三級分析 / geneyx / APIs === ###### tags: `基因體/三級分析` ###### tags: `生物資訊`, `基因體`, `三級分析`, `geneyx`, `瑞林⽣技` ![](https://i.imgur.com/CEvnroE.png) [TOC] <br> ## API > https://github.com/geneyx/geneyx.analysis.api ### response - success - error - VCF samples > annotate > https://www.prisma-gene.com.tw/sample/annotate ``` { "Code": "error", "Info": "No pipeline was found ready to be annotated by version set v5.12", "NeedEval": false } ``` ### Q & A - docs/geneyx.analysis.api 沒有此檔案 <br> <hr> <br> ## pipeline (prod) ### Step1 - config.yaml > [loadYamlFile(](https://github.com/geneyx/geneyx.analysis.api/blob/main/scripts/ga_helperFunctions.py) - [ga.config.yml](https://github.com/geneyx/geneyx.analysis.api/blob/main/scripts/ga.config.yml) ```yaml= server: 'https://www.prisma-gene.com.tw' apiUserId: 'enter-your-userid' apiUserKey: 'enter-your-userkey' ``` - code ```python # add user connection fields data['ApiUserKey'] = config['apiUserKey'] data['ApiUserID'] = config['apiUserId'] # send request api = config['server'] + '/api/xxx' ``` ### Step2 - CreatePatient > - [API doc](https://github.com/geneyx/geneyx.analysis.api/wiki/CreatePatient) > - [templates / patient.json](https://github.com/geneyx/geneyx.analysis.api/blob/main/scripts/templates/patient.json) > - [scripts / ga_createPatient.py](https://github.com/geneyx/geneyx.analysis.api/blob/main/scripts/ga_createPatient.py) - request URL [`/api/CreatePatient`](https://github.com/geneyx/geneyx.analysis.api/wiki/CreatePatient) - payload ```json= { "ApiUserID": "enter-your-userid", "apiUserKey": "enter-your-userkey", "SerialNumber":"SN-TJ-0421" } ``` - required - `SerialNumber` (unique) - SN 已經存在時，create 會有 error ```json { "Code": "error", "Info": "An item with that name already exists.", "NeedEval": false } ``` - full payload - 透過 `https://www.prisma-gene.com.tw/patient/Create` ```json= { "isNewPatient":true, "isLocked":false, "Gender":"", "UseConsentPersonal":"", "UseConsentClinical":"", "Consang":"", "SerialNumber":"SN-TJ-0421", "ID":null } ``` - response > based on UI ```json= { "SerialNumber":"SN-TJ-0421", "Consang":0, "ConsangName":"Unknown", "ID":"e7b5e50d-6c54-430e-ad60-a0a9b0e4e8e6", "CreatedByUser":"Grace Wu", "CreateDate":"2023-04-21T01:38:37.962179Z", "ModifiedByUser":"Grace Wu", "ModifyDate":"2023-04-21T01:38:37.962179Z" } ``` - `/patient/getBySn` 仍是透過 `SerialNumber` ，而不用 `ID` - 在下一步 CreateSample 階段，SubjectId 用的是 `ID` 而不是 `SerialNumber` ### Step3 - CreateSample > - [API doc](https://github.com/geneyx/geneyx.analysis.api/wiki/Create-Sample) > - [templates / sample.json](https://github.com/geneyx/geneyx.analysis.api/blob/main/scripts/templates/sample.json) > - [scripts / ga_uploadSample_json.py](https://github.com/geneyx/geneyx.analysis.api/blob/main/scripts/ga_uploadSample_json.py) > - [scripts / ga_uploadSamples.py](https://github.com/geneyx/geneyx.analysis.api/blob/main/scripts/ga_uploadSamples.py) - request URL `/api/createSample` - payload ```json= { "ApiUserID": "enter-your-userid", "apiUserKey": "enter-your-userkey", "SampleSerialNumber": "HG002.hiseqx.pcr-free.30x-0418.vcf.gz", "SubjectId": } ``` - required - `SerialNumber` (unique) - response > based on UI ```json= { "fileUrl": "HG002.hiseqx.pcr-free.30x-0418.vcf.gz" } ``` <br> <hr> <br> ## pipeline (study based on UI) ### Step1 - config.yaml - 準備 - [ga.config.yml](https://github.com/geneyx/geneyx.analysis.api/blob/main/scripts/ga.config.yml) ### Step3 - UploadSampleFile - request URL > 透過 `https://www.prisma-gene.com.tw/File/UploadSampleFile` - payload - response > based on UI ```json= { "fileUrl": "HG002.hiseqx.pcr-free.30x-0418.vcf.gz" } ``` (TODO, on-going) ### Step4: 開始分析 可能有兩個地方： - https://www.prisma-gene.com.tw/case/Create , POST > 開始分析? > [![](https://i.imgur.com/fUGRCZr.png)](https://i.imgur.com/fUGRCZr.png) - payload ```json= { "ID":"6ea4143b-4ba1-4898-b137-dd11c744e883", "ProtocolId":"b5f89905-8585-4e77-8dd0-00b9fef22b0a", "Name":"Single Sample Analysis", "PhenAlleleFreq":0.001, "GeneticModels":[ 1, 2, 4, 128, 256, 1073741824 ], "Phenotypes":"", "IsAdvancedPhenotypes":false, "PatientId":"0e85fc55-6fd3-41b9-9fa7-5d205b502bdb", "SerialNumber":"SN-HG002-SSA", "MainSampleId":"3f194b42-a54c-4058-b123-5aff1bdb72a6" } ``` - https://www.prisma-gene.com.tw/case/initializeCase , POST > 開始分析? > ![](https://i.imgur.com/WcrYMGK.png) - payload ```**** { "caseId": "6ea4143b-4ba1-4898-b137-dd11c744e883" } ``` - response ```true``` - https://www.prisma-gene.com.tw/sample/getCurrentVariantSummary , POST > 回傳狀態 > ![](https://i.imgur.com/19YLRGb.png) <br> ![](https://i.imgur.com/KsIWOEY.png) <br> - payload ```json= { "sampleId": "3f194b42-a54c-4058-b123-5aff1bdb72a6", "versionSetId": "8587f3bd-eba1-446e-b388-8c7bf115e090" } ``` - response ```json= { "ID":"578e7b12-4d01-474f-b006-2fd519edabde", "VersionSetId":"8587f3bd-eba1-446e-b388-8c7bf115e090", "VersionSetName":"v5.12", "StatusName":"ExecSnpEff", "Status":4, "TimeStamp":"2023-04-18T10:34:01.24Z", "Notes":"started", "Stats":{ "Variants":0, "Lines":0, "AaChangeCount":0, "DepthMedian":0 }, "Pipeline":1, "PipelineName":"Snv", "IsDone":false, "Disabled":false, "InArchive":false } ``` ### Step5: 產生報表 `https://analysis.geneyx.com/caseReport/CreateReport` <br> <hr> <br> ## files <!-- [ChatGPT] 請說明底下程式碼每個函數的用途： --> ### [scripts/UnifiedVcf.py](https://github.com/geneyx/geneyx.analysis.api/blob/1c741ec00a5823649f8a213af2f8bff07447b25d/scripts/UnifiedVcf.py) 這個程式碼主要是將不同格式的 VCF 文件（SNV, CNV, 重複序列）合併成一個 VCF 文件。以下是每個函數的用途： - `__get_lines__(file_path: str) -> []`: 這個函數會讀取指定路徑的文件，並回傳文件的所有行。這個函數可以處理 gzip 格式的壓縮文件。 - `__modify_repeat_line__(repeat_line: str) -> str`: 這個函數會修改重複序列文件中的一行，增加 SVTYPE=REP 到 INFO 欄位。 - `__is_valid_line__(line: str) -> bool`: 這個函數會檢查指定的 VCF 行是否合法。如果行是 header 或者是空行，就視為合法。如果行中包含 SVTYPE=，也視為合法。否則，需要檢查 GT（基因型）欄位，如果 GT 是 0 或者是 ./.，就視為不合法。 - `__write_vcf_content__(ftype: str, lines_dict: dict, output_h)`: 這個函數會將指定文件類型的 VCF 內容寫入到輸出文件。如果文件類型是 repeat，會先呼叫 __modify_repeat_line__ 函數來修改行中的 INFO 欄位。 - `__get_vcf_header__(vcf_file: str)`: 這個函數會從指定的 VCF 文件中讀取 header。 - `__get_vcf_header_from_lines__(vcf_lines: [])`: 這個函數會從指定的 VCF 行中讀取 header。 - `__is_empty__(lines: []) -> bool`: 這個函數會檢查指定的行是否都是空行或者是 header 行。 - `__create_unified_file__(files_lines: dict, output_path: str)`： 創建一個合併的 VCF 文件。如果 sv 檔案不為空，則先寫入 sv 檔案的內容；否則，寫入 cnv 和 repeat 檔案的內容。在寫入 repeat 檔案的內容之前，需要先從檔案中讀取 VCF 標頭。對於 cnv 和 repeat 檔案，必須檢查每一行是否有效，並且必須在寫入之前修改 info 段落。 **細節：** 函數的目的是將 files_lines 中的 sv、cnv 和 repeat 三種 vcf 檔案合併成一個統一的 vcf 檔案，並將合併後的檔案存儲到 output_path 中。在執行此函數時，會先將 sv 檔案的內容寫入輸出檔案，接著將 cnv 檔案和 repeat 檔案的內容寫入輸出檔案。如果 sv 檔案為空，則只有 cnv 檔案和 repeat 檔案的內容會被寫入輸出檔案。如果 cnv 檔案為空，則只有 repeat 檔案的內容會被寫入輸出檔案。如果所有檔案都為空或不存在，則會輸出警告信息。 - `run(output_path: str, sv_path: str = None, cnv_path: str = None, repeat_path: str = None)`： 運行整個程序，將三個不同類型的 VCF 檔案合併成一個 VCF 檔案。如果某個檔案不存在或是空的，則發出警告。 <br> ### [scripts/ga.config.yml](https://github.com/geneyx/geneyx.analysis.api/blob/1c741ec00a5823649f8a213af2f8bff07447b25d/scripts/ga.config.yml) 程式碼中的設定檔，其中 - server 指定了連接的伺服器位址， - apiUserId 和 apiUserKey 是需要填入使用者的 ID 和 Key，用於授權和驗證該使用者的身份。透過這些設定，程式碼可以透過提供的使用者身份，連接到指定的伺服器，並存取該伺服器提供的資源和服務。 <br> ### [scripts/ga_CreateCase.py](https://github.com/geneyx/geneyx.analysis.api/blob/1c741ec00a5823649f8a213af2f8bff07447b25d/scripts/ga_CreateCase.py) 用於建立一個 Geneyx Analysis 平台上的案例。程式中包含以下功能： - 匯入 argparse 模組，用於解析命令列參數。 - 匯入 requests 模組，用於向 Geneyx Analysis 平台發送 HTTP 請求。 - 匯入 ga_helperFunctions 模組，這是一個自定義的模組，其中包含一些用於輔助處理的函式。 - 定義 _verifyRequiredFields 函式，用於驗證必要欄位是否存在於輸入的 JSON 數據中。 - 解析命令列參數，其中包括： - --data：指定案例數據的 JSON 文件的路徑。 - --config：指定配置文件的路徑，其中包含 Geneyx Analysis 平台的 API 金鑰等信息。 - 讀取配置文件。 - 讀取案例數據 JSON 文件。 - 驗證必要欄位是否存在於案例數據 JSON 中。 - 將 API 金鑰和用戶 ID 添加到案例數據中。 - 向 Geneyx Analysis 平台發送 HTTP POST 請求以創建案例。 - 在控制台中打印 HTTP 請求的結果和響應內容。 <br> ### [scripts/ga_uploadSample_json.py](https://github.com/geneyx/geneyx.analysis.api/blob/1c741ec00a5823649f8a213af2f8bff07447b25d/scripts/ga_uploadSample_json.py) 用來上傳一個或多個 VCF 檔案到 Geneyx Analysis 的平台，並透過一個 JSON 檔案，設定檔案相關屬性。其中，程式的核心功能涵蓋了以下幾個部分： - 匯入 argparse、os、requests、ntpath 等 Python 標準函式庫以及自定義的 ga_helperFunctions 模組。 - 定義一些輔助函式，例如 _verifyRequiredFields 用來驗證資料是否符合規定。 - 使用 argparse 建立命令列參數解析器，以便在命令列執行時，使用者可以輸入相關參數，例如 snvVcf、svVcf、cnvVcf 等。 - 讀取配置檔案 ga.config.yml，並載入其中的設定。 - 檢查所提供的 SNV、SV、CNV 檔案是否存在，若不存在則會產生例外。 - 如果同時提供了 SV 與 CNV 檔案，則會將這兩個檔案合併成一個檔案；如果只提供了其中一個檔案，則直接使用該檔案。 - 讀取並驗證所提供的 JSON 檔案，並根據該檔案中的設定，設定檔案相關屬性。 - 上傳檔案到 Geneyx Analysis 的平台。 <br> ### [scripts/ga_uploadSamples.py](https://github.com/geneyx/geneyx.analysis.api/blob/1c741ec00a5823649f8a213af2f8bff07447b25d/scripts/ga_uploadSamples.py) 上傳一組 VCF 檔案作為樣本到 Geneyx Analysis。使用 argparse 套件解析命令列參數，程式能夠處理多種不同格式的 VCF 檔案，並能自動合併 SV 與 CNV 檔案。 程式還提供了多種選項，例如可以指定樣本的生物標本 ID、取樣日期、樣本類型、樣本來源、樣本的父母親等資訊，也可以附加樣本的 BAM 檔案 URL 或甲基化資料的 URL。 除了必填參數外，也提供了許多可選參數，如跳過上傳後的注釋、指定配置檔等。 - 相關資料 - sample data 樣本資料 - sample external files 樣本外部檔案 - BAM 檔案 URL - 甲基化資料的 URL - patient data 病患資料 <br> <hr> <br> ## [Geneyx Analysis API Collection](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json) - 全都是 - **method**: POST - **protocol**: https - **host**: analysis.geneyx.com - **body.options.raw.language**: json (raw 內容都是 json 格式) - **body.raw**: 都要攜帶底下兩個參數 - `ApiUserId: "enter_apiId"` - `ApiUserKey: "enter_apiKey"` - info - "_postman_id": "dc8b1c84-ceeb-4ca2-938b-c5c27a3f38b9", - "name": "Geneyx Analysis