2c:null 2d:["$","title",null,{"children":"23andMe data from PGP | lorenasandoval88 | Observable"}] 32:T78e,

Workflow

PGP Data Retrieval →

Chip Manifests → Overlap & Fingerprints → Classification Results

33:T652,## 2. Pipeline The pipeline performs the following operations: 1. Obtains a list of PGP participants with 23andMe files. 2. Downloads each supported `.txt` or `.zip` file. 3. Extracts ZIP archives into raw 23andMe text. 4. Checks whether the downloaded file is a valid 23andMe file. 5. detects the genome build from the file header. 6. Saves the raw text file in Google Cloud Storage. 7. Downloads the participant’s PGP profile. 8. Records successful, skipped and failed downloads. 9. Consolidates multiple files belonging to the same participant. 10. Produces detailed run reports. ```text PGP 23andMe participant page | v fetch23andMeParticipants() | v Participant/file metadata | +-------------------------+ | | v v load23andMeFileCloud_unknwn() fetchProfile() | | v v Download and extract file Participant profile | v Validate 23andMe format | v Detect GRCh36, GRCh37 or GRCh38 | v Save raw TXT to geneticFiles/ | v Create flat and consolidated JSON files | v Create error and import reports ``` --- *Observable note:* JavaScript template expressions are written as `\${...}` in this Markdown source so Observable does not try to execute them. When rendered, Observable displays the normal JavaScript `{...}` syntax. ---34:Tdd6,## 3. Required packages The script imports Google Cloud Storage: ```javascript import { Storage } from "@google-cloud/storage"; ``` It also imports three functions from the Personal Genomes Project SDK: ```javascript import { fetch23andMeParticipants, load23andMeFileCloud_unknwn, fetchProfile } from "personal_genomes_project_sdk/cloud_sdk.mjs"; ``` These functions have different responsibilities: | Function | Purpose | |---|---| | `fetch23andMeParticipants()` | Retrieves participant and genetic-file metadata from the PGP website | | `load23andMeFileCloud_unknwn()` | Downloads a file, handles TXT or ZIP content, validates the file and detects its genome build | | `fetchProfile()` | Retrieves the participant’s public PGP profile | --- ## 4. Cloud Run environment variables The job is controlled through environment variables. | Variable | Default | Purpose | |---|---:|---| | `BUCKET_NAME` | Automatically generated | Destination Google Cloud Storage bucket | | `LIMIT` | `6` | Maximum number of participant/file records requested | | `BATCH_SIZE` | `10` | Batch size used when retrieving participant metadata | | `PARTICIPANT_SOURCE` | `fetch` | Determines whether participant metadata is downloaded or reused | | `INPUT_PARTICIPANT_JSON` | `participantList/participants_LIMIT.json` | Existing participant-list object to reuse | ### Participant-source modes #### Fresh mode ```text PARTICIPANT_SOURCE=fetch ``` The job: 1. Retrieves a new participant list from PGP. 2. Saves the list in the bucket. 3. Processes the associated files. #### Existing mode ```text PARTICIPANT_SOURCE=existing ``` The job: 1. Reads an existing participant list from the bucket. 2. Does not retrieve a new list from PGP. 3. Reprocesses the file records in that list. Example: ```bash --set-env-vars \ LIMIT=1100,\ PARTICIPANT_SOURCE=existing,\ INPUT_PARTICIPANT_JSON=participantList/participants_1100.json,\ BATCH_SIZE=10 ``` --- ## 5. Bucket selection and creation If `BUCKET_NAME` is supplied, the job uses that bucket: ```text BUCKET_NAME=all_23_v2 ``` If it is not supplied, the script constructs a name using the UTC date and time: ```text all23_MMDDYYYY_HHMM ``` Example: ```text all23_07212026_1530 ``` The `ensureBucketExists()` function checks whether the bucket already exists. If it does not exist, the function attempts to create it in `US-EAST4` using the `STANDARD` storage class. The Cloud Run service account therefore needs appropriate Cloud Storage permissions. --- ## 6. File eligibility The job normally accepts metadata identifying a file as: ```text txt zip ``` Known unsupported file types