diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000..b949761e --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,24 @@ + +# Changelog + +## 0.7.0 - latest + +### Features + +### Bug Fixes + +## 0.6.0 + +### Features + +- Importing cases for analysis, with support of automated configured annotations of genomic units with support at + curating evidence for analysis review. +- Attachment of supporting evidence as files or URLs +- Support for researchers entering case relevant information to be disseminated to research team +- Multi image attachment for curated figures for analyses +- Attachment of visual annotations associated with genomic units +- Viewing annotations for the genomic units in a case for analysis +- CAS user login, enabling organizations to connect to their Center Authentication Service for user credentials +- Filtering available analyses by data presented on analysis cards in the analysis feed +- Workflows to change analyses from being in preparation to ready, active, approved, declined, on-hold +- 3rd party attachments to link Monday.com and Phenotips to the specific analysis diff --git a/README.md b/README.md index 4f1b6d94..3931d2ff 100644 --- a/README.md +++ b/README.md @@ -298,6 +298,38 @@ registry. For additional information on the `build.sh` script, refer to the [build.sh script documentation](./build.sh) within the script itself. +The local production docker compose yaml must be updated if you would like to test the docker images created from the +`build.sh` script. Modify the `docker-compose.local-production.yml` by: + +- Commenting out the build configuration designated within the compose yaml. + +```yaml + #build: + #context: ./frontend/ + #target: production-stage + #dockerfile: Dockerfile + #args: + #VERSION_BUILD_TAG: "local-production@latest" +``` + +- Uncommenting the docker image tags for the `frontend` and `backend` services + +```yaml +image: ghcr.io/uab-cgds-worthey/rosalution/frontend:${ROSALUTION_VERSION} +``` + +- Setting the ROSALUTION_VERSION environment variable to be the 'build tag' used with the `build.sh` script. + +```bash +export ROSALUTION_VERSION=0.6.0 +``` + +- Deploy the Rosalution Build as indicated in the following section + +```bash +docker-compose -f docker-compose.local-production.yml up --build +``` + #### Local deployment of a Production Build To deploy a production build locally, the following command can be uses. diff --git a/build.sh b/build.sh index 14c84096..b9a70652 100755 --- a/build.sh +++ b/build.sh @@ -146,7 +146,7 @@ build(){ # Making this a comment now to preserve code in the event we need the npmrc for future CGDS modules # docker_build_command="DOCKER_BUILDKIT=1 docker build --no-cache=true --secret id=npmrc,src=$npmrc_filepath --target=$build_target $(build_args "$service_name") --tag=$image_name -f ./$service_name/Dockerfile $build_context" - docker_build_command="DOCKER_BUILDKIT=1 docker build --no-cache=true --target=$build_target $(build_args "$service_name") --tag=$image_name -f ./$service_name/Dockerfile $build_context" + docker_build_command="DOCKER_BUILDKIT=1 docker build --no-cache=true --target=$build_target --build-arg=\"VERSION_BUILD_TAG=$build_tag\" $(build_args "$service_name") --tag=$image_name -f ./$service_name/Dockerfile $build_context" echo "Building $service_name..." eval "$docker_build_command" diff --git a/docker-compose.local-production.yml b/docker-compose.local-production.yml index db927ab7..6ad3130c 100644 --- a/docker-compose.local-production.yml +++ b/docker-compose.local-production.yml @@ -25,6 +25,9 @@ services: context: ./frontend/ target: production-stage dockerfile: Dockerfile + args: + VERSION_BUILD_TAG: "local-production@latest" + # image: ghcr.io/uab-cgds-worthey/rosalution/frontend:${ROSALUTION_VERSION} networks: - rosalution-network labels: @@ -43,6 +46,7 @@ services: context: ./backend/ target: production-stage dockerfile: Dockerfile + # image: ghcr.io/uab-cgds-worthey/rosalution/backend:${ROSALUTION_VERSION} networks: - rosalution-network environment: @@ -64,6 +68,7 @@ services: context: ./etc/fixtures/ target: production-stage dockerfile: production.Dockerfile + # image: ghcr.io/uab-cgds-worthey/rosalution/database-fixture:${ROSALUTION_VERSION} networks: - rosalution-network environment: diff --git a/docker-compose.yml b/docker-compose.yml index 2137da35..8830e475 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -27,6 +27,8 @@ services: dockerfile: Dockerfile volumes: - ./frontend/src:/app/src + environment: + VITE_ROSALUTION_VERSION: "local@latest" networks: - rosalution-network labels: diff --git a/frontend/Dockerfile b/frontend/Dockerfile index 4863e67c..474e3310 100644 --- a/frontend/Dockerfile +++ b/frontend/Dockerfile @@ -17,6 +17,9 @@ COPY package.json /app/ COPY yarn.lock /app/ COPY index.html /app/ COPY vite.config.js /app/ +ARG VERSION_BUILD_TAG=latest + +ENV VITE_ROSALUTION_VERSION=$VERSION_BUILD_TAG RUN yarn install --frozen-lockfile && yarn build --base=/rosalution/ diff --git a/frontend/index.html b/frontend/index.html index c4067226..229124d2 100644 --- a/frontend/index.html +++ b/frontend/index.html @@ -4,7 +4,7 @@ - rosalution v0.1 + rosalution %VITE_ROSALUTION_VERSION%
diff --git a/frontend/package.json b/frontend/package.json index 0f97159f..c6fb019c 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -24,16 +24,16 @@ "vue-router": "4.1.6" }, "devDependencies": { - "@vitejs/plugin-vue": "4.0.0", + "@vitejs/plugin-vue": "4.3.4", "@vitest/coverage-c8": "0.27.2", "@vitest/ui": "0.27.2", - "@vue/test-utils": "2.2.7", + "@vue/test-utils": "2.4.1", "eslint": "8.32.0", "eslint-config-google": "0.14.0", "eslint-plugin-vue": "9.9.0", "happy-dom": "6.0.4", "sinon": "15.0.1", - "vite": "4.0.4", + "vite": "4.4.9", "vitest": "0.27.2" } } diff --git a/frontend/yarn.lock b/frontend/yarn.lock index ae0826dc..39f850d7 100644 --- a/frontend/yarn.lock +++ b/frontend/yarn.lock @@ -17,111 +17,221 @@ resolved "https://registry.yarnpkg.com/@esbuild/android-arm64/-/android-arm64-0.16.17.tgz#cf91e86df127aa3d141744edafcba0abdc577d23" integrity sha512-MIGl6p5sc3RDTLLkYL1MyL8BMRN4tLMRCn+yRJJmEDvYZ2M7tmAf80hx1kbNEUX2KJ50RRtxZ4JHLvCfuB6kBg== 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braces@^3.0.2: version "3.0.2" resolved "https://registry.yarnpkg.com/braces/-/braces-3.0.2.tgz#3454e1a462ee8d599e236df336cd9ea4f8afe107" @@ -647,6 +777,11 @@ combined-stream@^1.0.6: dependencies: delayed-stream "~1.0.0" +commander@^10.0.0: + version "10.0.1" + resolved "https://registry.yarnpkg.com/commander/-/commander-10.0.1.tgz#881ee46b4f77d1c1dccc5823433aa39b022cbe06" + integrity sha512-y4Mg2tXshplEbSGzx7amzPwKKOCGuoSRP/CjEdwwk0FOGlUbq6lKuoyDZTNZkmxHdJtp54hdfY/JUrdL7Xfdug== + concat-map@0.0.1: version "0.0.1" resolved "https://registry.yarnpkg.com/concat-map/-/concat-map-0.0.1.tgz#d8a96bd77fd68df7793a73036a3ba0d5405d477b" @@ -662,6 +797,14 @@ concat-stream@^1.6.0, concat-stream@^1.6.2: readable-stream "^2.2.2" typedarray "^0.0.6" +config-chain@^1.1.13: + version "1.1.13" + resolved "https://registry.yarnpkg.com/config-chain/-/config-chain-1.1.13.tgz#fad0795aa6a6cdaff9ed1b68e9dff94372c232f4" + integrity 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"@esbuild/win32-x64" "0.16.17" +esbuild@^0.18.10: + version "0.18.20" + resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.18.20.tgz#4709f5a34801b43b799ab7d6d82f7284a9b7a7a6" + integrity sha512-ceqxoedUrcayh7Y7ZX6NdbbDzGROiyVBgC4PriJThBKSVPWnnFHZAkfI1lJT8QFkOwH4qOS2SJkS4wvpGl8BpA== + optionalDependencies: + "@esbuild/android-arm" "0.18.20" + "@esbuild/android-arm64" "0.18.20" + "@esbuild/android-x64" "0.18.20" + "@esbuild/darwin-arm64" "0.18.20" + "@esbuild/darwin-x64" "0.18.20" + "@esbuild/freebsd-arm64" "0.18.20" + "@esbuild/freebsd-x64" "0.18.20" + "@esbuild/linux-arm" "0.18.20" + "@esbuild/linux-arm64" "0.18.20" + "@esbuild/linux-ia32" "0.18.20" + "@esbuild/linux-loong64" "0.18.20" + "@esbuild/linux-mips64el" "0.18.20" + "@esbuild/linux-ppc64" "0.18.20" + "@esbuild/linux-riscv64" "0.18.20" + "@esbuild/linux-s390x" "0.18.20" + "@esbuild/linux-x64" "0.18.20" + "@esbuild/netbsd-x64" "0.18.20" + "@esbuild/openbsd-x64" "0.18.20" + "@esbuild/sunos-x64" "0.18.20" + "@esbuild/win32-arm64" "0.18.20" + "@esbuild/win32-ia32" "0.18.20" + "@esbuild/win32-x64" "0.18.20" + escalade@^3.1.1: version "3.1.1" resolved "https://registry.yarnpkg.com/escalade/-/escalade-3.1.1.tgz#d8cfdc7000965c5a0174b4a82eaa5c0552742e40" @@ -1075,6 +1256,17 @@ glob@^7.1.4: once "^1.3.0" path-is-absolute "^1.0.0" +glob@^8.1.0: + version "8.1.0" + resolved "https://registry.yarnpkg.com/glob/-/glob-8.1.0.tgz#d388f656593ef708ee3e34640fdfb99a9fd1c33e" + integrity sha512-r8hpEjiQEYlF2QU0df3dS+nxxSIreXQS1qRhMJM0Q5NDdR386C7jb7Hwwod8Fgiuex+k0GFjgft18yvxm5XoCQ== + dependencies: + fs.realpath "^1.0.0" + inflight "^1.0.4" + inherits "2" + minimatch "^5.0.1" + once "^1.3.0" + globals@^13.19.0: version "13.19.0" resolved "https://registry.yarnpkg.com/globals/-/globals-13.19.0.tgz#7a42de8e6ad4f7242fbcca27ea5b23aca367b5c8" @@ -1182,6 +1374,11 @@ inherits@2, inherits@^2.0.3, inherits@~2.0.3: resolved 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config-chain "^1.1.13" + editorconfig "^1.0.3" + glob "^8.1.0" + nopt "^6.0.0" + js-sdsl@^4.1.4: version "4.3.0" resolved "https://registry.yarnpkg.com/js-sdsl/-/js-sdsl-4.3.0.tgz#aeefe32a451f7af88425b11fdb5f58c90ae1d711" @@ -1380,6 +1587,13 @@ mime-types@^2.1.12: dependencies: mime-db "1.52.0" +minimatch@9.0.1: + version "9.0.1" + resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-9.0.1.tgz#8a555f541cf976c622daf078bb28f29fb927c253" + integrity sha512-0jWhJpD/MdhPXwPuiRkCbfYfSKp2qnn2eOc279qI7f+osl/l+prKSrvhg157zSYvx/1nmgn2NqdT6k2Z7zSH9w== + dependencies: + brace-expansion "^2.0.1" + minimatch@^3.0.4: version "3.0.5" resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-3.0.5.tgz#4da8f1290ee0f0f8e83d60ca69f8f134068604a3" @@ -1394,6 +1608,13 @@ minimatch@^3.0.5, minimatch@^3.1.1, minimatch@^3.1.2: dependencies: brace-expansion "^1.1.7" +minimatch@^5.0.1: + version "5.1.6" + resolved 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"https://registry.yarnpkg.com/natural-compare/-/natural-compare-1.4.0.tgz#4abebfeed7541f2c27acfb29bdbbd15c8d5ba4f7" @@ -1442,6 +1668,13 @@ node-fetch@^2.x.x: dependencies: whatwg-url "^5.0.0" +nopt@^6.0.0: + version "6.0.0" + resolved "https://registry.yarnpkg.com/nopt/-/nopt-6.0.0.tgz#245801d8ebf409c6df22ab9d95b65e1309cdb16d" + integrity sha512-ZwLpbTgdhuZUnZzjd7nb1ZV+4DoiC6/sfiVKok72ym/4Tlf+DFdlHYmT2JPmcNNWV6Pi3SDf1kT+A4r9RTuT9g== + dependencies: + abbrev "^1.0.0" + nth-check@^2.0.1: version "2.1.1" resolved "https://registry.yarnpkg.com/nth-check/-/nth-check-2.1.1.tgz#c9eab428effce36cd6b92c924bdb000ef1f1ed1d" @@ -1577,6 +1810,15 @@ postcss@^8.1.10, postcss@^8.4.20: picocolors "^1.0.0" source-map-js "^1.0.2" +postcss@^8.4.27: + version "8.4.29" + resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.29.tgz#33bc121cf3b3688d4ddef50be869b2a54185a1dd" + integrity sha512-cbI+jaqIeu/VGqXEarWkRCCffhjgXc0qjBtXpqJhTBohMUjUQnbBr0xqX3vEKudc4iviTewcJo5ajcec5+wdJw== + dependencies: + nanoid "^3.3.6" + picocolors "^1.0.0" + source-map-js "^1.0.2" + prelude-ls@^1.2.1: version "1.2.1" resolved "https://registry.yarnpkg.com/prelude-ls/-/prelude-ls-1.2.1.tgz#debc6489d7a6e6b0e7611888cec880337d316396" @@ -1594,6 +1836,11 @@ promise@^8.0.0: dependencies: asap "~2.0.6" +proto-list@~1.2.1: + version "1.2.4" + resolved "https://registry.yarnpkg.com/proto-list/-/proto-list-1.2.4.tgz#212d5bfe1318306a420f6402b8e26ff39647a849" + integrity sha512-vtK/94akxsTMhe0/cbfpR+syPuszcuwhqVjJq26CuNDgFGj682oRBXOP5MJpv2r7JtE8MsiepGIqvvOTBwn2vA== + punycode@^2.1.0: version "2.1.1" resolved "https://registry.yarnpkg.com/punycode/-/punycode-2.1.1.tgz#b58b010ac40c22c5657616c8d2c2c02c7bf479ec" @@ -1660,6 +1907,13 @@ rimraf@^3.0.2: dependencies: glob "^7.1.3" +rollup@^3.27.1: + version "3.28.1" + resolved "https://registry.yarnpkg.com/rollup/-/rollup-3.28.1.tgz#fb44aa6d5e65c7e13fd5bcfff266d0c4ea9ba433" + integrity sha512-R9OMQmIHJm9znrU3m3cpE8uhN0fGdXiawME7aZIpQqvpS/85+Vt1Hq1/yVIcYfOmaQiHjvXkQAoJukvLpau6Yw== + optionalDependencies: + fsevents "~2.3.2" + rollup@^3.7.0: version "3.10.1" resolved "https://registry.yarnpkg.com/rollup/-/rollup-3.10.1.tgz#56278901ed11fc2898421e8e3e2c8155bc7b40b4" @@ -1703,6 +1957,13 @@ semver@^7.3.6: dependencies: lru-cache "^6.0.0" +semver@^7.5.3: + version "7.5.4" + resolved "https://registry.yarnpkg.com/semver/-/semver-7.5.4.tgz#483986ec4ed38e1c6c48c34894a9182dbff68a6e" + integrity sha512-1bCSESV6Pv+i21Hvpxp3Dx+pSD8lIPt8uVjRrxAUt/nbswYc+tK6Y2btiULjd4+fnq15PX+nqQDC7Oft7WkwcA== + dependencies: + lru-cache "^6.0.0" + shebang-command@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/shebang-command/-/shebang-command-2.0.0.tgz#ccd0af4f8835fbdc265b82461aaf0c36663f34ea" @@ -1971,7 +2232,18 @@ vite-node@0.27.2: source-map-support "^0.5.21" vite "^3.0.0 || ^4.0.0" -vite@4.0.4, "vite@^3.0.0 || ^4.0.0": +vite@4.4.9: + version "4.4.9" + resolved "https://registry.yarnpkg.com/vite/-/vite-4.4.9.tgz#1402423f1a2f8d66fd8d15e351127c7236d29d3d" + integrity sha512-2mbUn2LlUmNASWwSCNSJ/EG2HuSRTnVNaydp6vMCm5VIqJsjMfbIWtbH2kDuwUVW5mMUKKZvGPX/rqeqVvv1XA== + dependencies: + esbuild "^0.18.10" + postcss "^8.4.27" + rollup "^3.27.1" + optionalDependencies: + fsevents "~2.3.2" + +"vite@^3.0.0 || ^4.0.0": version "4.0.4" resolved "https://registry.yarnpkg.com/vite/-/vite-4.0.4.tgz#4612ce0b47bbb233a887a54a4ae0c6e240a0da31" integrity sha512-xevPU7M8FU0i/80DMR+YhgrzR5KS2ORy1B4xcX/cXLsvnUWvfHuqMmVU6N0YiJ4JWGRJJsLCgjEzKjG9/GKoSw== @@ -2007,6 +2279,11 @@ vitest@0.27.2: vite-node "0.27.2" why-is-node-running "^2.2.2" +vue-component-type-helpers@1.8.4: + version "1.8.4" + resolved "https://registry.yarnpkg.com/vue-component-type-helpers/-/vue-component-type-helpers-1.8.4.tgz#302d85fac912519cdf0dd2fb51402e5215d85628" + integrity sha512-6bnLkn8O0JJyiFSIF0EfCogzeqNXpnjJ0vW/SZzNHfe6sPx30lTtTXlE5TFs2qhJlAtDFybStVNpL73cPe3OMQ== + vue-eslint-parser@^9.0.1: version "9.1.0" resolved "https://registry.yarnpkg.com/vue-eslint-parser/-/vue-eslint-parser-9.1.0.tgz#0e121d1bb29bd10763c83e3cc583ee03434a9dd5"