From e80a4b67a7484027dfa6943c36360768906b607a Mon Sep 17 00:00:00 2001 From: Birm Date: Wed, 29 Jul 2026 17:09:21 -0400 Subject: [PATCH 1/5] first security review and mongo update --- .github/dependabot.yml | 22 + .github/workflows/main.yml | 21 +- .gitignore | 4 + .travis.yml | 15 - README.md | 41 +- backups/.gitignore | 2 + caMicroscope.yml | 32 +- certs/.gitignore | 2 + config/nginx.conf | 34 + config/routes.json | 28 + config/seed_dicomweb_sources.js | 28 + config/test_seed.js | 2 +- db-upgrade.sh | 459 +++ develop.yml | 33 +- kc_caMicroscope.yml | 6 +- kubernetes/caMicroscope.yml | 8 +- kubernetes/develop.yml | 4 +- kubernetes/quip-pathdb.yml | 6 +- migrate/README.md | 2 +- .../deployment/heatmaploader-deployment.yaml | 2 +- osi_camicroscope.yml | 2 +- quip-pathdb.yml | 2 +- test/package-lock.json | 2545 ++++++++++------- test/package.json | 18 +- test/test_mctile.js | 72 + test/test_seed_dicomweb_sources.js | 60 + 26 files changed, 2367 insertions(+), 1083 deletions(-) create mode 100644 .github/dependabot.yml delete mode 100644 .travis.yml create mode 100644 backups/.gitignore create mode 100644 certs/.gitignore create mode 100644 config/nginx.conf create mode 100644 config/seed_dicomweb_sources.js create mode 100755 db-upgrade.sh create mode 100644 test/test_mctile.js create mode 100644 test/test_seed_dicomweb_sources.js diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..c6de68bf --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,22 @@ +version: 2 +updates: + - package-ecosystem: "npm" + directory: "/test" + schedule: + interval: "weekly" + open-pull-requests-limit: 10 + + - package-ecosystem: "docker-compose" + directory: "/" + schedule: + interval: "weekly" + + - package-ecosystem: "docker-compose" + directory: "/kubernetes" + schedule: + interval: "weekly" + + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "weekly" diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 9b6b3e7c..fd6bd27b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -4,6 +4,25 @@ jobs: test: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 + with: + node-version: '22' - name: Build the develop stack run: docker compose -f develop.yml build + - name: Start the develop stack + run: docker compose -f develop.yml up -d + - name: Wait for the back service to be healthy + run: timeout 180 bash -c 'until curl -sf http://localhost:4010/apps/viewer/viewer.html > /dev/null; do sleep 3; done' + - name: Install test dependencies + working-directory: test + run: npm ci + - name: Run test suite + working-directory: test + run: npm test + - name: Show container logs on failure + if: failure() + run: docker compose -f develop.yml logs + - name: Tear down + if: always() + run: docker compose -f develop.yml down diff --git a/.gitignore b/.gitignore index d27e5d4b..e119f82c 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,7 @@ .DS_Store/* test/node_modules/* data/pathdb/mysql/* +.db-upgrade.lock +db.pre-upgrade-* +db.pre-restore-* +db.newdata-* diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index b9a7d7a3..00000000 --- a/.travis.yml +++ /dev/null @@ -1,15 +0,0 @@ -sudo: required -language: node_js -node_js: - - "node" -before_script: - - cd test - - npm install - - npm install -g mocha -services: - - docker -script: - - docker-compose -f ../develop.yml build - - docker-compose -f ../develop.yml up -d - - sleep 120 - - mocha *.js --exit diff --git a/README.md b/README.md index 9c4c06f0..3bb8f37d 100644 --- a/README.md +++ b/README.md @@ -10,12 +10,18 @@ run with `docker-compose -f caMicroscope.yml up` this will build all services and run in the foreground. Use `docker-compose -f caMicroscope.yml build` to rebuild the services. -Once everything is up, go to http://localhost:4010/ to see the landing page. +Once everything is up, go to https://localhost/ to see the landing page (a self-signed-certificate warning is expected unless you provide a real certificate, see SSL below). Orthanc's DICOM REST API/GUI is available at https://localhost:8443/. 6GB memory is recommended (in total, 2GB RAM + 4GB swap should work well) ## SSL -To enable ssl, mount the private key and certificate files to the ca-back service in /root/src/ssl/privatekey.pem and /root/src/ssl/certificate.pem respectively. HTTPS mode will only be enabled if both of these files are present. +`caMicroscope.yml` fronts the whole stack with an nginx reverse proxy (the `proxy` service) that terminates TLS -- `ca-back` and `ca-dicomsrv` are no longer published directly to the host. To enable HTTPS, place your certificate and private key at `certs/certificate.pem` and `certs/privatekey.pem` respectively (this directory is gitignored). nginx will refuse to start without both files present, so for local testing you can generate a self-signed pair, e.g.: + +``` +openssl req -x509 -newkey rsa:4096 -keyout certs/privatekey.pem -out certs/certificate.pem -days 365 -nodes -subj "/CN=localhost" +``` + +Other compose variants (`kc_caMicroscope.yml`, `quip-pathdb.yml`) don't include this proxy and keep their own prior SSL setup (mounting certs directly into `ca-back` or configuring `config/httpd.conf`, respectively). ## Component Services mongo - vanilla mongo container @@ -28,6 +34,10 @@ back - security, data, and routing (see https://github.com/camicroscope/caracal) back/viewer - within back, viewer files ( see https://github.com/camicroscope/caMicroscope) +dicomsrv - Orthanc-based DICOM server/indexer, providing DICOMweb and raw DICOM protocol access to slides (see https://github.com/camicroscope/dicomsrv) + +proxy (`caMicroscope.yml` only) - nginx reverse proxy that TLS-terminates and fronts `back` (port 443) and `dicomsrv`'s REST API/GUI (port 8443). The raw DICOM protocol port (11112) is not published by default -- see "DICOM peer connectivity" below if you need it. + ## Configuration Logging - Logging is enabled by default with a set configurable maximum size. If you need to disable logs, for example due to HIPAA requirements, set the logging driver to none. @@ -35,8 +45,26 @@ See backend and security config notes [here](https://github.com/camicroscope/car Image Volume - This is, by default, the images directory in this directory. If this is changed, please make the same change across all impacted services. +## Upgrading the MongoDB data directory + +`caMicroscope.yml`, `kc_caMicroscope.yml`, and `quip-pathdb.yml` run `mongo:8.0` (previously `mongo:4.2-bionic`). MongoDB requires strictly sequential major-version upgrades, so if you have existing data in `./db` from before this change, starting `mongo:8.0` directly against it will fail with an error like: + +``` +Invalid feature compatibility version value '4.2'; expected '7.0' or '7.3' or '8.0' +``` + +If you're starting fresh (an empty or missing `./db`), there's nothing to do -- just start the stack normally. + +If you have existing data, run `./db-upgrade.sh` from the repo root. Rather than walking the on-disk files through every intermediate MongoDB version in place, it dumps the `camic` database out of wherever it currently lives, restores that dump into a freshly initialized `mongo:8.0` instance built alongside your existing data, and verifies every collection's document count matches before touching anything -- your original `./db` is never modified: it's only renamed aside (as a timestamped sidecar, kept indefinitely) once the new data has already been verified good, and a portable copy of the dump is also kept under `backups/`. Use `./db-upgrade.sh --dry-run` first to run the full dump-restore-verify rehearsal without installing anything, and `./db-upgrade.sh --help` for all options (including `--restore` to rebuild from a saved dump, optionally at a different `--target` version). + +**Compatibility caveat:** the `caracal` backend that performs all Mongo queries pins `"mongodb": "^3.6.6"`, a Node.js driver whose officially tested server-compatibility range predates MongoDB 8.0. The dump/restore itself is version-agnostic (it moves BSON documents, not on-disk storage format), but the driver talking to the resulting mongo:8.0 server afterward is running outside its documented range. Test the application thoroughly afterward. If you hit issues, `./db-upgrade.sh --restore --target 6.0` (or `7.0`) rebuilds the data at an earlier version instead. + +`develop.yml` also runs `mongo:8.0` -- if you have existing local dev data from before this change, run `./db-upgrade.sh` (with no `--data-dir` override, since it also points at `./db`) before starting `develop.yml`, the same as for the other compose files. + ## Securing caMicroscope +**`caMicroscope.yml` ships with security enabled by default (`DISABLE_SEC` is not set to `"true"`).** This is a behavior change: previously the flagship compose ran with authorization disabled out of the box. Before deploying `caMicroscope.yml`, you must either configure a real identity provider per the instructions below, or switch to `kc_caMicroscope.yml` for a self-contained Keycloak setup. Deploying `caMicroscope.yml` unmodified with no identity provider configured will lock you out of admin/write functionality. (`develop.yml`, used for local development, intentionally keeps `DISABLE_SEC: "true"` and is unaffected.) + ### Getting an Identity Provider and Setting up Login When selecting, an identity provider, note that we expect it to provide a JWT, and to have a certificate/public key/secret which can be used to verify such JWTs. @@ -65,6 +93,15 @@ Alternatively, you can use kc_caMicroscope.yml for a keycloak configuration. The email field is the email field (or failing that, sub field) in that priority from the identity provider. +### DICOM peer connectivity + +By default, `caMicroscope.yml` does not publish the raw DICOM protocol port (11112) to the host -- most deployments don't have an external PACS or modality that needs it, and Orthanc (`dicomsrv`) ships with no DICOM-level authentication or TLS of its own. If you do need real DICOM peer connectivity: + +1. Re-add `ports: ["11112:11112"]` to the `dicomsrv` service in `caMicroscope.yml`. +2. In `config/OrthancConfiguration.json`, enable `DicomTlsEnabled`, provide `DicomTlsPrivateKey`/`DicomTlsCertificate`, and populate `DicomModalities` with the AE title/IP/port of each trusted peer rather than leaving the `DicomAlwaysAllow*` flags open to everyone. + +Note that `config/OrthancConfiguration.json` is shared with `develop.yml` and `kc_caMicroscope.yml` -- changes here affect those too. + ## PathDB To use PathDB, use quip-pathdb.yml instead of caMicroscope.yml. diff --git a/backups/.gitignore b/backups/.gitignore new file mode 100644 index 00000000..d6b7ef32 --- /dev/null +++ b/backups/.gitignore @@ -0,0 +1,2 @@ +* +!.gitignore diff --git a/caMicroscope.yml b/caMicroscope.yml index 02990979..d326b46d 100644 --- a/caMicroscope.yml +++ b/caMicroscope.yml @@ -2,7 +2,7 @@ version: '3' services: mongo: - image: mongo:4.2-bionic + image: mongo:8.0 container_name: ca-mongo restart: always logging: @@ -18,8 +18,6 @@ services: viewer: "v3.12.2" depends_on: - "mongo" - ports: - - "4010:4010" container_name: ca-back restart: always logging: @@ -36,7 +34,7 @@ services: JWK_URL: "https://www.googleapis.com/oauth2/v3/certs" IIP_PATH: "http://ca-iip:8080/fcgi-bin/iipsrv.fcgi" MONGO_URI: "mongodb://ca-mongo" - DISABLE_SEC: "true" + DISABLE_SEC: "false" GENERATE_KEY_IF_MISSING: "true" iip: image: camicroscope/iipimage:version-3.11.0 @@ -70,9 +68,12 @@ services: restart: unless-stopped stdin_open: true tty: true - ports: - - "8042:8042" - - "11112:11112" + # Port 8042 (Orthanc REST/GUI) is reached only via the "proxy" service below. + # Port 11112 (raw DICOM protocol) is intentionally not published here -- most + # deployments have no external DICOM peers. If yours does, re-add + # `ports: ["11112:11112"]` and first complete the Orthanc-native DICOM TLS + # setup in config/OrthancConfiguration.json (DicomTlsEnabled/DicomModalities); + # see the README. volumes: - ./jwt_keys/:/root/keys/ - ./images/:/images/ @@ -81,3 +82,20 @@ services: DICOM_PORT: "11112" DICOM_UI_PORT: "8042" CARACAL_BACK_HOST_PORT: "ca-back:4010" + proxy: + image: nginx:1.27-alpine + container_name: ca-proxy + depends_on: + - back + - dicomsrv + ports: + - "443:443" + - "8443:8443" + volumes: + - ./config/nginx.conf:/etc/nginx/nginx.conf:ro + - ./certs/:/etc/nginx/certs/:ro + restart: always + logging: + options: + max-file: "5" + max-size: "10m" diff --git a/certs/.gitignore b/certs/.gitignore new file mode 100644 index 00000000..86c928bb --- /dev/null +++ b/certs/.gitignore @@ -0,0 +1,2 @@ +certificate.pem +privatekey.pem diff --git a/config/nginx.conf b/config/nginx.conf new file mode 100644 index 00000000..9e4bb543 --- /dev/null +++ b/config/nginx.conf @@ -0,0 +1,34 @@ +events {} + +http { + # Main app: viewer, API, loader, IIP, keycloak-proxy route (all handled internally by ca-back's own router) + server { + listen 443 ssl; + + ssl_certificate /etc/nginx/certs/certificate.pem; + ssl_certificate_key /etc/nginx/certs/privatekey.pem; + + location / { + proxy_pass http://ca-back:4010; + proxy_set_header Host $host; + proxy_set_header X-Forwarded-For $remote_addr; + proxy_set_header X-Forwarded-Proto https; + } + } + + # Orthanc REST API / Explorer GUI -- kept on a separate port rather than a + # sub-path, since Orthanc Explorer emits root-relative links. + server { + listen 8443 ssl; + + ssl_certificate /etc/nginx/certs/certificate.pem; + ssl_certificate_key /etc/nginx/certs/privatekey.pem; + + location / { + proxy_pass http://ca-dicomsrv:8042; + proxy_set_header Host $host; + proxy_set_header X-Forwarded-For $remote_addr; + proxy_set_header X-Forwarded-Proto https; + } + } +} diff --git a/config/routes.json b/config/routes.json index 908acafb..616a0107 100644 --- a/config/routes.json +++ b/config/routes.json @@ -43,6 +43,34 @@ ] }, + { + "method":"use", + "route": "/img/MCT/composited/", + "handlers":[ + {"function": "loginHandler", "args":[]}, + {"function": "preMct", "args":[]}, + {"function":"mctileHandler", "args": []} + ] + }, + + { + "method":"use", + "route": "/img/MCT/meta/", + "handlers":[ + {"function": "loginHandler", "args":[]}, + {"function":"proxyHandler", "args": ["http://ca-mctile:8008/", 3]} + ] + }, + + { + "method":"use", + "route": "/img/MCT/raw/", + "handlers":[ + {"function": "loginHandler", "args":[]}, + {"function":"proxyHandler", "args": ["http://ca-mctile:8008/", 3]} + ] + }, + { "route":"/data", "method":"use", diff --git a/config/seed_dicomweb_sources.js b/config/seed_dicomweb_sources.js new file mode 100644 index 00000000..75e34998 --- /dev/null +++ b/config/seed_dicomweb_sources.js @@ -0,0 +1,28 @@ +// One-time data seed (not a schema migration) for the DICOMweb sources list +// used by camicroscope's apps/dicom-web/table.html "DICOMweb" explorer. +// To run: either expose the mongo port (not recommended for production) or +// `docker exec -it ca-mongo mongosh`, then `use camic`, then load/paste this