are skipped. If the file-extension metadata is missing, the job still allows the SDK to inspect the download response. This is useful because some PGP URLs do not clearly identify whether the response is text or ZIP content. ZIP files are extracted by the SDK. The final loaded object must be a text file before it is saved. --- ## 7. Genome-build detection The SDK examines the raw 23andMe header to identify the reference genome assembly. Possible results can include: ```text GRCh36 GRCh37 GRCh38 null ``` The metadata recorded for a successful file includes: ```javascript { valid23File, matchedLineValid23File, genomeBuild, genomeBuildFiles } ``` The `genomeBuildFiles` array records: ```javascript { downloadUrl, filename, gcsPath, gcsfilename, sizeMB, matchedLine } ``` `matchedLine` preserves the header line that was used to determine the genome build. ---35:T255e,## 8. Unique filenames A participant may upload multiple files with identical inner filenames. To prevent one file from overwriting another, the script extracts the numeric PGP download identifier: ```text https://my.pgp-hms.org/user_file/download/4177 | v 4177 ``` The destination filename becomes: ```text participantID_downloadID_originalFilename ``` Example: ```text huBB5257_4177_genome.txt ``` This is safer than saving only: ```text huBB5257_genome.txt ``` because two uploaded files could otherwise produce the same destination path. Invalid filename characters are replaced with underscores. --- ## 9. Profile retrieval For each participant, profile retrieval starts before the genetic-file download finishes: ```javascript const profilePromise = fetchProfileSafe(participant.id); ``` This allows the profile request and file download to overlap. A profile error does not terminate the genetic-file download. Instead, the result records: ```javascript { profile: null, profileError: "error message" } ``` This design separates: ```text Genetic-file download success ``` from: ```text Profile-endpoint success ``` The participant can therefore have a successfully downloaded genotype file even when the profile request fails. --- ## 10. Processing behavior The job processes participant/file records in a sequential loop: ```javascript for (const participant of participants) { // Process one participant/file record. } ``` This means `BATCH_SIZE` controls participant-list retrieval, but it does not cause ten genotype files to download concurrently. For every record, the job: 1. Starts the profile request. 2. verifies that a download URL exists. 3. checks the reported filename extension. 4. downloads and extracts the genetic file. 5. verifies that the final result is text. 6. checks that the text is not empty. 7. constructs a unique filename. 8. saves the file in `geneticFiles/`. 9. records file size and genome-build metadata. 10. attaches the profile or profile error. --- ## 11. Skipped files A record is skipped when, for example: ```text No download URL is available. The known filename extension is unsupported. The downloaded content does not become a TXT file. ``` Skipped records remain in the updated participant list. They receive fields such as: ```javascript { valid23File: false, matchedLineValid23File: null, genomeBuild: null, genomeBuildFiles: [], processingNote: "reason for skipping" } ``` This preserves evidence that the record was considered by the pipeline. --- ## 12. Download failures A failed download does not terminate the entire job. The error handler captures: ```javascript { httpStatusDownloadAttempt, finalUrlAtFailure, requestedUrlAtFailure, failureSource, processingNote } ``` The SDK may provide structured error fields: ```text err.status err.requestedUrl err.finalUrl err.source ``` These fields make it possible to distinguish problems such as: ```text HTTP 401 unauthorized response Broken or redirected URL Unsupported response content Empty file SDK parsing error ``` HTTP `401` failures are also written to a dedicated report. --- ## 13. Flat output files The pipeline creates two flat metadata files. ### Build-only