API Collection", - "schema": "https://schema.getpostman.com/json/collection/v2.1.0/collection.json", - "_exporter_id": "18131911" <br> - Overview | API name | Usage| |----------|-------| | [AddClinicalRecord](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L10) | `/api/AddClinicalRecord`<br>- SubjectId: "Enter_SubjectID",<br>- RecordDate: "yyyy-mm-dd",<br>- Description: "recorded something new",<br>- PhenotypeCodes: [ "HP:0001903", "HP:0000005" ] | | [BatchReportList](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L40) | `/api/BatchReportList`<br>- batchName: "Enter_Batch_File_Name" | | [BatchSeqSamples](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L70) | `/api/BatchSeqSamples`<br>- batchName: "string"| | [BatchVcfSamples](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L100) | `/api/BatchVcfSamples`<br>- batchName: "string" | | [Cases](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L130) | `/api/Cases` | | [CaseAssignment](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L160) | `/api/CaseAssignment`<br>- SerialNumber: "string",<br>- AssignedToUserId: "00000000-0000-0000-0000-000000000000",<br>- AssignedToFullName: "string" | | [CaseReports](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L190) | `/api/CaseReports`<br>- caseSn: "enter_caseSn" | | [CreateCase](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L220) | `/api/CreateCase`<br>- SerialNumber: "string",<br>- Name: "string",<br>- Description: "string",<br>- PhenAlleleFreq: 0,<br>- Phenotypes: "string",<br>- Owner: "string",<br>- OwnerDepartment: "string",<br>- GeneList: "string",<br>- ProtocolId: "string",<br>- SubjectId: "string",<br>- ProbandSampleId: "string",<br>- AssociatedSamples: [ { Relation: 0, SampleId: "string", Affected: 0 } ],<br>- AssignedToUserId: "00000000-0000-0000-0000-000000000000",<br>- AssignedToFullName: "string",<br>- AssignedToUser: "string" | | CreatePatient | `/api/CreatePatient` (推測), [[empty doc]](https://github.com/geneyx/geneyx.analysis.api/wiki/CreatePatient)<br>`/api/Patient` ([來源](https://github.com/geneyx/geneyx.analysis.api/blob/main/scripts/ga_createPatient.py#L37)) | | CreateSample | `/api/CreateSample` (推測), [[doc]](https://github.com/geneyx/geneyx.analysis.api/wiki/Create-Sample) | | [DataEntryBatches](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L250) | `/api/DataEntryBatches` | | [enrichmentKits](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L280) | `/api/enrichmentKits` | | [GetVcfSampleQcData](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L310) | `/api/GetVcfSampleQcData`<br>- sampleSn: "string" | | [GetVcfSampleCoverage](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L340) | `/api/GetVcfSampleCoverage`<br>- sampleSn: "string" | | [GetVcfSampleFile](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L370) | `/api/GetVcfSampleFile`<br>- sampleSn: "string" | | [GetVcfSampleArtifact](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L400) | `/api/GetVcfSampleArtifact`<br>- sampleSn: "string",<br>- pipelineType: "string" | | [Patient](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L430) | `/api/patient`<br>- SerialNumber: "123456789",<br>- Name: "Patient-Name",<br>- DateOfBirth: "2001-06-25", <br>- Gender: "M",<br>- Consang: "NonConsang",<br>- PopulationType: "general population",<br>- PaternalAncestry: "string",<br>- MaternalAncestry: "string",<br>- PaternalGrandfather: "string",<br>- PaternalGrandmother: "string",<br>- MaternalGrandfather: "string",<br>- MaternalGrandmother: "string",<br>- FamilyHistory: "long long history of nothing",<br>- UseConsentPersonal: "true",<br>- UseConsentClinical: "false",<br>- HasBioSample: "true",<br>- GenerallyHealthy: "false",<br>- ClinicalRecords: [<br>{ RecordDate: "2005-06-25", Description: "recorded something", PhenotypeCodes: [ "HP:0002000" ] }<br>] | | [Patients](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L460) | `/api/patients` | | [Protocols](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L490) | `/api/Protocols` | | [ReportUrl](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L520) | `/api/ReportUrl`<br>- fileName: "string" | | [ReportList](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L550) | `/api/ReportList`<br>- startTime: "string" | | [Samples](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L580) | `/api/Samples` | | [SampleAssignment](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L610) | `/api/SampleAssignment`<br>- SerialNumber: "string",<br>- GroupAssignment: [ { Code: "string", Name: "string" } ],<br>- AssignedToUserId: "00000000-0000-0000-0000-000000000000",<br>- AssignedToFullName: "string" | | [SequenceMachines](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L640) | `/api/SequenceMachines` | | [UpdateSampleQc](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L670) | `/api/UpdateSampleQc`<br>- SampleSerialNumber: "string",<br>- SampleTakenDate: "2022-12-27T18:56:48.329Z",<br>- SampleSequenceDate: "2022-12-27T18:56:48.329Z",<br>- SampleReceivedDate: "2022-12-27T18:56:48.329Z",<br>- SampleType: "string",<br>- SampleTarget: "string",<br>- SampleSource: "string",<br>- SampleSequenceMachineId: "string",<br>- SampleEnrichmentKitId: "string",<br>- SampleNotes: "string",<br>- SampleRelation: "string",<br>- SampleGenomeBuild: "string",<br>- BamUrl: "string",<br>- SnvFile: "string",<br>- StructFile: "string",<br>- SampleQcData: "string",<br>- SubjectId: "string",<br>- SubjectName: "string",<br>- SubjectGender: "string",<br>- SubjectDateOfBirth: "2022-12-27T18:56:48.329Z",<br>- SubjectConsanguinity: "string",<br>- SubjectPopulationType: "string",<br>- SubjectPaternalAncestry: "string",<br>- SubjectMaternalAncestry: "string",<br>- SubjectFamilyHistory: "string",<br>- SubjectHasBioSample: true,<br>- SubjectUseConsentPersonal: true,<br>- SubjectUseConsentClinical: true,<br>- GroupAssignment: [ { Code: "string", Name: "string" } ],<br>- AssignedToUserId: "00000000-0000-0000-0000-000000000000",<br>- AssignedToFullName: "string",<br>- SkipAnnotation: true | <br> <hr> <br> ## API Responses ### [Cases](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L130) > `/api/Cases` [![](https://i.imgur.com/nUZdmHa.png)](https://i.imgur.com/nUZdmHa.png) ```json { "Items":[ ..., { "PatientId":"7bd15904-b14c-4a0d-9818-e202ab1c8dfc", "Patient":"HG002", "SerialNumber":"SN-HG002", "Name":"Single Sample Analysis", "VersionSetId":"6232d942-435a-4fe3-9075-e1ea1caf7ec4", "VersionSetName":"v5.12", "VersionSetNumber":41, "VersionSetArchived":false, "VersionSetLatest":true, "Status":0, "StatusName":"Open", "MainSampleId":"5e00cad6-5c52-4fea-945b-f8ef476ce755", "MainSampleSerialNumber":"HG002.hiseqx.pcr-free.30x.vcf.gz", "PhenAlleleFreq":0.001, "Phenotypes":"", "IsAdvancedPhenotypes":false, "GeneticModels":[1, 2, 4, 256], "GeneticModelNames":["Recessive HOM", "Recessive Compound HET", "Dominant HET", "Secondary Findings"], "ProtocolId":"73b911c9-2d81-46aa-b917-a87ed92d3676", "ProtocolName":"Single Sample Analysis", "ProtocolTypeName":"RareGenetics", "ProtocolSerialNumber":"RG_SINGLE", "AutoAnalyze":false, "AutoReport":false, "SortAsc":false, "ExpandColumns":{"COSMIC":true, "MitoEvidence":true, "Civic":true}, "CalcLocalFreq":false, "UnfilterEvidence":false, "ReadyForAnalysis":true, "SamplesReady":true, "HasAnalysis":true, "HasReport":true, "GenomeBuild":1, "AcmgCalcDate":"2023-03-27T07:12:40.767Z", "IbdParentsCalcStatus":"None", "IsTrio":false, "ID":"62beb88f-8eae-414c-83ff-f0c2fd4bf2d5", "CreatedByUser":"Grace Wu", "CreateDate":"2023-03-27T07:01:52.607Z", "ModifiedByUser":"Grace Wu", "ModifyDate":"2023-03-30T06:15:16.13Z" }, ... ], "Total":7 } ``` <br> ### [Patients](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L460) > `/api/patients` [![](https://i.imgur.com/AkuTk3M.png)](https://i.imgur.com/AkuTk3M.png) ```json= { "Items":[ ..., { "SerialNumber": "HG002", "Gender": "M", "Consang": 0, "ConsangName": "Unknown", "PopulationType": "White / Ashkenazim Jewish", "UseConsentPersonal": true, "ID": "7bd15904-b14c-4a0d-9818-e202ab1c8dfc", "CreatedByUser": "Grace Wu", "CreateDate": "2023-03-27T02:30:56.303Z", "ModifiedByUser": "Grace Wu", "ModifyDate": "2023-03-30T09:14:41.38Z" }, ... ], "Total":3 } ``` <br> ### [Protocols](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L490) > `/api/Protocols` [![](https://i.imgur.com/B9viaqd.png)](https://i.imgur.com/B9viaqd.png) ```json= { "Items":[ { "Name": "Single Sample Analysis", "SerialNumber": "RG_SINGLE", "Description": "Only the affected sample is available", "GeneticModelNames": [ "Recessive HOM", "Recessive Compound HET", "Dominant HET", "Secondary Findings" ], "GeneticModels": [ 1, 2, 4, 256 ], "PhenAlleleFreq": 0.001, "Ordinal": 1, "MainSampleSource": 1, "MainSampleSourceName": "GermLine", "IsAdvancedPhenotypes": false, "ReportTemplateId": "8fa4512d-78c1-4c3c-9728-da0ad4580800", "ReportTemplateName": "Rare Genetics Default", "SortAsc": false, "CalcLocalFreq": false, "Type": 2, "TypeName": "RareGenetics", "ExpandColumns": [ "COSMIC", "MitoEvidence", "Civic" ], "AutoAnalyze": false, "AutoReport": false, "AutoAnnotateBasedOnPrev": false, "AlwaysShowPatVars": false, "ID": "73b911c9-2d81-46aa-b917-a87ed92d3676", "CreatedByUser": "Grace Wu", "CreateDate": "2023-02-06T08:44:23.713Z", "ModifiedByUser": "Grace Wu", "ModifyDate": "2023-02-06T08:44:23.713Z" }, {"Name":"Trio Analysis",...