file. +// Safe to re-run: it upserts the single dicomweb_sources Configuration +// document by config_name rather than inserting duplicates. +// +// Endpoints below are the 2026 IHE Connectathon DICOMweb "Image Manager/ +// Archive" origin servers whose Query/Retrieve and Store transactions share a +// single DICOMweb root (the assumption camicroscope's dicom-web explorer and +// viewer make). Vendors that split QIDO-RS/WADO-RS into separate roots +// (Sectra, AGFA), require auth flows the app doesn't support (Visage's JWT), +// or don't expose a browsable Query/Retrieve root at all were intentionally +// left out; add them by hand through the "Add Source" UI if you confirm they +// work. +var dicomwebSources = [ + {id: 'google', name: 'Google', url: 'https://dicomwebproxy.app/dicomWeb'}, + {id: 'bmd', name: 'BMD Software', url: 'https://dicom-wg26.bmd-software.com/ext/dicom-web'}, + {id: 'proscia', name: 'Proscia', url: 'https://proscia-connectathon.com/dicom-web'}, + {id: 'ntunhs', name: 'NTUNHS', url: 'https://raccoon.dicom.org.tw/dicom-web'}, + {id: 'infinitt', name: 'Infinitt', url: 'http://121.170.194.140:88/dicomweb'}, +]; + +db.configuration.updateOne( + {config_name: 'dicomweb_sources'}, + {$set: {config_name: 'dicomweb_sources', configuration: dicomwebSources}}, + {upsert: true}, +); diff --git a/config/test_seed.js b/config/test_seed.js index 996c6b44..19452b20 100644 --- a/config/test_seed.js +++ b/config/test_seed.js @@ -1,5 +1,5 @@ // To add the test data, run this against mongo, either by modifying the ca-idx script, or directly. -// To access mongo, either expose the port (not recommended for production) or run `docker exec -it ca-mongo mongo` then `use camic` +// To access mongo, either expose the port (not recommended for production) or run `docker exec -it ca-mongo mongosh` then `use camic` var slides = [{ "_id": new ObjectId("5bec456369056d7e537c2a9b"), name: "CMU1", diff --git a/db-upgrade.sh b/db-upgrade.sh new file mode 100755 index 00000000..32b0de0d --- /dev/null +++ b/db-upgrade.sh @@ -0,0 +1,459 @@ +#!/usr/bin/env bash +# +# db-upgrade.sh - safely move an existing caMicroscope MongoDB data +# directory onto a new MongoDB major version, by dumping the data out +# of wherever it currently lives and restoring it into a freshly +# initialized instance of the target version -- rather than walking the +# on-disk files through every intermediate major version in place. +# See README.md, "Upgrading the MongoDB data directory", for when you +# need this. +# +# The original data directory is never modified: a fresh replacement is +# built and verified (collection-by-collection document counts compared +# against the source) entirely alongside it first, and is only swapped +# into place -- via a simple, cheap rename -- once that verification +# passes. The old directory is kept as a timestamped sidecar afterward, +# so rollback is just moving it back. +# +# Usage: +# ./db-upgrade.sh [--target VERSION] [--data-dir PATH] [--db NAME] [--yes] [--dry-run] +# ./db-upgrade.sh --restore ARCHIVE_FILE [--target VERSION] [--data-dir PATH] [--yes] +# +# With no arguments, moves ./db's "camic" database onto mongo:8.0, +# prompting for confirmation before touching the live data directory. + +set -uo pipefail + +SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" +ALL_VERSIONS=(4.2 4.4 5.0 6.0 7.0 8.0) + +DATA_DIR="./db" +TARGET="8.0" +DB_NAME="camic" +ASSUME_YES=0 +DRY_RUN=0 +RESTORE_ARCHIVE="" +TMP_CONTAINER="ca-mongo-upgrade-tmp" +LOCK_FILE="$SCRIPT_DIR/.db-upgrade.lock" + +log() { echo "$@"; } +err() { echo "ERROR: $@" >&2; } + +usage() { + cat <<'EOF' +Usage: ./db-upgrade.sh [options] + +Options: + --target VERSION Target MongoDB major version: one of 4.4, 5.0, 6.0, 7.0, 8.0. + Default: 8.0 (matches caMicroscope.yml / kc_caMicroscope.yml + / quip-pathdb.yml). + --data-dir PATH MongoDB data directory to move. Default: ./db + --db NAME Database to dump/restore. Default: camic + -y, --yes Don't prompt for confirmation. + --dry-run Do a full rehearsal (dump, restore into a scratch instance, + verify) without touching the real data directory or + leaving anything behind. + --restore ARCHIVE Restore --data-dir from a dump archive produced by this + script (found under backups/). Moves the current data + directory aside first rather than deleting it. + -h, --help Show this help. +EOF +} + +while [[ $# -gt 0 ]]; do + case "$1" in + --target) TARGET="$2"; shift 2 ;; + --data-dir) DATA_DIR="$2"; shift 2 ;; + --db) DB_NAME="$2"; shift 2 ;; + -y|--yes) ASSUME_YES=1; shift ;; + --dry-run) DRY_RUN=1; shift ;; + --restore) RESTORE_ARCHIVE="$2"; shift 2 ;; + -h|--help) usage; exit 0 ;; + *) err "Unknown option: $1"; usage; exit 1 ;; + esac +done + +is_known_version() { + local v="$1" x + for x in "${ALL_VERSIONS[@]}"; do [[ "$x" == "$v" ]] && return 0; done + return 1 +} + +if ! is_known_version "$TARGET"; then + err "Unknown --target '$TARGET'. Must be one of: ${ALL_VERSIONS[*]}" + exit 1 +fi + +require_docker() { + if ! command -v docker >/dev/null 2>&1; then + err "docker is not installed or not on PATH." + exit 1 + fi + if ! docker info >/dev/null 2>&1; then + err "docker daemon is not reachable (is Docker running?)." + exit 1 + fi +} + +resolve_abs_dir() { + local d="$1" parent + parent="$(cd "$(dirname "$d")" 2>/dev/null && pwd)" || return 1 + echo "${parent}/$(basename "$d")" +} + +looks_like_existing_data() { + local dir="$1" + [[ -d "$dir" ]] || return 1 + [[ -e "$dir/WiredTiger" ]] +} + +pick_shell() { + local name="$1" + if docker exec "$name" which mongosh >/dev/null 2>&1; then + echo mongosh + else + echo mongo + fi +} + +extract_fcv() { + local out="$1" + echo "$out" | grep -oE "version[\"']?[[:space:]]*:[[:space:]]*[\"'][0-9]+\.[0-9]+[\"']" \ + | head -1 | grep -oE '[0-9]+\.[0-9]+' +} + +# Start a temporary, no-host-port mongod container of the given version +# bound to the given data directory. Always (re)creates $TMP_CONTAINER. +start_tmp_container() { + local ver="$1" dir="$2" + docker rm -f "$TMP_CONTAINER" >/dev/null 2>&1 || true + docker run -d --rm --name "$TMP_CONTAINER" -v "${dir}:/data/db" "mongo:${ver}" >/dev/null 2>&1 +} + +wait_for_ready_or_exit() { + local name="$1" timeout="${2:-120}" waited=0 + while (( waited < timeout )); do + local running + running="$(docker inspect -f '{{.State.Running}}' "$name" 2>/dev/null || echo false)" + if [[ "$running" != "true" ]]; then + return 1 + fi + local shell; shell="$(pick_shell "$name")" + if docker exec "$name" "$shell" --quiet --eval 'db.adminCommand("ping")' >/dev/null 2>&1; then + return 0 + fi + sleep 2 + waited=$((waited + 2)) + done + return 1 +} + +stop_tmp_container() { + docker stop "$TMP_CONTAINER" >/dev/null 2>&1 || true + local waited=0 + while docker inspect "$TMP_CONTAINER" >/dev/null 2>&1 && (( waited < 20 )); do + sleep 1 + waited=$((waited + 1)) + done +} + +find_bound_container() { + local abs_dir="$1" cid + for cid in $(docker ps -q); do + if docker inspect "$cid" --format '{{range .Mounts}}{{.Source}}{{"\n"}}{{end}}' 2>/dev/null \ + | grep -qxF "$abs_dir"; then + echo "$cid" + return 0 + fi + done + return 1 +} + +# Prompts (unless --yes) and stops the container. Never called under +# --dry-run for a stop -- callers check DRY_RUN themselves, since a live +# container is safe to *read* from during a dry run, just not to stop. +stop_bound_container_with_confirmation() { + local cid="$1" name + name="$(docker inspect -f '{{.Name}}' "$cid" | sed 's#^/##')" + log "Container '$name' must be stopped to install the upgraded data directory." + if [[ $ASSUME_YES -eq 0 ]]; then + read -r -p "Stop '$name' now? [y/N] " REPLY + [[ "$REPLY" =~ ^[Yy]$ ]] || { log "Aborted. Stop it yourself and re-run, e.g.: docker stop $name"; exit 1; } + fi + docker stop "$cid" >/dev/null + log "Stopped '$name'." +} + +# Try binary versions oldest to newest until one starts successfully +# against $1; print the version that worked (this is also the version +# whose mongodump we'll use to read the data, and matches this app's +# on-disk data since binaries only start against data at or one step +# behind their own FCV). +detect_current_version() { + local abs_dir="$1" ver + for ver in "${ALL_VERSIONS[@]}"; do + log " trying mongo:$ver ..." >&2 + if start_tmp_container "$ver" "$abs_dir" && wait_for_ready_or_exit "$TMP_CONTAINER" 60; then + echo "$ver" + return 0 + fi + stop_tmp_container + done + return 1 +} + +# Prints "name:count,name:count,..." (sorted by name) for every +# collection in $DB_NAME inside the given running container. Used to +# verify the restored data matches the source before ever touching the +# real data directory. +collection_summary() { + local name="$1" shell db="$2" + shell="$(pick_shell "$name")" + docker exec "$name" "$shell" --quiet --eval " + (function(){ + var d = db.getSiblingDB('$db'); + var names = d.getCollectionNames().sort(); + var out = []; + names.forEach(function(n){ out.push(n + ':' + d.getCollection(n).countDocuments({})); }); + print(out.join(',')); + })(); + " admin 2>&1 | tail -1 +} + +# Runs mongodump for $DB_NAME inside container $1, copies the resulting +# gzip archive to host path $2. Returns non-zero on any failure. +dump_from_container() { + local name="$1" dest="$2" + docker exec "$name" sh -c "rm -f /tmp/db-upgrade-dump.archive.gz && mongodump --db=$DB_NAME --archive=/tmp/db-upgrade-dump.archive.gz --gzip" \ + >/dev/null 2>/tmp/db-upgrade-dump.err + if [[ $? -ne 0 ]]; then + err "mongodump failed:" + cat /tmp/db-upgrade-dump.err >&2 + return 1 + fi + docker cp "$name:/tmp/db-upgrade-dump.archive.gz" "$dest" >/dev/null 2>&1 + docker exec "$name" rm -f /tmp/db-upgrade-dump.archive.gz >/dev/null 2>&1 || true + [[ -s "$dest" ]] +} + +# Restores archive $1 into container $2 (must already be running). +restore_into_container() { + local archive="$1" name="$2" + docker cp "$archive" "$name:/tmp/db-upgrade-dump.archive.gz" >/dev/null 2>&1 + docker exec "$name" mongorestore --archive=/tmp/db-upgrade-dump.archive.gz --gzip \ + >/dev/null 2>/tmp/db-upgrade-restore.err + local rc=$? + docker exec "$name" rm -f /tmp/db-upgrade-dump.archive.gz >/dev/null 2>&1 || true + if [[ $rc -ne 0 ]]; then + err "mongorestore failed:" + cat /tmp/db-upgrade-restore.err >&2 + return 1 + fi + return 0 +} + +acquire_lock() { + if ! (set -o noclobber; echo "$$" > "$LOCK_FILE") 2>/dev/null; then + local pid; pid="$(cat "$LOCK_FILE" 2>/dev/null || echo unknown)" + err "Another db-upgrade.sh run appears to be in progress (lock held by pid $pid: $LOCK_FILE)." + err "If that's not the case, remove the lock file and retry: rm \"$LOCK_FILE\"" + exit 1 + fi + trap 'rm -f "$LOCK_FILE"' EXIT +} + +# Builds and verifies a fresh mongo:$TARGET data directory at $2 (a +# sibling of the eventual --data-dir, so the final install is a same- +# filesystem rename) by restoring $1 into it. Returns 0 and leaves the +# directory in place on success; on failure, removes it and returns 1. +build_target_data_dir() { + local archive="$1" new_dir="$2" expected_summary="${3:-}" + mkdir -p "$new_dir" + if ! start_tmp_container "$TARGET" "$new_dir" || ! wait_for_ready_or_exit "$TMP_CONTAINER" 120; then + err "Could not start a fresh mongo:$TARGET instance to restore into." + stop_tmp_container + rm -rf "$new_dir" + return 1 + fi + if ! restore_into_container "$archive" "$TMP_CONTAINER"; then + stop_tmp_container + rm -rf "$new_dir" + return 1 + fi + if [[ -n "$expected_summary" ]]; then + local actual_summary + actual_summary="$(collection_summary "$TMP_CONTAINER" "$DB_NAME")" + if [[ "$actual_summary" != "$expected_summary" ]]; then + err "Verification failed: restored data doesn't match the source." + err " source: $expected_summary" + err " restored: $actual_summary" + stop_tmp_container + rm -rf "$new_dir" + return 1 + fi + log "Verified: restored collection/document counts match the source ($actual_summary)." + fi + stop_tmp_container + return 0 +} + +do_restore() { + require_docker + local abs_dir + abs_dir="$(resolve_abs_dir "$DATA_DIR")" || { err "Invalid data directory path: $DATA_DIR"; exit 1; } + + if [[ ! -f "$RESTORE_ARCHIVE" ]]; then + err "Archive file not found: $RESTORE_ARCHIVE" + exit 1 + fi + if ! gzip -t "$RESTORE_ARCHIVE" >/dev/null 2>&1; then + err "Archive failed integrity check: $RESTORE_ARCHIVE" + exit 1 + fi + + local new_dir="${abs_dir}.newdata-$(date -u +%Y%m%dT%H%M%SZ)" + log "Restoring $RESTORE_ARCHIVE into a fresh mongo:$TARGET instance ..." + build_target_data_dir "$(cd "$(dirname "$RESTORE_ARCHIVE")" && pwd)/$(basename "$RESTORE_ARCHIVE")" "$new_dir" || { + err "Restore failed. $DATA_DIR has not been touched." + exit 1 + } + + local bound + bound="$(find_bound_container "$abs_dir")" || true + if [[ -n "${bound:-}" ]]; then + stop_bound_container_with_confirmation "$bound" + fi + + log "This will replace the current contents of $DATA_DIR with the restored data." + if [[ $ASSUME_YES -eq 0 ]]; then + read -r -p "Proceed? [y/N] " REPLY + [[ "$REPLY" =~ ^[Yy]$ ]] || { log "Aborted."; rm -rf "$new_dir"; exit 1; } + fi + + local sidecar="" + if [[ -d "$abs_dir" ]]; then + sidecar="${abs_dir}.pre-restore-$(date -u +%Y%m%dT%H%M%SZ)" + mv "$abs_dir" "$sidecar" + fi + mv "$new_dir" "$abs_dir" + + log "Restore complete. Data restored from: $RESTORE_ARCHIVE" + if [[ -n "$sidecar" ]]; then + log "Your previous data was moved aside to: $sidecar" + log "Once you've confirmed the restore is correct, it's safe to delete that directory." + fi +} + +main() { + if [[ -n "$RESTORE_ARCHIVE" ]]; then + do_restore + exit $? + fi + + require_docker + + local abs_dir + abs_dir="$(resolve_abs_dir "$DATA_DIR")" || { err "Data directory not found: $DATA_DIR"; exit 1; } + + if ! looks_like_existing_data "$abs_dir"; then + log "No existing MongoDB data found in $DATA_DIR." + log "Nothing to move -- you can start mongo:$TARGET directly." + exit 0 + fi + + local bound + bound="$(find_bound_container "$abs_dir")" || true + + local dump_source="" started_reader=0 + if [[ -n "${bound:-}" ]]; then + dump_source="$bound" + log "Using the already-running container bound to $DATA_DIR as the dump source (it does not need to be stopped for this step)." + else + log "Detecting current MongoDB data version in $DATA_DIR ..." + local ver + ver="$(detect_current_version "$abs_dir")" || { + err "Could not determine the current MongoDB version of the data in $DATA_DIR." + err "Nothing has been changed." + exit 1 + } + log "Detected current version: $ver. Starting a temporary instance to read from ..." + if ! start_tmp_container "$ver" "$abs_dir" || ! wait_for_ready_or_exit "$TMP_CONTAINER" 120; then + err "Could not start mongo:$ver against $DATA_DIR." + stop_tmp_container + exit 1 + fi + dump_source="$TMP_CONTAINER" + started_reader=1 + fi + + mkdir -p "$SCRIPT_DIR/backups" + local ts archive + ts="$(date -u +%Y%m%dT%H%M%SZ)" + archive="$SCRIPT_DIR/backups/ca-mongo-dump-${ts}.archive.gz" + + log "Dumping database '$DB_NAME' ..." + local source_summary + source_summary="$(collection_summary "$dump_source" "$DB_NAME")" + if ! dump_from_container "$dump_source" "$archive"; then + [[ $started_reader -eq 1 ]] && stop_tmp_container + err "Dump failed. Nothing has been changed." + rm -f "$archive" + exit 1 + fi + log "Dump written to: $archive" + [[ $started_reader -eq 1 ]] && stop_tmp_container + + local new_dir="${abs_dir}.newdata-${ts}" + log "Restoring into a fresh mongo:$TARGET instance for verification ..." + if ! build_target_data_dir "$archive" "$new_dir" "$source_summary"; then + err "The upgrade has been aborted before touching $DATA_DIR." + log "Your original data is untouched. The dump is still saved at: $archive" + exit 1 + fi + + if [[ $DRY_RUN -eq 1 ]]; then + log "(dry run: verification succeeded, but not installing -- cleaning up)" + rm -rf "$new_dir" + rm -f "$archive" + exit 0 + fi + + if [[ -n "${bound:-}" ]]; then + stop_bound_container_with_confirmation "$bound" + fi + + if [[ $ASSUME_YES -eq 0 ]]; then + log "About to install the verified mongo:$TARGET data in place of $DATA_DIR." + read -r -p "Proceed? [y/N] " REPLY + if [[ ! "$REPLY" =~ ^[Yy]$ ]]; then + log "Aborted. Your original data is untouched. Verified upgrade data is at: $new_dir" + log "The dump is saved at: $archive" + exit 1 + fi + fi + + acquire_lock + + local sidecar="${abs_dir}.pre-upgrade-${ts}" + mv "$abs_dir" "$sidecar" + mv "$new_dir" "$abs_dir" + + log "========================================================================" + log "MongoDB data directory upgraded successfully to $TARGET." + log "Your pre-upgrade data is preserved (untouched) at: $sidecar" + log "A portable dump of it is also saved at: $archive" + log "Neither has been deleted. Once you've confirmed the app works correctly" + log "against mongo:$TARGET, it is safe to remove them." + log "" + log "*** IMPORTANT COMPATIBILITY CAVEAT ***" + log "The caracal backend (github.com/camicroscope/caracal), which performs all" + log "Mongo queries for this app, pins \"mongodb\": \"^3.6.6\" -- a ~2020-era" + log "Node.js MongoDB driver whose documented/tested server-compatibility range" + log "does not officially extend to MongoDB $TARGET. Test the application" + log "thoroughly before considering this upgrade done. If you hit driver/server" + log "issues, you can restore from the dump at $archive into an earlier target" + log "version (--restore \"$archive\" --target 6.0, for example)." + log "========================================================================" +} + +main diff --git a/develop.yml b/develop.yml index 4238e903..25f2fa93 100644 --- a/develop.yml +++ b/develop.yml @@ -2,16 +2,19 @@ version: '2' services: mongo: - image: mongo:4.2-bionic + image: mongo:8.0 container_name: ca-mongo volumes: - ./db:/data/db back: - build: - context: "https://github.com/camicroscope/caracal.git#develop" - args: - viewer: "develop" - fork: "camicroscope" + # TEMPORARY local-build override for building/testing against local sibling + # repo checkouts -- revert to the github context below before committing. + #build: + # context: "https://github.com/camicroscope/caracal.git#develop" + # args: + # viewer: "develop" + # fork: "camicroscope" + build: "../caracal/" depends_on: - "mongo" ports: @@ -28,18 +31,28 @@ services: environment: JWK_URL: "https://www.googleapis.com/oauth2/v3/certs" IIP_PATH: "http://ca-iip:8080/fcgi-bin/iipsrv.fcgi" + MC_TILE_PATH: "http://ca-mctile:8008/" MONGO_URI: "mongodb://ca-mongo" DISABLE_SEC: "true" ALLOW_PUBLIC: "true" NUM_THREADS: 1 iip: - build: "https://github.com/camicroscope/iipImage.git#develop" + #build: "https://github.com/camicroscope/alt_iip.git#develop" + build: "../alt_iip/" container_name: ca-iip restart: unless-stopped volumes: - ./images/:/images/ + mctile: + build: "../camicroscope-mctile/" + container_name: ca-mctile + restart: unless-stopped + volumes: + - ./images/:/images/ loader: - build: "https://github.com/camicroscope/SlideLoader.git#develop" + # TEMPORARY local-build override -- revert before committing. + #build: "https://github.com/camicroscope/SlideLoader.git#develop" + build: "../slideloader/" container_name: ca-load volumes: - ./images/:/images/ @@ -48,7 +61,9 @@ services: DICOM_PORT: "11112" DICOM_UI_PORT: "8042" dicomsrv: - build: "https://github.com/camicroscope/dicomsrv.git" + # TEMPORARY local-build override -- revert before committing. + #build: "https://github.com/camicroscope/dicomsrv.git" + build: "../dicomsrv/" container_name: ca-dicomsrv restart: unless-stopped stdin_open: true diff --git a/kc_caMicroscope.yml b/kc_caMicroscope.yml index 92a1c6c6..ae8635ee 100644 --- a/kc_caMicroscope.yml +++ b/kc_caMicroscope.yml @@ -6,7 +6,7 @@ volumes: services: postgres: - image: postgres:15 + image: postgres:17 container_name: ca-key-db volumes: - postgres_data:/var/lib/postgresql/data @@ -21,7 +21,7 @@ services: max-size: "10m" keycloak: container_name: ca-key - image: quay.io/keycloak/keycloak:latest + image: quay.io/keycloak/keycloak:26.7 command: start-dev environment: KC_DB: postgres @@ -40,7 +40,7 @@ services: depends_on: - postgres mongo: - image: mongo:4.2-bionic + image: mongo:8.0 container_name: ca-mongo restart: always logging: diff --git a/kubernetes/caMicroscope.yml b/kubernetes/caMicroscope.yml index b27c55aa..d109622d 100644 --- a/kubernetes/caMicroscope.yml +++ b/kubernetes/caMicroscope.yml @@ -61,10 +61,12 @@ items: name: camic-login containers: - name: mongo - image: mongo:4.2-bionic + image: mongo:8.0 ports: - containerPort: 27017 - name: back + # TODO: no versioned (semver) image is published for caracal on ghcr.io today, + # only floating branch tags -- pin to a release tag once upstream publishes one. image: ghcr.io/camicroscope/caracal:master ports: - containerPort: 4010 @@ -85,13 +87,15 @@ items: - name: GENERATE_KEY_IF_MISSING value: "true" - name: iip - image: camicroscope/iipimage:latest + image: camicroscope/iipimage:version-3.11.0 ports: - containerPort: 8080 volumeMounts: - name: images mountPath: /images/ - name: loader + # TODO: no versioned (semver) image is published for slideloader on ghcr.io today, + # only floating branch tags -- pin to a release tag once upstream publishes one. image: ghcr.io/camicroscope/slideloader:master ports: - containerPort: 4000 diff --git a/kubernetes/develop.yml b/kubernetes/develop.yml index 54fd029b..bb26024f 100644 --- a/kubernetes/develop.yml +++ b/kubernetes/develop.yml @@ -28,7 +28,7 @@ items: emptyDir: {} containers: - name: mongo - image: mongo:4.2-bionic + image: mongo:8.0 ports: - containerPort: 27017 - name: back @@ -51,7 +51,7 @@ items: - name: DISABLE_CSP value: "true" - name: iip - image: camicroscope/iipimage:latest + image: camicroscope/iipimage:version-3.11.0 ports: - containerPort: 8080 volumeMounts: diff --git a/kubernetes/quip-pathdb.yml b/kubernetes/quip-pathdb.yml index 4b7f0dd1..3cae375d 100644 --- a/kubernetes/quip-pathdb.yml +++ b/kubernetes/quip-pathdb.yml @@ -99,10 +99,12 @@ items: name: pathdb-config containers: - name: mongo - image: mongo:4.2-bionic + image: mongo:8.0 ports: - containerPort: 27017 - name: back + # TODO: no versioned (semver) image is published for caracal on ghcr.io today, + # only floating branch tags -- pin to a release tag once upstream publishes one. image: ghcr.io/camicroscope/caracal:master ports: - containerPort: 4010 @@ -127,7 +129,7 @@ items: - name: "DISABLE_CSP" value: "true" - name: iip - image: camicroscope/iipimage:latest + image: camicroscope/iipimage:version-3.11.0 