flat output ```text participants_LIMIT_with_build_DATE.json ``` This contains one record per participant/file entry and excludes: ```text profile profileError ``` ### Build-and-profile flat output ```text participants_LIMIT_with_build_and_profile_DATE.json ``` This contains the same file-level records but also includes: ```text profile profileError ``` If one participant has three files, the flat outputs can contain three records with the same participant ID. --- ## 14. Consolidated output files The `consolidateById()` function groups records by participant ID. Flat input: ```javascript [ { id: "hu123", filename: "file1.txt" }, { id: "hu123", filename: "file2.txt" } ] ``` Consolidated output: ```javascript [ { id: "hu123", number_of_files: 2, files: [ { filename: "file1.txt" }, { filename: "file2.txt" } ] } ] ``` Two consolidated versions are created: | Output | Profile included? | |---|---:| | `consolidated_with_build` | No | | `consolidated_with_build_and_profile` | Yes | In the profile version, `profile` and `profileError` are stored once at the participant level instead of being duplicated inside every file. --- ## 15. Output structure ```text gs://BUCKET_NAME/ ├── participantList/ │ └── participants_LIMIT.json ├── geneticFiles/ │ ├── participant_downloadID_file1.txt │ └── participant_downloadID_file2.txt ├── updatedParticipantsList/ │ ├── participants_LIMIT_with_build_DATE.json │ ├── participants_LIMIT_with_build_and_profile_DATE.json │ ├── participants_LIMIT_consolidated_with_build_DATE.json │ └── participants_LIMIT_consolidated_with_build_and_profile_DATE.json └── runReports/ ├── unauthorized_401s_LIMIT_DATE.json └── import_report_LIMIT_DATE.json ``` --- ## 16. Import report The final import report summarizes the run: ```javascript { bucketName, dateStamp, participantSource, participantSourcePath, totalParticipants, saved, failed, skipped, unauthorized401s, profiled, profileFailed, uniqueParticipants, withBuildJson, updatedParticipantJson, consolidatedBuildJson, consolidatedBuildProfileJson, unauthorizedFailuresJson } ``` Important distinctions include: ```text totalParticipants Number of participant/file records processed. saved Number of genetic files successfully saved. uniqueParticipants Number of distinct participant IDs after consolidation. ``` These values can differ because one participant may have multiple files. --- ## 17. Cloud deployment Build the container: ```bash gcloud builds submit \ --tag gcr.io/nih-nci-dceg-episphere-dev/all23andme-job \ --project nih-nci-dceg-episphere-dev ``` Deploy the Cloud Run Job: ```bash gcloud run jobs deploy all23andme-job \ --image gcr.io/nih-nci-dceg-episphere-dev/all23andme-job \ --region us-east4 \ --project nih-nci-dceg-episphere-dev \ --memory 32Gi \ --cpu 8 \ --task-timeout 14400 \ --max-retries 0 \ --set-env-vars LIMIT=6,PARTICIPANT_SOURCE=fetch,BATCH_SIZE=10 ``` Execute the job: ```bash gcloud run jobs execute all23andme-job \ --region us-east4 \ --project nih-nci-dceg-episphere-dev ``` --- ## 18. Important implementation notes - The job runs in full download, build-detection and profile mode. - File records are processed sequentially. - Profile retrieval overlaps with the current file download. - An existing participant list causes the files to be reprocessed; it is not automatically a resume-from-last-file operation. - The generated bucket name must be globally unique if `BUCKET_NAME` is not specified. - The service account requires permission to create a bucket when automatic bucket creation is used. - A fixed `BUCKET_NAME` is easier for repeatable production runs. - Public PGP genotype and profile data should still be stored with appropriate access controls. - The `LIMIT` value controls the requested participant/file records and is not necessarily equal to the number of unique participants. - The program writes several complete JSON arrays, so memory and object sizes should be monitored for very large runs. --- # 19. Complete JavaScript source ```javascript /** * Cloud Run worker: fetch PGP 23andMe