}, {"Name":"Tumor Only Analysis",...}, {"Name":"Tumor / Normal Analysis",...}, {"Name":"Carrier Screening",...}, {"Name":"Cancer Screening",...}, {"Name":"Mitochondria Analysis",...}, {"Name":"Germline - SV",...} ], "Total":8 } ``` <br> ### [Samples](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L580) > 列出樣本清單 > - from backend API > `/api/Samples` > - [docs/Samples.md](https://github.com/geneyx/geneyx.analysis.api/blob/main/docs/Samples.md) > used to retrieve the list of samples in the account. > - from UI portal > `https://www.prisma-gene.com.tw/sample/getItems` (列出樣本清單) > `https://www.prisma-gene.com.tw/sample/GetFormOptions` (取得編輯 sample 的表單選項清單) > `https://www.prisma-gene.com.tw/sample/Update` (更新某個 samlpe) [![](https://i.imgur.com/sbhU0f1.png)](https://i.imgur.com/sbhU0f1.png) - `https://www.prisma-gene.com.tw/sample/getItems` ```json= { "Items":[ ..., { "PatientId":"7bd15904-b14c-4a0d-9818-e202ab1c8dfc", "Patient":"HG002", "SerialNumber":"HG002.hiseqx.pcr-free.30x.vcf.gz", "EnrichmentKitId":"cd52c5cd-5b13-4add-915b-18c80d8a45a1", "EnrichmentKit":"Twist Human Core Exome", "EnrichmentKitDescription":"Twist Human Core Exome", "Target":1, "TargetName":"WholeGenome", "Source":1, "SourceName":"GermLine", "BamUrl":"", "BamFileExists":false, "MethylationFileExists":false, "Relation":0, "RelationName":"Self", "GenomeBuild":1, "GenomeBuildName":"hg38", "Assignment":{ "AssignDate":"0001-01-01T00:00:00Z", "GroupCodes":[ ], "Groups":[ ] }, "Files":[ { "ID":"a4a5423d-e6c2-4009-8a7c-b225975639a0", "FileTypeName":"SNV", "FileType":1, "FileName":"HG002.hiseqx.pcr-free.30x.vcf.gz", "CreateDate":"2023-03-27T06:38:20.073Z" } ], "ExcludeFromLAF":false, "ID":"5e00cad6-5c52-4fea-945b-f8ef476ce755", "CreatedByUser":"Grace Wu", "CreateDate":"2023-03-27T06:38:20.077Z", "ModifiedByUser":"Grace Wu", "ModifyDate":"2023-03-27T06:59:49.037Z" }, ... ], "Total":3 } ``` - `https://www.prisma-gene.com.tw/sample/GetFormOptions` - UI [![](https://i.imgur.com/6Z9gBVz.png)](https://i.imgur.com/6Z9gBVz.png) - request payload ```json { "patientId":"7bd15904-b14c-4a0d-9818-e202ab1c8dfc", "sampleId":"5e00cad6-5c52-4fea-945b-f8ef476ce755" } ``` - response ```json { "EnrichmentKits":[ { "Text":"Twist Human Core Exome", "Value":"cd52c5cd-5b13-4add-915b-18c80d8a45a1" } ], "SequenceMachines":[ { "Text":"HiSeq 2500", "Value":"758aeef1-71d2-4366-9900-d0f2b6f04684" }, { "Text":"HiSeq 4000", "Value":"d0c7cadb-b2cb-45a9-b97f-3afa04da77fc" }, { "Text":"MiSeq", "Value":"651c1397-2893-44f3-8db1-c4ac41d87437" }, { "Text":"NextSeq 500", "Value":"586d71f5-814e-4a13-9209-7ec6f4b946b8" }, { "Text":"NovaSeq 6000", "Value":"c82ecff9-fb53-440f-bbe7-19e91c32e56f" } ], "DataFiles":[ { "Text":"demo-germline-sample.vcf.gz", "Value":"demo-germline-sample.vcf.gz" }, { "Text":"HG002.hiseqx.pcr-free.30x.R_.vcf.gz", "Value":"HG002.hiseqx.pcr-free.30x.R_.vcf.gz" }, { "Text":"HG002.hiseqx.pcr-free.30x.vcf.gz", "Value":"HG002.hiseqx.pcr-free.30x.vcf.gz" }, { "Text":"output (1).vcf.gz", "Value":"output (1).vcf.gz" }, { "Text":"output (2).vcf.gz", "Value":"output (2).vcf.gz" }, { "Text":"output.vcf.gz", "Value":"output.vcf.gz" }, { "Text":"SRR7890824.vcf.gz", "Value":"SRR7890824.vcf.gz" } ], "IsSnvAnnotated":true, "IsSvAnnotated":false, "AllowChangeGenomeBuild":false } ``` <br> ### [SampleAssignment](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L610) > `/api/SampleAssignment` - request payload - SerialNumber: "string" - GroupAssignment: [ { Code: "string", Name: "string" } ] - AssignedToUserId: "00000000-0000-0000-0000-000000000000" - AssignedToFullName: "string" - 用途 > "assigned to user ID"（指派給用戶ID）通常是指將某個任務、工作或資源指派給特定的用戶。這個用戶負責完成這個任務、工作或資源，並承擔責任。在軟件開發、項目管理和工作流程中，指派給用戶ID通常用於追蹤和管理任務的分配和進度。 - 將 sample 指派到其他 group ? (分享 sample?) - 指派到某個 user (id & name) ? <br> ### [SequenceMachines](https://github.com/geneyx/geneyx.analysis.api/blob/main/Geneyx%20Analysis%20%20API%20Collection.postman_collection.json#L640) > 列出定序儀清單 > - from backend API > `/api/SequenceMachines` > - [docs/SequencingMachines.md](https://github.com/geneyx/geneyx.analysis.api/blob/main/docs/SequencingMachines.md) > used to retrieve the list of sequence machines in the account. > - from UI portal > `https://www.prisma-gene.com.tw/SequenceMachine/Create` > `https://www.prisma-gene.com.tw/SequenceMachine/Search` > `https://www.prisma-gene.com.tw/SequenceMachine/Update` > `https://www.prisma-gene.com.tw/SequenceMachine/Delete` [![](https://i.imgur.com/ZhHplEP.png)](https://i.imgur.com/ZhHplEP.png) - `https://www.prisma-gene.com.tw/SequenceMachine/Create` - request payload ```json= { "SerialNumber":"NovaSeq 6000", "Description":"Illumina NovaSeq 6000 System" } ``` - response ```json= { "SerialNumber":"NovaSeq 6000", "Description":"Illumina NovaSeq 6000 System", "ID":"c82ecff9-fb53-440f-bbe7-19e91c32e56f", "CreatedByUser":"Grace Wu", "CreateDate":"2023-02-06T08:44:23.103Z", "ModifiedByUser":"Grace Wu", "ModifyDate":"2023-02-06T08:44:23.103Z" } ``` - `https://www.prisma-gene.com.tw/SequenceMachine/Search` ```json= { "Items":[ ..., { "SerialNumber":"NovaSeq 6000", "Description":"Illumina NovaSeq 6000 System", "ID":"c82ecff9-fb53-440f-bbe7-19e91c32e56f", "CreatedByUser":"Grace Wu", "CreateDate":"2023-02-06T08:44:23.103Z", "ModifiedByUser":"Grace Wu", "ModifyDate":"2023-02-06T08:44:23.103Z" }, ... ], "Total":5 } ``` - `https://www.prisma-gene.com.tw/SequenceMachine/Update` - request payload ```json= { "SerialNumber":"NovaSeq 6000", "Description":"Illumina NovaSeq 6000 System", "ID":"c82ecff9-fb53-440f-bbe7-19e91c32e56f", "CreatedByUser":"Grace Wu", "CreateDate":"2023-02-06T08:44:23.103Z", "ModifiedByUser":"Grace Wu", "ModifyDate":"2023-02-06T08:44:23.103Z" } ``` - response - 同 request payload - `https://www.prisma-gene.com.tw/SequenceMachine/Delete` - request payload ```json= { "id": "47c3245d-4736-48eb-889f-2f7221c50ff4" } ``` - response ```json= { "SerialNumber":"NovaSeq 6000", "Description":"Illumina NovaSeq 6000 System", "ID":"c82ecff9-fb53-440f-bbe7-19e91c32e56f", "CreatedByUser":"Grace Wu", "CreateDate":"2023-02-06T08:44:23.103Z", "ModifiedByUser":"Grace Wu", "ModifyDate":"2023-02-06T08:44:23.103Z" } ```