ports: - containerPort: 8080 volumeMounts: diff --git a/migrate/README.md b/migrate/README.md index f562346d..753e5bc3 100644 --- a/migrate/README.md +++ b/migrate/README.md @@ -20,4 +20,4 @@ Before migration, move heatmaps to a different collection, as to not confuse the The other collections use a single script which should run in mongo. This makes needed changes to the collections, and puts the results in the camic database. These utilities may behave strangely with non-standard or older form data. ## Authorization -Authorization is handled differently in the 3.0 version. See config/add_mongo_users.js for an example. Edit that file to add your original users. Name should match the subject of the jwt. This is not needed for deployments which rely on pathdb, or use another custom authorization service. +Authorization is handled differently in the 3.0 version. See config/users.json for an example. Edit that file to add your original users. Name should match the subject of the jwt. This is not needed for deployments which rely on pathdb, or use another custom authorization service. diff --git a/openshift/deployment/heatmaploader-deployment.yaml b/openshift/deployment/heatmaploader-deployment.yaml index a9a26483..52bc983d 100644 --- a/openshift/deployment/heatmaploader-deployment.yaml +++ b/openshift/deployment/heatmaploader-deployment.yaml @@ -30,7 +30,7 @@ spec: value: noninteractive - name: TZ value: America/New_York - image: heatmaploader:last + image: heatmaploader:latest imagePullPolicy: "" name: quip-hmloader resources: {} diff --git a/osi_camicroscope.yml b/osi_camicroscope.yml index fa5eb362..58adefc8 100644 --- a/osi_camicroscope.yml +++ b/osi_camicroscope.yml @@ -28,7 +28,7 @@ services: max-size: "10m" keycloak: container_name: ca-key - image: quay.io/keycloak/keycloak:latest + image: quay.io/keycloak/keycloak:26.7 command: start-dev environment: KC_DB: postgres diff --git a/quip-pathdb.yml b/quip-pathdb.yml index 6e488325..3d0527fa 100644 --- a/quip-pathdb.yml +++ b/quip-pathdb.yml @@ -2,7 +2,7 @@ version: '3' services: mongo: - 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"string-width": "^4.2.0", + "string-width": "^4.2.3", "y18n": "^5.0.5", - "yargs-parser": "^20.2.2" + "yargs-parser": "^21.1.1" }, "engines": { - "node": ">=10" + "node": ">=12" } }, "node_modules/yargs-parser": { - "version": "20.2.4", - "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.4.tgz", - "integrity": "sha512-WOkpgNhPTlE73h4VFAFsOnomJVaovO8VqLDzy5saChRBFQFBoMYirowyW+Q9HB4HFF4Z7VZTiG3iSzJJA29yRA==", + "version": "21.1.1", + "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz", + "integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw==", + "license": "ISC", "engines": { - "node": ">=10" + "node": ">=12" } }, "node_modules/yargs-unparser": { @@ -2060,6 +2506,47 @@ "node": ">=10" } }, + "node_modules/yargs/node_modules/ansi-regex": { + "version": "5.0.1", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz", + "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==", + "license": "MIT", + "engines": { + "node": ">=8" + } + }, + "node_modules/yargs/node_modules/emoji-regex": { + "version": "8.0.0", + "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", + "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==", + "license": "MIT" + }, + "node_modules/yargs/node_modules/string-width": { + "version": "4.2.3", + "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz", + "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==", + "license": "MIT", + "dependencies": { + "emoji-regex": "^8.0.0", + "is-fullwidth-code-point": "^3.0.0", + "strip-ansi": "^6.0.1" + }, + "engines": { + "node": ">=8" + } + }, + "node_modules/yargs/node_modules/strip-ansi": { + "version": "6.0.1", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", + "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", + "license": "MIT", + "dependencies": { + "ansi-regex": "^5.0.1" + }, + "engines": { + "node": ">=8" + } + }, "node_modules/yocto-queue": { "version": "0.1.0", "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", diff --git a/test/package.json b/test/package.json index de00c456..9d8adeca 100644 --- a/test/package.json +++ b/test/package.json @@ -8,11 +8,17 @@ "author": "", "license": "ISC", "dependencies": { - "chai": "^4.1.2", - "express": "^4.18.2", - "jsdom": "^16.5.0", - "mocha": "^10.2.0", - "node-fetch": "^2.6.7", - "whatwg-fetch": "^3.0.0" + "chai": "^4.5.0", + "express": "^5.2.1", + "jsdom": "^27.0.0", + "mocha": "^11.7.6", + "node-fetch": "^2.7.0", + "whatwg-fetch": "^3.6.20" + }, + "overrides": { + "brace-expansion": "^5.0.8", + "diff": "^9.0.0", + "serialize-javascript": "^7.0.7", + "js-yaml": "^4.1.1" } } diff --git a/test/test_mctile.js b/test/test_mctile.js new file mode 100644 index 00000000..fa684fd9 --- /dev/null +++ b/test/test_mctile.js @@ -0,0 +1,72 @@ +// Black-box smoke tests for the /img/MCT/* routes (config/routes.json), which +// proxy to the ca-mctile service. The actual response contract (JSON shape for +// meta, image format for composited, etc.) is defined in the external +// camicroscope-mctile repo, not here -- so these tests only assert that the +// routing/proxy wiring is intact (the request reaches ca-mctile and doesn't +// blow up), not the business-logic contents of the response. + +const assert = require('assert'); +const fetch = require("node-fetch") + +const posturl = "http://localhost:4010/data/Slide/post" +const findurl = "http://localhost:4010/data/Slide/find?name=TEST_MCT" + +let slideId; + +describe('MCT Slide Setup', function () { + it('Posts a multi-channel OME-TIFF slide for MCT testing', function (done) { + this.timeout(5000); + var slideData = {"name": "TEST_MCT", "specimen": '', "study": '', "location": "/images/exemplar_panel0_real.ome.tif", "mpp": 0.499}; + fetch(posturl, { + method: "POST", + mode: "cors", + headers: {"Content-Type": "application/json; charset=utf-8"}, + body: JSON.stringify(slideData) + }).then(x => x.json()).then(x => { + assert.equal(x.result.ok, 1, "Post Reported Successful") + done() + }).catch(e => done(e)) + }) + + it('Finds the added slide and captures its id', function (done) { + this.timeout(5000); + fetch(findurl).then(x => x.json()).then(x => { + assert.equal(x.length, 1, "Slide Shows up in API List") + slideId = x[0]._id; + assert.ok(slideId, "Slide has an id") + done() + }).catch(e => done(e)) + }); +}) + +describe('MCT Meta Route', function () { + it('reaches ca-mctile via /img/MCT/meta/ without a routing failure', function (done) { + this.timeout(10000); + fetch(`http://localhost:4010/img/MCT/meta/${slideId}`).then(res => { + // Asserting reachability, not the response shape -- the mctile API + // contract lives in the camicroscope-mctile repo, not this one. + assert.ok(res.status < 500, `expected a non-5xx response, got ${res.status}`) + done() + }).catch(e => done(e)) + }); +}) + +describe('MCT Raw Route', function () { + it('reaches ca-mctile via /img/MCT/raw/ without a routing failure', function (done) { + this.timeout(10000); + fetch(`http://localhost:4010/img/MCT/raw/${slideId}`).then(res => { + assert.ok(res.status < 500, `expected a non-5xx response, got ${res.status}`) + done() + }).catch(e => done(e)) + }); +}) + +describe('MCT Composited Route', function () { + it('does not crash the backend on a request with no compositing params', function (done) { + this.timeout(10000); + fetch(`http://localhost:4010/img/MCT/composited/${slideId}`).then(res => { + assert.ok(res.status < 500, `expected a non-5xx response (crash guard), got ${res.status}`) + done() + }).catch(e => done(e)) + }); +}) diff --git a/test/test_seed_dicomweb_sources.js b/test/test_seed_dicomweb_sources.js new file mode 100644 index 00000000..2b1d912a --- /dev/null +++ b/test/test_seed_dicomweb_sources.js @@ -0,0 +1,60 @@ +// Runs config/seed_dicomweb_sources.js (a mongosh script, not require()-able) +// against the stack's mongo the same way its own header comment documents, +// then verifies the upsert via the caracal API, including idempotency. + +const assert = require('assert'); +const fetch = require("node-fetch") +const { execFileSync } = require('child_process'); +const fs = require('fs'); +const path = require('path'); + +const findurl = "http://localhost:4010/data/Configuration/find?config_name=dicomweb_sources" +const scriptPath = path.join(__dirname, '..', 'config', 'seed_dicomweb_sources.js'); +const expectedIds = ['google', 'bmd', 'proscia', 'ntunhs', 'infinitt']; + +// mongo:6.0+ only bundles mongosh; mongo:5.0 and earlier only bundle the +// legacy `mongo` shell -- detect which is actually present rather than +// hardcoding one, since ca-mongo's version varies by compose file. +function mongoShellBinary() { + try { + execFileSync('docker', ['exec', 'ca-mongo', 'which', 'mongosh']); + return 'mongosh'; + } catch (e) { + return 'mongo'; + } +} + +function runSeedScript() { + const script = fs.readFileSync(scriptPath); + execFileSync('docker', ['exec', '-i', 'ca-mongo', mongoShellBinary(), 'camic', '--quiet'], { input: script }); +} + +describe('Seed DICOMweb Sources', function () { + it('upserts the dicomweb_sources configuration document', function (done) { + this.timeout(15000); + try { + runSeedScript(); + } catch (e) { + return done(e); + } + fetch(findurl).then(x => x.json()).then(x => { + assert.equal(x.length, 1, "Exactly one dicomweb_sources configuration document exists") + const ids = x[0].configuration.map(s => s.id); + expectedIds.forEach(id => assert.ok(ids.includes(id), `expected source "${id}" to be seeded`)) + done() + }).catch(e => done(e)) + }); + + it('is idempotent when run again', function (done) { + this.timeout(15000); + try { + runSeedScript(); + } catch (e) { + return done(e); + } + fetch(findurl).then(x => x.json()).then(x => { + assert.equal(x.length, 1, "Re-running the seed script does not create a duplicate document") + done() + }).catch(e => done(e)) + }); +}) From b10a5e278457d0de7d03d245ed76217da9237d63 Mon Sep 17 00:00:00 2001 From: Birm Date: Wed, 29 Jul 2026 17:44:17 -0400 Subject: [PATCH 2/5] more checks --- .github/workflows/main.yml | 23 ++++++++++++++---- .github/workflows/scorecard.yml | 41 +++++++++++++++++++++++++++++++++ README.md | 2 ++ SECURITY.md | 18 +++++++++++++++ check-hardening.sh | 25 ++++++++++++++++++++ 5 files changed, 104 insertions(+), 5 deletions(-) create mode 100644 .github/workflows/scorecard.yml create mode 100644 SECURITY.md create mode 100755 check-hardening.sh diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index fd6bd27b..0f1be5b8 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -1,22 +1,35 @@ name: Docker Compose Test on: push + +permissions: + contents: read + jobs: + hardening-guard: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4.4.0 + - run: ./check-hardening.sh + test: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: actions/setup-node@v4 + - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4.4.0 + - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4.4.0 with: node-version: '22' + - name: Install test dependencies + working-directory: test + run: npm ci + - name: Audit dependencies + working-directory: test + run: npm audit --audit-level=high - name: Build the develop stack run: docker compose -f develop.yml build - name: Start the develop stack run: docker compose -f develop.yml up -d - name: Wait for the back service to be healthy run: timeout 180 bash -c 'until curl -sf http://localhost:4010/apps/viewer/viewer.html > /dev/null; do sleep 3; done' - - name: Install test dependencies - working-directory: test - run: npm ci - name: Run test suite working-directory: test run: npm test diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml new file mode 100644 index 00000000..40ba31b6 --- /dev/null +++ b/.github/workflows/scorecard.yml @@ -0,0 +1,41 @@ +name: Scorecard supply-chain security +on: + branch_protection_rule: + schedule: + - cron: '30 1 * * 6' + push: + branches: [ "master" ] + +permissions: read-all + +jobs: + analysis: + name: Scorecard analysis + runs-on: ubuntu-latest + permissions: + security-events: write + id-token: write + steps: + - name: Checkout code + uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4.4.0 + with: + persist-credentials: false + + - name: Run analysis + uses: ossf/scorecard-action@2d1146689b8cda280b9bc96326124645441f03bc # v2.4.4 + with: + results_file: results.sarif + results_format: sarif + publish_results: true + + - name: Upload artifact + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 + with: + name: SARIF file + path: results.sarif + retention-days: 5 + + - name: Upload to code-scanning + uses: github/codeql-action/upload-sarif@e4fba868fa4b1b91e1fdab776edc8cfbe6e9fb81 # v4.37.3 + with: + sarif_file: results.sarif diff --git a/README.md b/README.md index 3bb8f37d..605e62fd 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,8 @@ # caMicroscope distribution +![Docker Compose Test](https://github.com/camicroscope/distro/actions/workflows/main.yml/badge.svg) +![License](https://img.shields.io/github/license/camicroscope/distro) run with `docker-compose -f caMicroscope.yml up` diff --git a/SECURITY.md b/SECURITY.md new file mode 100644 index 00000000..fde49c01 --- /dev/null +++ b/SECURITY.md @@ -0,0 +1,18 @@ +# Security Policy + +## Reporting a Vulnerability + +If you believe you've found a security vulnerability in this repository, please report it privately using [GitHub's Security Advisories](https://github.com/camicroscope/distro/security/advisories/new) rather than opening a public issue. This lets us assess and fix the issue before it's publicly disclosed. + +Please include: +- A description of the vulnerability and its potential impact +- Steps to reproduce it +- Any relevant configuration (which compose file, environment variables, etc.) + +## Supported Versions + +This repository tracks the latest state of the `master` branch. There is no separate long-term-support branch; fixes land on `master` and are not backported. + +## Non-Security Questions + +For general questions, bugs, or feature discussion that aren't security-sensitive, please use the [caMicroscope discussion forum](https://github.com/orgs/camicroscope/discussions) instead. diff --git a/check-hardening.sh b/check-hardening.sh new file mode 100755 index 00000000..1b795c54 --- /dev/null +++ b/check-hardening.sh @@ -0,0 +1,25 @@ +#!/usr/bin/env bash +# +# check-hardening.sh - guards caMicroscope.yml (the flagship production +# compose) against regressing on the auth/secrets hardening decisions +# made for it. Run locally before pushing, or from CI. + +set -uo pipefail + +FAIL=0 + +if grep -q 'DISABLE_SEC: "true"' caMicroscope.yml; then + echo "FAIL: caMicroscope.yml has DISABLE_SEC set to true (the production compose must ship with auth enabled)." + FAIL=1 +fi + +if grep -inE '(PASSWORD|SECRET|_KEY):[[:space:]]*"?