participants, download each genetic file, * detect genome build, add profile data, and write consolidated lists. * * FULL MODE (download + build + profile all enabled). * * PARTICIPANT_SOURCE controls where the participant list comes from: * PARTICIPANT_SOURCE=fetch -> pulls a fresh participant list from the PGP * site, saves it, then downloads every file. * PARTICIPANT_SOURCE=existing -> loads a participant list already in the bucket * (path in INPUT_PARTICIPANT_JSON) and reprocesses. * * For each participant whose file is .txt/.zip: download the file, detect genome * build from the header, save the TXT to geneticFiles/, and fetch the profile. * profile / profileError are merged onto every record exactly once. * * On failure, the SDK attaches structured fields to the thrown error: * err.status / err.requestedUrl / err.finalUrl / err.source * * Outputs: * participantList/participants_\${LIMIT}.json * updatedParticipantsList/participants_\${LIMIT}_with_build_\${dateStamp}.json * updatedParticipantsList/participants_\${LIMIT}_with_build_and_profile_\${dateStamp}.json * updatedParticipantsList/participants_\${LIMIT}_consolidated_with_build_\${dateStamp}.json * updatedParticipantsList/participants_\${LIMIT}_consolidated_with_build_and_profile_\${dateStamp}.json * runReports/unauthorized_401s_\${LIMIT}_\${dateStamp}.json * runReports/import_report_\${LIMIT}_\${dateStamp}.json */ import { Storage } from "@google-cloud/storage"; import { fetch23andMeParticipants, load23andMeFileCloud_unknwn, fetchProfile } from "personal_genomes_project_sdk/cloud_sdk.mjs"; const storage = new Storage(); function getDateStamp() { ... ``` ## SEE attached index.js, package.json and Dockerfile36:Te75,toc = { const slugify = text => text .toLowerCase() .normalize("NFKD") .replace(/[\u0300-\u036f]/g, "") .replace(/[^a-z0-9]+/g, "-") .replace(/^-|-$/g, ""); return function toc({ selector = "h1, h2",// h3", title = "Table of Contents" } = {}) { const nav = document.createElement("nav"); nav.className = "notebook-toc"; let scheduled = false; function getAllHeaders() { const cells = [ ...document.querySelectorAll(".observablehq") ]; const headers = cells.flatMap(cell => [...cell.querySelectorAll(selector)] ); // Remove duplicates and headings inside the TOC. return [...new Set(headers)] .filter(header => !nav.contains(header)) .filter(header => header.textContent.trim()) .filter(header => header.isConnected); } function render() { scheduled = false; const headers = getAllHeaders(); const usedIds = new Set( [...document.querySelectorAll("[id]")] .filter(element => !headers.includes(element)) .map(element => element.id) ); for (const header of headers) { if (!header.id) { const base = slugify(header.textContent.trim()) || "section"; let id = base; let number = 2; while (usedIds.has(id)) { id = `${base}-${number++}`; } header.id = id; } usedIds.add(header.id); } const levels = headers.map(header => Number(header.tagName.substring(1)) ); const minimumLevel = levels.length ? 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\n\n

\n PGP 23andMe Data Retrieval\n

\n\n

\n Public 23andMe genotype files and participant metadata were retrieved from the\n \n Personal Genome Project (PGP)\n \n and stored in Google Cloud. These data provide the source for chip manifests,\n fingerprint analysis, and chip-version classification.\n

\n\n

\n \n

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":271,"value":"## Explore all 23and Me Participants\n855 participants with 1070 23andme files","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":53,"value":"participants = FileAttachment(\n \"participants_1020_consolidated_with_build_and_profile_07102026_2053.json\"\n).json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":93,"value":"viewof chipFilter = Inputs.select(\n [\n \"All\",\n ...new Set(\n participantTable\n .map(d => d.chipVersion)\n .filter(Boolean)\n )\n ].sort(),\n {\n label: \"Chip version\",\n value: \"v5\"\n }\n)\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":88,"value":"viewof buildFilter = Inputs.select(\n [\n \"All\",\n ...new Set(\n participantTable\n .map(d => d.genomeBuild)\n .filter(Boolean)\n )\n ].sort(),\n {\n label: \"Genome build\",\n value: \"37\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":292,"value":"viewof raceFilter = Inputs.select(\n raceOptions,\n {\n label: \"Race\",\n value: \"All\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":295,"value":"viewof ethnicityFilter = Inputs.select(\n ethnicityOptions,\n {\n label: \"Ethnicity\",\n value: \"All\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":114,"value":"### Filtered Participants: ${filteredFirstFiles.length.toLocaleString()}\nBuild: ${buildFilter} Chip: ${chipFilter} Race: ${raceFilter} Ethnicity: ${ethnicityFilter}","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":371,"value":"filteredParticipantsList = filteredParticipants","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":82,"value":"Inputs.table(\n [...filteredParticipants].sort(\n (a, b) => b.numberOfFiles - a.numberOfFiles\n ),\n {\n columns: [\n \"id\",\n // \"name\",\n \"chipVersion\",\n \"genomeBuild\",\n \"race\",\n \"ethnicity\",\n \"veritas\",\n \"veritasFileCount\",\n \"profile\",\n \"survey\",\n \"zip\",\n \"numberOfFiles\",\n \"profileUrl\"\n ],\n\n width: {\n id: 90,\n name: 90,\n chipVersion: 80,\n genomeBuild: 80,\n race: 180,\n ethnicity: 180,\n veritas: 70,\n veritasFileCount: 90,\n profile: 70,\n survey: 70,\n zip: 70,\n numberOfFiles: 90,\n profileUrl: 180\n },\n\n rows: 15\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":401,"value":"DOM.download(\n new Blob(\n [filteredParticipantsList.map(x=>x.id)],\n {type: \"text/plain\"}\n ),\n `filtered_participant_ids_${filteredParticipantsList.length}.txt`,\n \"Download participant ID list\"\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":237,"value":"---\n### Filtered 23andMe files: ${filteredFirstFiles.length} (First qualifying file per participant)\nBuild: ${buildFilter} Chip: ${chipFilter} Race: ${raceFilter} Ethnicity: ${ethnicityFilter}\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":460,"value":"files = filteredFirstFiles","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":382,"value":"filenameList = filteredFirstFiles.map(x=>x.filename)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":252,"value":"Inputs.table(\n [...filteredFirstFiles].sort(\n (a, b) => b.numberOfFiles - a.numberOfFiles\n ),\n {\n columns: [\n \"participantId\",\n \"numberOfFiles\",\n \"filename\",\n \"chipVersion\",\n \"genomeBuild\",\n \"dataType\",\n \"sizeMB\",\n \"valid23File\",\n \"publishedDate\",\n \"downloadUrl\"\n ],\n\n width: {\n participantId: 90,\n numberOfFiles: 90,\n filename: 420,\n chipVersion: 80,\n genomeBuild: 80,\n dataType: 90,\n sizeMB: 80,\n valid23File: 90,\n publishedDate: 110,\n downloadUrl: 150\n },\n\n rows: 10\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":396,"value":"DOM.download(\n new Blob(\n [filenameList.join(\"\\n\")],\n {type: \"text/plain\"}\n ),\n `v5_build37_filenames_${filenameList.length}.txt`,\n \"Download filename list\"\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":263,"value":"---\n### Warning! Duplicate files: ${multiFileParticipants.length} files belonging to ${multiFileParticipantCount} participants ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":472,"value":"$${multiFileParticipantCount} files were ultimately kept in the file list above. Some participants had up to four different 23andme files. In cases with two same version files, the first was kept (probably duplicate file).","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":267,"value":"Inputs.table(multiFileParticipants.sort(\n (a, b) => b.numberOfFiles - a.numberOfFiles\n ), {\n columns: [\n \"participantId\",\n \"numberOfFiles\",\n \"filename\",\n \"chipVersion\",\n \"genomeBuild\",\n \"dataType\",\n \"sizeMB\",\n \"valid23File\",\n \"publishedDate\",\n \"downloadUrl\"\n ],\n\n width: {\n participantId: 90,\n numberOfFiles: 90,\n filename: 420,\n chipVersion: 80,\n genomeBuild: 80,\n dataType: 90,\n