From 5fe70abdd4c64f232048c214615fe749fb5fa9a1 Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Wed, 25 Oct 2023 13:28:23 +0200 Subject: [PATCH 01/11] build: set prerelease to false --- .github/workflows/release-please.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml index c5f695c..0182682 100644 --- a/.github/workflows/release-please.yml +++ b/.github/workflows/release-please.yml @@ -28,4 +28,4 @@ jobs: release-type: node package-name: release-please-action token: ${{ secrets.GITHUB_TOKEN }} - prerelease: true \ No newline at end of file + prerelease: false \ No newline at end of file From 3f32b019ec48b958525148bf8acaaa47d8d449f3 Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Wed, 25 Oct 2023 16:20:40 +0200 Subject: [PATCH 02/11] fix: move nmrium url to ENV. fixes #4 --- .env.example | 4 +++- .env.test | 2 ++ app/Controllers/Http/SpectraController.ts | 4 ++-- env.ts | 2 ++ 4 files changed, 9 insertions(+), 3 deletions(-) diff --git a/.env.example b/.env.example index f4870c0..db292c0 100644 --- a/.env.example +++ b/.env.example @@ -2,4 +2,6 @@ PORT=3333 HOST=0.0.0.0 NODE_ENV=production APP_KEY=NZu-mbqukZjV_65cT3ckDB21exh17-ws -DRIVE_DISK=local \ No newline at end of file +DRIVE_DISK=local +NMRIUM_DEV_URL=https://nmriumdev.nmrxiv.org +NMRIUM_PROD_URL=https://nmrium.nmrxiv.org/ \ No newline at end of file diff --git a/.env.test b/.env.test index 2c87534..ba76b1a 100644 --- a/.env.test +++ b/.env.test @@ -1 +1,3 @@ NODE_ENV=test +NMRIUM_DEV_URL=https://nmriumdev.nmrxiv.org +NMRIUM_PROD_URL=https://nmrium.nmrxiv.org/ diff --git a/app/Controllers/Http/SpectraController.ts b/app/Controllers/Http/SpectraController.ts index a12751c..4d1590b 100644 --- a/app/Controllers/Http/SpectraController.ts +++ b/app/Controllers/Http/SpectraController.ts @@ -48,8 +48,8 @@ export default class SpectraController { private generateNMRiumURL() { const baseURL = Env.get('NODE_ENV') === 'development' - ? 'https://nmriumdev.nmrxiv.org' - : 'https://nmrium.nmrxiv.org/' + ? Env.get('NMRIUM_DEV_URL') + : Env.get('NMRIUM_PROD_URL') const url = new URL(baseURL) const preferences = JSON.stringify({ diff --git a/env.ts b/env.ts index 3ac1661..3a68b7c 100644 --- a/env.ts +++ b/env.ts @@ -21,4 +21,6 @@ export default Env.rules({ APP_NAME: Env.schema.string(), DRIVE_DISK: Env.schema.enum(['local'] as const), NODE_ENV: Env.schema.enum(['development', 'production', 'test'] as const), + NMRIUM_DEV_URL: Env.schema.string(), + NMRIUM_PROD_URL: Env.schema.string(), }) From 9e0120fe334f404b0deda249e4b077ef2f76fea4 Mon Sep 17 00:00:00 2001 From: hamed musallam Date: Tue, 14 Nov 2023 10:10:16 +0100 Subject: [PATCH 03/11] feat: prefer loading Ft and auto processing fid --- app/Controllers/Http/SpectraController.ts | 8 +++++- package-lock.json | 30 +++++++++++------------ package.json | 4 +-- 3 files changed, 24 insertions(+), 18 deletions(-) diff --git a/app/Controllers/Http/SpectraController.ts b/app/Controllers/Http/SpectraController.ts index a12751c..4f0ec53 100644 --- a/app/Controllers/Http/SpectraController.ts +++ b/app/Controllers/Http/SpectraController.ts @@ -41,7 +41,13 @@ export default class SpectraController { } return { relativePath: refURL.pathname, baseURL: refURL.origin } }, []) - const state: NmriumState = (await readFromWebSource({ entries })) as NmriumState + const state: NmriumState = (await readFromWebSource( + { entries }, + { + onLoadProcessing: { autoProcessing: true }, + sourceSelector: { general: { dataSelection: 'preferFT' } }, + } + )) as NmriumState return resolveState(state) } diff --git a/package-lock.json b/package-lock.json index 624d77c..5775390 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,7 +11,7 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.22.4", + "nmr-load-save": "^0.23.2", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", @@ -6625,9 +6625,9 @@ } }, "node_modules/nmr-load-save": { - "version": "0.22.4", - "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.22.4.tgz", - "integrity": "sha512-U3HAOz67ilLKLKoCKVQciGma8e/FPE9bM/J9k+1BJEU+JgmWuLPt4bqIoGz8E2A5huvKD1/JW38SrMXZvOWCVg==", + "version": "0.23.2", + "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.2.tgz", + "integrity": "sha512-QSBYdjENOAhznJoZWYzn8aLQc3Df24xSWzwn/maK5dHd015XKy35p4+O5u2KmGW6lmyF8KysWemjmiKHUXdv7Q==", "dependencies": { "@lukeed/uuid": "^2.0.1", "@types/lodash.merge": "^4.6.7", @@ -6642,7 +6642,7 @@ "lodash.merge": "^4.6.2", "ml-spectra-processing": "^12.5.1", "nmr-correlation": "^2.3.3", - "nmr-processing": "^11.4.1", + "nmr-processing": "^11.5.0", "nmredata": "^0.9.7", "openchemlib": "^8.7.0", "openchemlib-utils": "^5.4.0", @@ -6651,9 +6651,9 @@ } }, "node_modules/nmr-processing": { - "version": "11.4.1", - "resolved": "https://registry.npmjs.org/nmr-processing/-/nmr-processing-11.4.1.tgz", - "integrity": "sha512-pA/Z5vWcQcetaB3UHip0+XahjNQh7c9JPAE9uC+HHpRoagb13U4cnO4RLApdxOTKzjKwsXC4sSwtZKqJbpES4A==", + "version": "11.5.0", + "resolved": "https://registry.npmjs.org/nmr-processing/-/nmr-processing-11.5.0.tgz", + "integrity": "sha512-WnrHPd6aYmiBW2a2bk743Id6XD9UJ3uLZSL7HDYrFhfjGzAiNK2d+SMn8fm7PmuKGV7Q6SChxb5Zdthgqo//dQ==", "dependencies": { "@lukeed/uuid": "^2.0.1", "binary-search": "^1.3.6", @@ -14802,9 +14802,9 @@ } }, "nmr-load-save": { - "version": "0.22.4", - "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.22.4.tgz", - "integrity": "sha512-U3HAOz67ilLKLKoCKVQciGma8e/FPE9bM/J9k+1BJEU+JgmWuLPt4bqIoGz8E2A5huvKD1/JW38SrMXZvOWCVg==", + "version": "0.23.2", + "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.2.tgz", + "integrity": "sha512-QSBYdjENOAhznJoZWYzn8aLQc3Df24xSWzwn/maK5dHd015XKy35p4+O5u2KmGW6lmyF8KysWemjmiKHUXdv7Q==", "requires": { "@lukeed/uuid": "^2.0.1", "@types/lodash.merge": "^4.6.7", @@ -14819,7 +14819,7 @@ "lodash.merge": "^4.6.2", "ml-spectra-processing": "^12.5.1", "nmr-correlation": "^2.3.3", - "nmr-processing": "^11.4.1", + "nmr-processing": "^11.5.0", "nmredata": "^0.9.7", "openchemlib": "^8.7.0", "openchemlib-utils": "^5.4.0", @@ -14828,9 +14828,9 @@ } }, "nmr-processing": { - "version": "11.4.1", - "resolved": "https://registry.npmjs.org/nmr-processing/-/nmr-processing-11.4.1.tgz", - "integrity": "sha512-pA/Z5vWcQcetaB3UHip0+XahjNQh7c9JPAE9uC+HHpRoagb13U4cnO4RLApdxOTKzjKwsXC4sSwtZKqJbpES4A==", + "version": "11.5.0", + "resolved": "https://registry.npmjs.org/nmr-processing/-/nmr-processing-11.5.0.tgz", + "integrity": "sha512-WnrHPd6aYmiBW2a2bk743Id6XD9UJ3uLZSL7HDYrFhfjGzAiNK2d+SMn8fm7PmuKGV7Q6SChxb5Zdthgqo//dQ==", "requires": { "@lukeed/uuid": "^2.0.1", "binary-search": "^1.3.6", diff --git a/package.json b/package.json index 6e1bd13..de8d37a 100644 --- a/package.json +++ b/package.json @@ -60,10 +60,10 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.22.4", + "nmr-load-save": "^0.23.2", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", "source-map-support": "^0.5.21" } -} \ No newline