 type: "string" 541 x-nullable: true 542 x-go-custom-tag: "db:\"opened_date\"" 543 panel_assay_screened: 544 type: "number" 545 format: "int" 546 x-nullable: true 547 x-go-custom-tag: "db:\"panel_assay_screened\"" 548 pcr: 549 type: "string" 550 x-nullable: true 551 x-go-custom-tag: "db:\"pcr\"" 552 priority: 553 type: "number" 554 format: "int" 555 x-nullable: true 556 x-go-custom-tag: "db:\"priority\"" 557 procedure_order_datetime: 558 type: "string" 559 x-nullable: true 560 x-go-custom-tag: "db:\"procedure_order_datetime\"" 561 project_id: 562 type: "string" 563 x-nullable: true 564 x-go-custom-tag: "db:\"project_id\"" 565 project_name: 566 type: "string" 567 x-nullable: true 568 x-go-custom-tag: "db:\"project_name\"" 569 sample_id: 570 type: "string" 571 x-nullable: true 572 x-go-custom-tag: "db:\"sample_id\"" 573 study_id: 574 type: "string" 575 x-nullable: true 576 x-go-custom-tag: "db:\"study_id\"" 577 test_date: 578 type: "string" 579 x-nullable: true 580 x-go-custom-tag: "db:\"test_date\"" 581 Result: 582 type: "object" 583 properties: 584 sample_id: 585 type: "string" 586 x-nullable: true 587 x-go-custom-tag: "db:\"sample_id\"" 588 uid: 589 type: "string" 590 x-nullable: true 591 x-go-custom-tag: "db:\"uid\"" 592 results_id: 593 type: "string" 594 x-nullable: true 595 x-go-custom-tag: "db:\"results_id\"" 596 failed_regions: 597 type: "string" 598 x-nullable: true 599 x-go-custom-tag: "db:\"failed_regions\"" 600 mutation: 601 type: "string" 602 x-nullable: true 603 x-go-custom-tag: "db:\"mutation\"" 604 verification_pcr: 605 type: "string" 606 x-nullable: true 607 x-go-custom-tag: "db:\"verification_pcr\"" 608 mlpa_pcr: 609 type: "string" 610 x-nullable: true 611 x-go-custom-tag: "db:\"mlpa_pcr\"" 612 overall_quality_threshold: 613 type: "number" 614 format: "float" 615 x-nullable: true 616 x-go-custom-tag: "db:\"overall_quality_threshold\"" 617 overall_hotspots_threshold: 618 type: "number" 619 format: "float" 620 x-nullable: true 621 x-go-custom-tag: "db:\"overall_hotspots_threshold\"" 622 mean_depth_of_coveage: 623 type: "number" 624 format: "float" 625 x-nullable: true 626 x-go-custom-tag: "db:\"mean_depth_of_coveage\"" 627 Resultdetails: 628 type: "object" 629 properties: 630 uid: 631 type: "string" 632 x-nullable: true 633 x-go-custom-tag: "db:\"uid\"" 634 results_id: 635 type: "string" 636 x-nullable: true 637 x-go-custom-tag: "db:\"results_id\"" 638 results_details_id: 639 type: "string" 640 x-nullable: true 641 x-go-custom-tag: "db:\"results_details_id\"" 642 pcr: 643 type: "string" 644 x-nullable: true 645 x-go-custom-tag: "db:\"pcr\"" 646 sample_id: 647 type: "string" 648 x-nullable: true 649 x-go-custom-tag: "db:\"sample_id\"" 650 gene: 651 type: "string" 652 x-nullable: true 653 x-go-custom-tag: "db:\"gene\"" 654 exon: 655 type: "number" 656 format: "int" 657 x-nullable: true 658 x-go-custom-tag: "db:\"exon\"" 659 p_nomenclature: 660 type: "string" 661 x-nullable: true 662 x-go-custom-tag: "db:\"p_nomenclature\"" 663 c_nomenclature: 664 type: "string" 665 x-nullable: true 666 x-go-custom-tag: "db:\"c_nomenclature\"" 667 VAF: 668 type: "number" 669 format: "float" 670 x-nullable: true 671 x-go-custom-tag: "db:\"VAF\"" 672 quality_score: 673 type: "number" 674 format: "float" 675 x-nullable: true 676 x-go-custom-tag: "db:\"quality_score\"" 677 coverage: 678 type: "number" 679 format: "int" 680 x-nullable: true 681 x-go-custom-tag: "db:\"coverage\"" 682 risk_score: 683 type: "number" 684 format: "float" 685 x-nullable: true 686 x-go-custom-tag: "db:\"risk_score\"" 687 result: 688 type: "string" 689 x-nullable: true 690 x-go-custom-tag: "db:\"result\"" 691 Record: 692 type: "object" 693 properties: 694 Sample: 695 $ref: "#/definitions/Sample" 696 Patient: 697 $ref: "#/definitions/Patient" 698 Experiment: 699 $ref: "#/definitions/Experiment" 700 Result: 701 $ref: "#/definitions/Result" 702 Resultdetails: 703 $ref: "#/definitions/Resultdetails"