sizeMB: 80,\n valid23File: 90,\n publishedDate: 110,\n downloadUrl: 150\n },\n\n rows: 11\n\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":164,"value":"---\n# Inspect a single participant by ID","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":146,"value":"viewof participantId = Inputs.text({\n label: \"Participant ID\",\n placeholder: \"e.g. hu7ECB9C\",\n value: \"\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":148,"value":"selectedParticipant = participantId.trim()\n ? participants.find(\n p => p.id?.toLowerCase() === participantId.trim().toLowerCase()\n )\n : null","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":159,"value":"Inputs.table(selectedParticipantData, {\n columns: [\n \"field\",\n \"value\"\n ],\n rows: 20\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":42,"value":"---\n# Code for Retrieveing 23andme files\n## 1. Purpose\n\nThis Node.js Cloud Run Job downloads publicly shared 23andMe files from the [Personal Genome Project](https://my.pgp-hms.org/public_genetic_data?data_type=23andMe), detects their genome builds, retrieves participant profiles, saves the genetic files to Google Cloud Storage, and creates participant-level metadata files.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":27,"value":"toc()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"$33","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":50,"value":"$34","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":14,"value":"$35","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":20,"value":"---\n### Notebook Helper Functions","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":17,"value":"$36","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":117,"value":"d3 = require(\"d3@7\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":76,"value":"getChipVersions = (p) => {\n const fileVersions = new Set();\n\n for (const f of p.files ?? []) {\n const versions = getFileChipVersions(f);\n\n if (versions.length > 0) {\n fileVersions.add(versions.join(\"_\"));\n }\n }\n\n return [...fileVersions]\n .sort()\n .join(\", \") || \"Unknown\";\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":290,"value":"ethnicityOptions = [\n \"All\",\n ...[...new Set(\n participantTable.map(d => d.ethnicity)\n )]\n .filter(Boolean)\n .sort()\n]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":434,"value":"getFileChipVersion = f => {\n const names = [\n f.filename,\n f.fileName,\n f.innerFilename,\n f.innerFileName,\n ...(f.genomeBuildFiles ?? []).flatMap(g => [\n g.filename,\n g.gcsfilename\n ])\n ].filter(Boolean);\n\n const versions = new Set();\n\n for (const name of names) {\n for (const match of String(name).matchAll(\n /(?:^|[_\\-.])v([1-5])(?=[_\\-.]|$)/gi\n )) {\n versions.add(`v${match[1]}`);\n }\n }\n\n const found = [...versions].sort();\n\n if (found.length === 1) return found[0];\n\n // Keep mixed-chip files separate, e.g. v3_v5\n if (found.length > 1) return found.join(\"_\");\n\n return \"unknown\";\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":418,"value":"getFileChipVersions = (f) => {\n const name = String(f?.filename ?? \"\");\n const versions = new Set();\n\n // Finds groups such as:\n // v5\n // v4_v5\n // v3_v4_5\n // v2_v3_v4_v5\n for (const match of name.matchAll(\n /(?:^|_)v([2345](?:_v?[2345])*)(?=_|\\.|$)/gi\n )) {\n const parts = match[1].split(\"_\");\n\n for (const part of parts) {\n const version = part.replace(/^v/i, \"\");\n\n if ([\"2\", \"3\", \"4\", \"5\"].includes(version)) {\n versions.add(`v${version}`);\n }\n }\n }\n\n return [...versions].sort(\n (a, b) => Number(a.slice(1)) - Number(b.slice(1))\n );\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":288,"value":"raceOptions = [\n \"All\",\n ...[...new Set(\n participantTable.map(d => d.race)\n )]\n .filter(Boolean)\n .sort()\n]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":282,"value":"getParticipantNames = p =>\n p.profile?.name ??\n p.profile?.display_name ??\n p.profile?.full_name ??\n p.name ??