[^"$]' caMicroscope.yml | grep -v '^\s*#'; then + echo "FAIL: caMicroscope.yml appears to contain a hardcoded credential." + FAIL=1 +fi + +if [[ $FAIL -eq 0 ]]; then + echo "OK: caMicroscope.yml hardening checks passed." +fi + +exit $FAIL From a1924f9695bc203f83861debbea5ba4a0cb61576 Mon Sep 17 00:00:00 2001 From: Birm Date: Thu, 30 Jul 2026 18:53:11 -0400 Subject: [PATCH 3/5] undo local dev versions --- develop.yml | 26 +++++++++----------------- 1 file changed, 9 insertions(+), 17 deletions(-) diff --git a/develop.yml b/develop.yml index 25f2fa93..669407f8 100644 --- a/develop.yml +++ b/develop.yml @@ -7,14 +7,11 @@ services: volumes: - ./db:/data/db back: - # TEMPORARY local-build override for building/testing against local sibling - # repo checkouts -- revert to the github context below before committing. - #build: - # context: "https://github.com/camicroscope/caracal.git#develop" - # args: - # viewer: "develop" - # fork: "camicroscope" - build: "../caracal/" + build: + context: "https://github.com/camicroscope/caracal.git#develop" + args: + viewer: "develop" + fork: "camicroscope" depends_on: - "mongo" ports: @@ -27,7 +24,7 @@ services: - ./jwt_keys/:/src/keys/ - ./config/routes.json:/src/routes.json - ./config/contentSecurityPolicy.json:/src/contentSecurityPolicy.json - - ../camicroscope/:/src/camicroscope/ + # - ../camicroscope/:/src/camicroscope/ environment: JWK_URL: "https://www.googleapis.com/oauth2/v3/certs" IIP_PATH: "http://ca-iip:8080/fcgi-bin/iipsrv.fcgi" @@ -37,8 +34,7 @@ services: ALLOW_PUBLIC: "true" NUM_THREADS: 1 iip: - #build: "https://github.com/camicroscope/alt_iip.git#develop" - build: "../alt_iip/" + build: "https://github.com/camicroscope/alt_iip.git#develop" container_name: ca-iip restart: unless-stopped volumes: @@ -50,9 +46,7 @@ services: volumes: - ./images/:/images/ loader: - # TEMPORARY local-build override -- revert before committing. - #build: "https://github.com/camicroscope/SlideLoader.git#develop" - build: "../slideloader/" + build: "https://github.com/camicroscope/SlideLoader.git#develop" container_name: ca-load volumes: - ./images/:/images/ @@ -61,9 +55,7 @@ services: DICOM_PORT: "11112" DICOM_UI_PORT: "8042" dicomsrv: - # TEMPORARY local-build override -- revert before committing. - #build: "https://github.com/camicroscope/dicomsrv.git" - build: "../dicomsrv/" + build: "https://github.com/camicroscope/dicomsrv.git" container_name: ca-dicomsrv restart: unless-stopped stdin_open: true From 49fcb6d9b4c394c73629e39316b97f146651ef51 Mon Sep 17 00:00:00 2001 From: Birm Date: Thu, 30 Jul 2026 19:08:27 -0400 Subject: [PATCH 4/5] cleanup mctile --- README.md | 2 ++ develop.yml | 2 +- local_dev.yml | 73 +++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 76 insertions(+), 1 deletion(-) create mode 100644 local_dev.yml diff --git a/README.md b/README.md index 605e62fd..113af980 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,8 @@ Once everything is up, go to https://localhost/ to see the landing page (a self- 6GB memory is recommended (in total, 2GB RAM + 4GB swap should work well) +For local development, use `develop.yml` instead -- it builds each service from its GitHub `develop` branch and runs with security disabled for convenience. If you're actively developing against local sibling checkouts of the component repos (`../caracal/`, `../alt_iip/`, ...), use `local_dev.yml` instead, which is identical to `develop.yml` but builds from those local directories rather than GitHub. + ## SSL `caMicroscope.yml` fronts the whole stack with an nginx reverse proxy (the `proxy` service) that terminates TLS -- `ca-back` and `ca-dicomsrv` are no longer published directly to the host. To enable HTTPS, place your certificate and private key at `certs/certificate.pem` and `certs/privatekey.pem` respectively (this directory is gitignored). nginx will refuse to start without both files present, so for local testing you can generate a self-signed pair, e.g.: diff --git a/develop.yml b/develop.yml index 669407f8..8407cc89 100644 --- a/develop.yml +++ b/develop.yml @@ -40,7 +40,7 @@ services: volumes: - ./images/:/images/ mctile: - build: "../camicroscope-mctile/" + build: "https://github.com/camicroscope/multichannel_tile.git" container_name: ca-mctile restart: unless-stopped volumes: diff --git a/local_dev.yml b/local_dev.yml new file mode 100644 index 00000000..6606839f --- /dev/null +++ b/local_dev.yml @@ -0,0 +1,73 @@ +# Local development against sibling repo checkouts, instead of building +# from each repo's GitHub "develop" branch as develop.yml does. Requires +# ../caracal/, ../alt_iip/, ../slideloader/, ../multichannel_tile/ and ../dicomsrv/ to exist as +# sibling directories of this repo. +version: '2' + +services: + mongo: + image: mongo:8.0 + container_name: ca-mongo + volumes: + - ./db:/data/db + back: + build: "../caracal/" + depends_on: + - "mongo" + ports: + - "4010:4010" + - "9229:9229" + container_name: ca-back + command: node --inspect=0.0.0.0:9229 --prof caracal.js + volumes: + - ./config/login.html:/src/static/login.html + - ./jwt_keys/:/src/keys/ + - ./config/routes.json:/src/routes.json + - ./config/contentSecurityPolicy.json:/src/contentSecurityPolicy.json + - ../camicroscope/:/src/camicroscope/ + environment: + JWK_URL: "https://www.googleapis.com/oauth2/v3/certs" + IIP_PATH: "http://ca-iip:8080/fcgi-bin/iipsrv.fcgi" + MC_TILE_PATH: "http://ca-mctile:8008/" + MONGO_URI: "mongodb://ca-mongo" + DISABLE_SEC: "true" + ALLOW_PUBLIC: "true" + NUM_THREADS: 1 + iip: + build: "../iipimage/" + container_name: ca-iip + restart: unless-stopped + volumes: + - ./images/:/images/ + mctile: + build: "../multichannel_tile/" + container_name: ca-mctile + restart: unless-stopped + volumes: + - ./images/:/images/ + loader: + build: "../slideloader/" + container_name: ca-load + volumes: + - ./images/:/images/ + - ./cloud-upload-apis/:/cloud-upload-apis/ + environment: + DICOM_PORT: "11112" + DICOM_UI_PORT: "8042" + dicomsrv: + build: "../dicomsrv/" + container_name: ca-dicomsrv + restart: unless-stopped + stdin_open: true + tty: true + ports: + - "8042:8042" + - "11112:11112" + volumes: + - ./jwt_keys/:/root/keys/ + - ./images/:/images/ + - ./config/OrthancConfiguration.json:/root/src/Configuration.json + environment: + DICOM_PORT: "11112" + DICOM_UI_PORT: "8042" + CARACAL_BACK_HOST_PORT: "ca-back:4010" From 1116ae4685236cae9e815e78bcc94be8175292ba Mon Sep 17 00:00:00 2001 From: Birm Date: Fri, 31 Jul 2026 09:39:23 -0400 Subject: [PATCH 5/5] fix post test --- test/test_add_slide.js | 2 +- test/test_mctile.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/test/test_add_slide.js b/test/test_add_slide.js index 2baf4657..763c6a07 100644 --- a/test/test_add_slide.js +++ b/test/test_add_slide.js @@ -23,7 +23,7 @@ describe('Slide Loading Step 1', function () { body:JSON.stringify(slideData)}) postProcess.then(x=>x.json()).then(x=>{ console.log(x) - assert.equal(x.result.ok,1, "Post Reported Successful") + assert.equal(x.acknowledged, true, "Post Reported Successful") done() }).catch(e=>{ console.log("err") diff --git a/test/test_mctile.js b/test/test_mctile.js index fa684fd9..26253bc7 100644 --- a/test/test_mctile.js +++ b/test/test_mctile.js @@ -23,7 +23,7 @@ describe('MCT Slide Setup', function () { headers: {"Content-Type": "application/json; charset=utf-8"}, body: JSON.stringify(slideData) }).then(x => x.json()).then(x => { - assert.equal(x.result.ok, 1, "Post Reported Successful") + assert.equal(x.acknowledged, true, "Post Reported Successful") done() }).catch(e => done(e)) })