\n \"Unknown\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":321,"value":"filteredParticipantIds = new Set(\n filteredFirstFiles.map(d => d.participantId)\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":86,"value":"filteredParticipants = participantTable.filter(d =>\n filteredParticipantIds.has(d.id)\n)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":119,"value":"downloadFile = (content, filename, type, label) => {\n const blob = new Blob([content], {type});\n const url = URL.createObjectURL(blob);\n\n return htl.html`\n \n ${label}\n \n `;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":437,"value":"filteredParticipantObjects = participants.filter(p =>\n chipFilter === \"All\" ||\n (p.files ?? []).some(f =>\n getFileChipVersion(f) === chipFilter\n )\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":133,"value":"participantTable = participants.map(p => {\n const veritasFiles = getVeritasFiles(p);\n\n return {\n id: p.id,\n\n name: getParticipantNames(p),\n\n chipVersion: getChipVersions(p),\n\n genomeBuild: [\n ...new Set(\n (p.files ?? [])\n .map(f => f.genomeBuild)\n .filter(Boolean)\n )\n ].join(\", \") || \"Unknown\",\n\n race: getRace(p),\n\n ethnicity: getEthnicity(p),\n\n veritas: veritasFiles.length > 0\n ? \"Yes\"\n : \"No\",\n\n veritasFileCount: veritasFiles.length,\n\n profile: p.profile ? \"Yes\" : \"No\",\n\n survey:\n getSurveyRows(p).length > 0\n ? \"Yes\"\n : \"No\",\n\n zip: p.profile?.zip ?? \"\",\n\n numberOfFiles: p.number_of_files ?? 0,\n\n profileUrl: p.profileUrl ?? \"\"\n };\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":139,"value":"getEthnicity = p => {\n const rows = getSurveyRows(p);\n\n // Prefer newer separate ethnicity question\n const modern = rows.find(([question]) =>\n question?.trim() === \"What is your ethnicity?\"\n );\n\n if (modern?.[1]) {\n return modern[1];\n }\n\n // Fall back to older combined Race/ethnicity question\n const legacy = rows.find(([question]) =>\n question?.trim() === \"Race/ethnicity\"\n );\n\n if (!legacy?.[1] || legacy[1] === \"No response\") {\n return \"Unknown\";\n }\n\n if (legacy[1].includes(\"Hispanic or Latino\")) {\n return \"Hispanic or Latino or Spanish Origin\";\n }\n\n return \"Not Hispanic or Latino or Spanish Origin\";\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":137,"value":"getRace = p => {\n const rows = getSurveyRows(p);\n\n // Prefer newer separate race question\n const modern = rows.find(([question]) =>\n question?.trim() === \"What is your race? Pick all that apply.\"\n );\n\n if (modern?.[1]) {\n return modern[1];\n }\n\n // Fall back to older combined Race/ethnicity question\n const legacy = rows.find(([question]) =>\n question?.trim() === \"Race/ethnicity\"\n );\n\n if (!legacy?.[1] || legacy[1] === \"No response\") {\n return \"Unknown\";\n }\n\n // Remove ethnicity component so this column contains race only\n const races = legacy[1]\n .split(\",\")\n .map(d => d.trim())\n .filter(d =>\n d &&\n d !== \"Hispanic or Latino\" &&\n d !== \"No response\"\n )\n .map(d =>\n d === \"American Indian / Alaska Native\"\n ? \"American Indian or Alaska Native\"\n : d\n );\n\n return races.length\n ? races.join(\", \")\n : \"Unknown\";\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":135,"value":"getSurveyRows = p =>\n (p.profile?.google_survey_results ?? []).flat()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":131,"value":"getVeritasFiles = p =>\n [\n ...(p.files ?? []),\n ...(p.profile?.files ?? [])\n ].filter(f =>\n [\n f.filename,\n f.name,\n f.dataType,\n f.data_type,\n f.description,\n f.downloadUrl,\n f.download_url\n ]\n .filter(Boolean)\n .join(\" \")\n .toLowerCase()\n .includes(\"veritas\")\n )","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":157,"value":"selectedParticipantData = selectedParticipant\n ? flattenObject(selectedParticipant)\n : []","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":154,"value":"flattenObject = function walk(obj, prefix = \"\") {\n if (obj === null || obj === undefined) {\n return [{\n field: prefix,\n value: \"\"\n }];\n }\n\n if (typeof obj !== \"object\") {\n return [{\n field: prefix,\n value: String(obj)\n }];\n }\n\n return Object.entries(obj).flatMap(([key, value]) => {\n const field = prefix\n ? `${prefix}.${key}`\n : key;\n\n if (\n value !== null &&\n typeof value === \"object\"\n ) {\n return walk(value, field);\n }\n\n return [{\n field,\n value: value ?? \"\"\n }];\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":188,"value":"formatBytes = bytes => {\n if (bytes === null || bytes === undefined || bytes === \"\") {\n return \"Unknown\";\n }\n\n if (typeof bytes === \"string\" && isNaN(Number(bytes))) {\n return bytes;\n }\n\n const n = Number(bytes);\n\n if (n < 1024) return `${n} B`;\n if (n < 1024 ** 2) return `${(n / 1024).toFixed(1)} KB`;\n if (n < 1024 ** 3) return `${(n / 1024 ** 2).toFixed(1)} MB`;\n\n return `${(n / 1024 ** 3).toFixed(2)} GB`;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":191,"value":"getFileSize = f =>\n f.sizeBytes ??\n f.fileSizeBytes ??\n f.fileSize ??\n f.size ??\n f.contentLength ??\n f.bytes ??\n null","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":200,"value":"displayedParticipantIds = new Set(\n filteredParticipants.map(d => d.id)\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":194,"value":"displayedFiles = participants\n .filter(p => displayedParticipantIds.has(p.id))\n .flatMap(p =>\n (p.files ?? []).map(f => ({\n participantId: p.id,\n\n numberOfFiles:\n p.number_of_files ?? (p.files ?? []).length,\n\n filename:\n f.filename ??\n f.name ??\n f.innerFilename ??\n \"\",\n\n chipVersion:\n getFileChipVersions(f).join(\", \") || \"Unknown\",\n\n genomeBuild:\n f.genomeBuild ?? \"Unknown\",\n\n dataType:\n f.dataType ?? \"\",\n\n sizeMB:\n getFileSizeMB(f),\n\n valid23File:\n f.valid23File === true\n ? \"Yes\"\n : \"No\",\n\n publishedDate:\n f.publishedDate ?? \"\",\n\n downloadUrl:\n f.downloadUrl ?? \"\"\n }))\n )","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":444,"value":"filteredFiles = participants.flatMap(p =>\n (p.files ?? [])\n .filter(f =>\n chipFilter === \"All\" ||\n getFileChipVersion(f) === chipFilter\n )\n .map(f => ({\n participantId: p.id,\n\n numberOfFiles: p.number_of_files ?? (p.files ?? []).length,\n\n // Original PGP filename\n originalFilename: f.filename,\n\n // Exact filename stored in GCP\n filename:\n f.genomeBuildFiles?.[0]?.gcsfilename ??\n f.filename,\n\n // Full GCS path, if you also want it\n gcsPath:\n f.genomeBuildFiles?.[0]?.gcsPath ??\n null,\n\n chipVersion: getFileChipVersion(f),\n\n genomeBuild: f.genomeBuild,\n\n dataType: f.dataType,\n\n valid23File: f.valid23File,\n\n downloadUrl: f.downloadUrl,\n\n publishedDate: f.publishedDate,\n\n profileUrl: p.profileUrl\n }))\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":377,"value":"qualifyingFilteredFiles = filteredFiles.filter(d =>\n (buildFilter === \"All\" ||\n String(d.genomeBuild) === String(buildFilter)) &&\n\n d.dataType === \"23andMe\" &&\n d.valid23File === true\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":235,"value":"filteredFirstFiles = {\n const seen = new Set();\n\n return qualifyingFilteredFiles.filter(d => {\n if (seen.has(d.participantId)) {\n return false;\n }\n\n seen.add(d.participantId);\n return true;\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":197,"value":"// getFileChipVersions = f => {\n// const filename = f.filename ?? \"\";\n\n// return [\n// ...new Set(\n// filename\n// .match(/v[2-5]/gi)\n// ?.map(d => d.toLowerCase()) ?? []\n// )\n// ];\n// }","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":226,"value":"getFileSizeMB = f =>\n f.genomeBuildFiles?.[0]?.sizeMB ?? null","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":259,"value":"multiFileParticipants = displayedFiles.filter(\n d => d.numberOfFiles > 1\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":261,"value":"multiFileParticipantCount = new Set(\n multiFileParticipants.map(d => d.participantId)\n).size","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W37","stdlib":"1"}} 31:"$30:body"