at end of file +} From b72a7a9446f3e46ea8d79731a747cdb08cffc37a Mon Sep 17 00:00:00 2001 From: hamed musallam Date: Tue, 21 Nov 2023 19:55:00 +0100 Subject: [PATCH 04/11] feat: update nmr-load-save to version 0.23.3 --- package-lock.json | 46 +++++++++++++++++++++++----------------------- package.json | 4 ++-- 2 files changed, 25 insertions(+), 25 deletions(-) diff --git a/package-lock.json b/package-lock.json index 624d77c..1698bd2 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,7 +11,7 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.22.4", + "nmr-load-save": "^0.23.3", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", @@ -5316,9 +5316,9 @@ } }, "node_modules/jcampconverter": { - "version": "9.2.2", - "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.2.2.tgz", - "integrity": "sha512-+mZK6QzbwnDBorK6lzccFuBNiTSGgwQGKczdhxNzpYjKS1osEQwtmgPJVEp9JGqbI7ClxXJU6IAyxivIBN/jLA==", + "version": "9.4.1", + "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.4.1.tgz", + "integrity": "sha512-P+0FRkDx4hYCZ0q5BWdoiQTa1kf2maw9A12iUMvnkrQ18f04rZ1WDUhPFEFaMquNujucqNQ9lbYUoR08PFmlXg==", "dependencies": { "cheminfo-types": "^1.7.2", "dynamic-typing": "^1.0.0", @@ -6625,9 +6625,9 @@ } }, "node_modules/nmr-load-save": { - "version": "0.22.4", - "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.22.4.tgz", - "integrity": "sha512-U3HAOz67ilLKLKoCKVQciGma8e/FPE9bM/J9k+1BJEU+JgmWuLPt4bqIoGz8E2A5huvKD1/JW38SrMXZvOWCVg==", + "version": "0.23.3", + "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.3.tgz", + "integrity": "sha512-g8p0Ympb+UiE4PXQoCA2pR4q9wRCWEk/8bpKKLEUrugDZbUzq+f6B5ws3eG1P0caUkof832gqgQLH4pC5Q9S3A==", "dependencies": { "@lukeed/uuid": "^2.0.1", "@types/lodash.merge": "^4.6.7", @@ -6637,12 +6637,12 @@ "filelist-utils": "^1.10.2", "gyromagnetic-ratio": "^1.0.0", "is-any-array": "^2.0.1", - "jcampconverter": "^9.2.2", + "jcampconverter": "^9.4.1", "jeolconverter": "^1.0.2", "lodash.merge": "^4.6.2", "ml-spectra-processing": "^12.5.1", "nmr-correlation": "^2.3.3", - "nmr-processing": "^11.4.1", + "nmr-processing": "^11.6.0", "nmredata": "^0.9.7", "openchemlib": "^8.7.0", "openchemlib-utils": "^5.4.0", @@ -6651,9 +6651,9 @@ } }, "node_modules/nmr-processing": { - "version": "11.4.1", - "resolved": "https://registry.npmjs.org/nmr-processing/-/nmr-processing-11.4.1.tgz", - "integrity": "sha512-pA/Z5vWcQcetaB3UHip0+XahjNQh7c9JPAE9uC+HHpRoagb13U4cnO4RLApdxOTKzjKwsXC4sSwtZKqJbpES4A==", + "version": "11.6.0", + "resolved": "https://registry.npmjs.org/nmr-processing/-/nmr-processing-11.6.0.tgz", + "integrity": "sha512-Hqh3h3WYlZNTuXODgd7LJh7Qt04pHb4gJedpcZoex8f7wL6vyWsAF7F85KwXDCrsZ4nEGPxh5a004VYZdVEHSg==", "dependencies": { "@lukeed/uuid": "^2.0.1", "binary-search": "^1.3.6", @@ -13705,9 +13705,9 @@ "integrity": "sha512-mJtsQGFfAphKdVuRitEpc0eon4v5fuaB6v9ZJIrLnIyybh02sIIwJ2RQbLMp6UICVCfquezllupZIVcqzGzCPg==" }, "jcampconverter": { - "version": "9.2.2", - "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.2.2.tgz", - "integrity": "sha512-+mZK6QzbwnDBorK6lzccFuBNiTSGgwQGKczdhxNzpYjKS1osEQwtmgPJVEp9JGqbI7ClxXJU6IAyxivIBN/jLA==", + "version": "9.4.1", + "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.4.1.tgz", + "integrity": "sha512-P+0FRkDx4hYCZ0q5BWdoiQTa1kf2maw9A12iUMvnkrQ18f04rZ1WDUhPFEFaMquNujucqNQ9lbYUoR08PFmlXg==", "requires": { "cheminfo-types": "^1.7.2", "dynamic-typing": "^1.0.0", @@ -14802,9 +14802,9 @@ } }, "nmr-load-save": { - "version": "0.22.4", - "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.22.4.tgz", - "integrity": "sha512-U3HAOz67ilLKLKoCKVQciGma8e/FPE9bM/J9k+1BJEU+JgmWuLPt4bqIoGz8E2A5huvKD1/JW38SrMXZvOWCVg==", + "version": "0.23.3", + "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.3.tgz", + "integrity": "sha512-g8p0Ympb+UiE4PXQoCA2pR4q9wRCWEk/8bpKKLEUrugDZbUzq+f6B5ws3eG1P0caUkof832gqgQLH4pC5Q9S3A==", "requires": { "@lukeed/uuid": "^2.0.1", "@types/lodash.merge": "^4.6.7", @@ -14814,12 +14814,12 @@ "filelist-utils": "^1.10.2", "gyromagnetic-ratio": "^1.0.0", "is-any-array": "^2.0.1", - "jcampconverter": "^9.2.2", + "jcampconverter": "^9.4.1", "jeolconverter": "^1.0.2", "lodash.merge": "^4.6.2", "ml-spectra-processing": "^12.5.1", "nmr-correlation": "^2.3.3", - "nmr-processing": "^11.4.1", + "nmr-processing": "^11.6.0", "nmredata": "^0.9.7", "openchemlib": "^8.7.0", "openchemlib-utils": "^5.4.0", @@ -14828,9 +14828,9 @@ } }, "nmr-processing": { - "version": "11.4.1", - "resolved": "https://registry.npmjs.org/nmr-processing/-/nmr-processing-11.4.1.tgz", - "integrity": "sha512-pA/Z5vWcQcetaB3UHip0+XahjNQh7c9JPAE9uC+HHpRoagb13U4cnO4RLApdxOTKzjKwsXC4sSwtZKqJbpES4A==", + "version": "11.6.0", + "resolved": "https://registry.npmjs.org/nmr-processing/-/nmr-processing-11.6.0.tgz", + "integrity": "sha512-Hqh3h3WYlZNTuXODgd7LJh7Qt04pHb4gJedpcZoex8f7wL6vyWsAF7F85KwXDCrsZ4nEGPxh5a004VYZdVEHSg==", "requires": { "@lukeed/uuid": "^2.0.1", "binary-search": "^1.3.6", diff --git a/package.json b/package.json index 6e1bd13..e9ba518 100644 --- a/package.json +++ b/package.json @@ -60,10 +60,10 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.22.4", + "nmr-load-save": "^0.23.3", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", "source-map-support": "^0.5.21" } -} \ No newline at end of file +} From d5ee2bfe30b94ca89e88af478594c809d68b3bbc Mon Sep 17 00:00:00 2001 From: hamed musallam Date: Wed, 22 Nov 2023 11:58:20 +0100 Subject: [PATCH 05/11] fix: serialize spectra object --- app/Controllers/Http/SpectraController.ts | 4 +- package-lock.json | 50 +++++++++++------------ package.json | 2 +- 3 files changed, 28 insertions(+), 28 deletions(-) diff --git a/app/Controllers/Http/SpectraController.ts b/app/Controllers/Http/SpectraController.ts index 4d1590b..7148194 100644 --- a/app/Controllers/Http/SpectraController.ts +++ b/app/Controllers/Http/SpectraController.ts @@ -10,7 +10,7 @@ interface SpectrumSnapshot { id: string } -function omitKeys(source: T, excludeKeys: Array): Partial { +function omitKeys(source: T, excludeKeys: Array): Partial { const target: Partial = {} for (const key in source) { if (!excludeKeys.includes(key)) { @@ -24,7 +24,7 @@ function omitKeys(source: T, excludeKeys: Array): Partial { function resolveState(state: NmriumState) { let { data, version, ...others } = state data.spectra = data?.spectra.map((spectrum) => - omitKeys(spectrum, ['data', 'originalData']) + omitKeys(spectrum, ['data', 'originalData', 'logger', 'keepSource']) ) as Spectrum[] return { data, version, ...others } diff --git a/package-lock.json b/package-lock.json index 1698bd2..a8c1ebb 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,7 +11,7 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.23.3", + "nmr-load-save": "^0.23.4", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", @@ -4598,9 +4598,9 @@ "dev": true }, "node_modules/gyromagnetic-ratio": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/gyromagnetic-ratio/-/gyromagnetic-ratio-1.0.0.tgz", - "integrity": "sha512-s55NtJPxoplsW/8OnM1C7tNWd2gEXXt+roF3NPNDKFb7YchBy9JXdxmzztf3d4JL1zCiQz5cn6HSC8M0osN78w==" + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/gyromagnetic-ratio/-/gyromagnetic-ratio-1.1.1.tgz", + "integrity": "sha512-M1y9bAhK11moqAPRZ5oUoDCEIQCogjKYXDMlkXJiSjkLFmOAp1qevrjThF+6KrtwkSpmT7Vgy8C/mgBlIdZPSg==" }, "node_modules/has": { "version": "1.0.3", @@ -5316,14 +5316,14 @@ } }, "node_modules/jcampconverter": { - "version": "9.4.1", - "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.4.1.tgz", - "integrity": "sha512-P+0FRkDx4hYCZ0q5BWdoiQTa1kf2maw9A12iUMvnkrQ18f04rZ1WDUhPFEFaMquNujucqNQ9lbYUoR08PFmlXg==", + "version": "9.4.2", + "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.4.2.tgz", + "integrity": "sha512-yTC4PgSMYeo+hHY/n9G+WgjGbjgwsdvEcu9FaJx55iRelHshulZ2HF3qPfwR4lH5vVpI0aQoplRYsE0MTUz18w==", "dependencies": { "cheminfo-types": "^1.7.2", "dynamic-typing": "^1.0.0", "ensure-string": "^1.2.0", - "gyromagnetic-ratio": "^1.0.0", + "gyromagnetic-ratio": "^1.1.1", "ml-array-median": "^1.1.6" } }, @@ -6625,9 +6625,9 @@ } }, "node_modules/nmr-load-save": { - "version": "0.23.3", - "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.3.tgz", - "integrity": "sha512-g8p0Ympb+UiE4PXQoCA2pR4q9wRCWEk/8bpKKLEUrugDZbUzq+f6B5ws3eG1P0caUkof832gqgQLH4pC5Q9S3A==", + "version": "0.23.4", + "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.4.tgz", + "integrity": "sha512-A7PFWXBEwlFjjrTcvNAK++Lafl/nca6GGWuLB0uQ8ni6qAsBQ4Xnr6Inv0ZKJfpR6bR17hJgX2EL+A5BPi8xwg==", "dependencies": { "@lukeed/uuid": "^2.0.1", "@types/lodash.merge": "^4.6.7", @@ -6635,9 +6635,9 @@ "cheminfo-types": "^1.7.2", "convert-to-jcamp": "^5.4.9", "filelist-utils": "^1.10.2", - "gyromagnetic-ratio": "^1.0.0", + "gyromagnetic-ratio": "^1.1.0", "is-any-array": "^2.0.1", - "jcampconverter": "^9.4.1", + "jcampconverter": "^9.4.2", "jeolconverter": "^1.0.2", "lodash.merge": "^4.6.2", "ml-spectra-processing": "^12.5.1", @@ -13172,9 +13172,9 @@ "dev": true }, "gyromagnetic-ratio": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/gyromagnetic-ratio/-/gyromagnetic-ratio-1.0.0.tgz", - "integrity": "sha512-s55NtJPxoplsW/8OnM1C7tNWd2gEXXt+roF3NPNDKFb7YchBy9JXdxmzztf3d4JL1zCiQz5cn6HSC8M0osN78w==" + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/gyromagnetic-ratio/-/gyromagnetic-ratio-1.1.1.tgz", + "integrity": "sha512-M1y9bAhK11moqAPRZ5oUoDCEIQCogjKYXDMlkXJiSjkLFmOAp1qevrjThF+6KrtwkSpmT7Vgy8C/mgBlIdZPSg==" }, "has": { "version": "1.0.3", @@ -13705,14 +13705,14 @@ "integrity": "sha512-mJtsQGFfAphKdVuRitEpc0eon4v5fuaB6v9ZJIrLnIyybh02sIIwJ2RQbLMp6UICVCfquezllupZIVcqzGzCPg==" }, "jcampconverter": { - "version": "9.4.1", - "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.4.1.tgz", - "integrity": "sha512-P+0FRkDx4hYCZ0q5BWdoiQTa1kf2maw9A12iUMvnkrQ18f04rZ1WDUhPFEFaMquNujucqNQ9lbYUoR08PFmlXg==", + "version": "9.4.2", + "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.4.2.tgz", + "integrity": "sha512-yTC4PgSMYeo+hHY/n9G+WgjGbjgwsdvEcu9FaJx55iRelHshulZ2HF3qPfwR4lH5vVpI0aQoplRYsE0MTUz18w==", "requires": { "cheminfo-types": "^1.7.2", "dynamic-typing": "^1.0.0", "ensure-string": "^1.2.0", - "gyromagnetic-ratio": "^1.0.0", + "gyromagnetic-ratio": "^1.1.1", "ml-array-median": "^1.1.6" } }, @@ -14802,9 +14802,9 @@ } }, "nmr-load-save": { - "version": "0.23.3", - "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.3.tgz", - "integrity": "sha512-g8p0Ympb+UiE4PXQoCA2pR4q9wRCWEk/8bpKKLEUrugDZbUzq+f6B5ws3eG1P0caUkof832gqgQLH4pC5Q9S3A==", + "version": "0.23.4", + "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.4.tgz", + "integrity": "sha512-A7PFWXBEwlFjjrTcvNAK++Lafl/nca6GGWuLB0uQ8ni6qAsBQ4Xnr6Inv0ZKJfpR6bR17hJgX2EL+A5BPi8xwg==", "requires": { "@lukeed/uuid": "^2.0.1", "@types/lodash.merge": "^4.6.7", @@ -14812,9 +14812,9 @@ "cheminfo-types": "^1.7.2", "convert-to-jcamp": "^5.4.9", "filelist-utils": "^1.10.2", - "gyromagnetic-ratio": "^1.0.0", + "gyromagnetic-ratio": "^1.1.0", "is-any-array": "^2.0.1", - "jcampconverter": "^9.4.1", + "jcampconverter": "^9.4.2", "jeolconverter": "^1.0.2", "lodash.merge": "^4.6.2", "ml-spectra-processing": "^12.5.1", diff --git a/package.json b/package.json index e9ba518..9fd0ee6 100644 --- a/package.json +++ b/package.json @@ -60,7 +60,7 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.23.3", + "nmr-load-save": "^0.23.4", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", From b1f072dac10ebe4191310720fdc6c136335e9ac0 Mon Sep 17 00:00:00 2001 From: hamed musallam Date: Mon, 27 Nov 2023 12:01:35 +0100 Subject: [PATCH 06/11] chore: update nmr-load-save --- package-lock.json | 30 +++++++++++++++--------------- package.json | 2 +- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/package-lock.json b/package-lock.json index a8c1ebb..dfdda41 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,7 +11,7 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.23.4", + "nmr-load-save": "^0.23.6", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", @@ -5316,9 +5316,9 @@ } }, "node_modules/jcampconverter": { - "version": "9.4.2", - "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.4.2.tgz", - "integrity": "sha512-yTC4PgSMYeo+hHY/n9G+WgjGbjgwsdvEcu9FaJx55iRelHshulZ2HF3qPfwR4lH5vVpI0aQoplRYsE0MTUz18w==", + "version": "9.5.0", + "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.5.0.tgz", + "integrity": "sha512-xsuZXcUd+YkF0Rlt0IZa1+4XbMYq/fR6+gewwDJd5M17y2+SbjrgESKZH73+GokzLC7H1KTS0/l5/7cQFFLgiA==", "dependencies": { "cheminfo-types": "^1.7.2", "dynamic-typing": "^1.0.0", @@ -6625,9 +6625,9 @@ } }, "node_modules/nmr-load-save": { - "version": "0.23.4", - "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.4.tgz", - "integrity": "sha512-A7PFWXBEwlFjjrTcvNAK++Lafl/nca6GGWuLB0uQ8ni6qAsBQ4Xnr6Inv0ZKJfpR6bR17hJgX2EL+A5BPi8xwg==", + "version": "0.23.6", + "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.6.tgz", + "integrity": "sha512-F+z7IdzDNM1mokybnhUq0nyQhxMif7oNqLloWBRS1HQjh44gdMw+EUuW75izEWPisKmU1qkgUbeRR/D7UQ8/9A==", "dependencies": { "@lukeed/uuid": "^2.0.1", "@types/lodash.merge": "^4.6.7", @@ -6637,7 +6637,7 @@ "filelist-utils": "^1.10.2", "gyromagnetic-ratio": "^1.1.0", "is-any-array": "^2.0.1", - "jcampconverter": "^9.4.2", + "jcampconverter": "^9.5.0", "jeolconverter": "^1.0.2", "lodash.merge": "^4.6.2", "ml-spectra-processing": "^12.5.1", @@ -13705,9 +13705,9 @@ "integrity": "sha512-mJtsQGFfAphKdVuRitEpc0eon4v5fuaB6v9ZJIrLnIyybh02sIIwJ2RQbLMp6UICVCfquezllupZIVcqzGzCPg==" }, "jcampconverter": { - "version": "9.4.2", - "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.4.2.tgz", - "integrity": "sha512-yTC4PgSMYeo+hHY/n9G+WgjGbjgwsdvEcu9FaJx55iRelHshulZ2HF3qPfwR4lH5vVpI0aQoplRYsE0MTUz18w==", + "version": "9.5.0", + "resolved": "https://registry.npmjs.org/jcampconverter/-/jcampconverter-9.5.0.tgz", + "integrity": "sha512-xsuZXcUd+YkF0Rlt0IZa1+4XbMYq/fR6+gewwDJd5M17y2+SbjrgESKZH73+GokzLC7H1KTS0/l5/7cQFFLgiA==", "requires": { "cheminfo-types": "^1.7.2", "dynamic-typing": "^1.0.0", @@ -14802,9 +14802,9 @@ } }, "nmr-load-save": { - "version": "0.23.4", - "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.4.tgz", - "integrity": "sha512-A7PFWXBEwlFjjrTcvNAK++Lafl/nca6GGWuLB0uQ8ni6qAsBQ4Xnr6Inv0ZKJfpR6bR17hJgX2EL+A5BPi8xwg==", + "version": "0.23.6", + "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.6.tgz", + "integrity": "sha512-F+z7IdzDNM1mokybnhUq0nyQhxMif7oNqLloWBRS1HQjh44gdMw+EUuW75izEWPisKmU1qkgUbeRR/D7UQ8/9A==", "requires": { "@lukeed/uuid": "^2.0.1", "@types/lodash.merge": "^4.6.7", @@ -14814,7 +14814,7 @@ "filelist-utils": "^1.10.2", "gyromagnetic-ratio": "^1.1.0", "is-any-array": "^2.0.1", - "jcampconverter": "^9.4.2", + "jcampconverter": "^9.5.0", "jeolconverter": "^1.0.2", "lodash.merge": "^4.6.2", "ml-spectra-processing": "^12.5.1", diff --git a/package.json b/package.json index 9fd0ee6..4837adf 100644 --- a/package.json +++ b/package.json @@ -60,7 +60,7 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.23.4", + "nmr-load-save": "^0.23.6", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", From 4268f51b62e5f748e75bb17b1f96da735ae46e0c Mon Sep 17 00:00:00 2001 From: hamed musallam Date: Thu, 30 Nov 2023 13:08:47 +0100 Subject: [PATCH 07/11] feat: update nmr-load-save to version 0.23.8 --- package-lock.json | 30 +++++++++++++++--------------- package.json | 2 +- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/package-lock.json b/package-lock.json index dfdda41..47d145e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,7 +11,7 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.23.6", + "nmr-load-save": "^0.23.8", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", @@ -6625,9 +6625,9 @@ } }, "node_modules/nmr-load-save": { - "version": "0.23.6", - "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.6.tgz", - "integrity": "sha512-F+z7IdzDNM1mokybnhUq0nyQhxMif7oNqLloWBRS1HQjh44gdMw+EUuW75izEWPisKmU1qkgUbeRR/D7UQ8/9A==", + "version": "0.23.8", + "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.8.tgz", + "integrity": "sha512-iyoYhaHWlEk280hKX8Dwq0HPdRk/gHuMT0eHvGWr58I0yfEU5IGAHsK4jMex/H0Eg4HgAhWGA0lCClLFVwpK2A==", "dependencies": { "@lukeed/uuid": "^2.0.1", "@types/lodash.merge": "^4.6.7", @@ -6643,7 +6643,7 @@ "ml-spectra-processing": "^12.5.1", "nmr-correlation": "^2.3.3", "nmr-processing": "^11.6.0", - "nmredata": "^0.9.7", + "nmredata": "^0.9.9", "openchemlib": "^8.7.0", "openchemlib-utils": "^5.4.0", "sdf-parser": "^6.0.1", @@ -6685,9 +6685,9 @@ } }, "node_modules/nmredata": { - "version": "0.9.7", - "resolved": "https://registry.npmjs.org/nmredata/-/nmredata-0.9.7.tgz", - "integrity": "sha512-Lp2Pjts420voq++NZevDcnCuv2b6qCb0haKoUAHSWAyQ6YUrCNZSqJuDPcX4FAC/pim7gsqM5peex7d+tWgNhA==", + "version": "0.9.9", + "resolved": "https://registry.npmjs.org/nmredata/-/nmredata-0.9.9.tgz", + "integrity": "sha512-FhqSIN3p37RE/e/8Lf8OG/bpAuT35WtKrhjo6W9YQ1ZvC6QV7xP/1IUYOfOjmMqafaMC8xdzED9aSgHnlE5VUA==", "dependencies": { "filelist-utils": "^1.2.0", "jszip": "^3.10.1", @@ -14802,9 +14802,9 @@ } }, "nmr-load-save": { - "version": "0.23.6", - "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.6.tgz", - "integrity": "sha512-F+z7IdzDNM1mokybnhUq0nyQhxMif7oNqLloWBRS1HQjh44gdMw+EUuW75izEWPisKmU1qkgUbeRR/D7UQ8/9A==", + "version": "0.23.8", + "resolved": "https://registry.npmjs.org/nmr-load-save/-/nmr-load-save-0.23.8.tgz", + "integrity": "sha512-iyoYhaHWlEk280hKX8Dwq0HPdRk/gHuMT0eHvGWr58I0yfEU5IGAHsK4jMex/H0Eg4HgAhWGA0lCClLFVwpK2A==", "requires": { "@lukeed/uuid": "^2.0.1", "@types/lodash.merge": "^4.6.7", @@ -14820,7 +14820,7 @@ "ml-spectra-processing": "^12.5.1", "nmr-correlation": "^2.3.3", "nmr-processing": "^11.6.0", - "nmredata": "^0.9.7", + "nmredata": "^0.9.9", "openchemlib": "^8.7.0", "openchemlib-utils": "^5.4.0", "sdf-parser": "^6.0.1", @@ -14862,9 +14862,9 @@ } }, "nmredata": { - "version": "0.9.7", - "resolved": "https://registry.npmjs.org/nmredata/-/nmredata-0.9.7.tgz", - "integrity": "sha512-Lp2Pjts420voq++NZevDcnCuv2b6qCb0haKoUAHSWAyQ6YUrCNZSqJuDPcX4FAC/pim7gsqM5peex7d+tWgNhA==", + "version": "0.9.9", + "resolved": "https://registry.npmjs.org/nmredata/-/nmredata-0.9.9.tgz", + "integrity": "sha512-FhqSIN3p37RE/e/8Lf8OG/bpAuT35WtKrhjo6W9YQ1ZvC6QV7xP/1IUYOfOjmMqafaMC8xdzED9aSgHnlE5VUA==", "requires": { "filelist-utils": "^1.2.0", "jszip": "^3.10.1", diff --git a/package.json b/package.json index 4837adf..f26c76c 100644 --- a/package.json +++ b/package.json @@ -60,7 +60,7 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.23.6", + "nmr-load-save": "^0.23.8", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", From 8d9ab83209e1c6e8d9326062f61f102efc3fc448 Mon Sep 17 00:00:00 2001 From: hamed musallam Date: Thu, 30 Nov 2023 13:14:27 +0100 Subject: [PATCH 08/11] chore: not omit 'logger' or 'keepSource' --- app/Controllers/Http/SpectraController.ts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/app/Controllers/Http/SpectraController.ts b/app/Controllers/Http/SpectraController.ts index 7148194..4d1590b 100644 --- a/app/Controllers/Http/SpectraController.ts +++ b/app/Controllers/Http/SpectraController.ts @@ -10,7 +10,7 @@ interface SpectrumSnapshot { id: string } -function omitKeys(source: T, excludeKeys: Array): Partial { +function omitKeys(source: T, excludeKeys: Array): Partial { const target: Partial = {} for (const key in source) { if (!excludeKeys.includes(key)) { @@ -24,7 +24,7 @@ function omitKeys(source: T, excludeKeys: Array - omitKeys(spectrum, ['data', 'originalData', 'logger', 'keepSource']) + omitKeys(spectrum, ['data', 'originalData']) ) as Spectrum[] return { data, version, ...others } From c0326dc5656a7065b6c4b6b6be7d93dd230cfeaa Mon Sep 17 00:00:00 2001 From: hamed musallam Date: Thu, 14 Dec 2023 12:36:00 +0100 Subject: [PATCH 09/11] chore: update dependencies --- package-lock.json | 2139 ++++++++++++++++++++++++++++++++------------- package.json | 24 +- 2 files changed, 1537 insertions(+), 626 deletions(-) diff --git a/package-lock.json b/package-lock.json index 47d145e..73244c1 100644 --- a/package-lock.json +++ b/package-lock.json @@ -12,25 +12,25 @@ "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", "nmr-load-save": "^0.23.8", - "playwright": "^1.39.0", + "playwright": "^1.40.1", "proxy-addr": "^2.0.7", - "reflect-metadata": "^0.1.13", + "reflect-metadata": "^0.2.0", "source-map-support": "^0.5.21" }, "devDependencies": { - "@adonisjs/assembler": "^5.9.5", + "@adonisjs/assembler": "^5.9.6", "@japa/preset-adonis": "^1.2.0", - "@japa/runner": "^2.5.1", + "@japa/runner": "^3.1.0", "adonis-preset-ts": "^2.1.0", - "eslint": "^8.45.0", - "eslint-config-prettier": "^8.9.0", + "eslint": "^8.55.0", + "eslint-config-prettier": "^9.1.0", "eslint-plugin-adonis": "^2.1.1", - "eslint-plugin-prettier": "^5.0.0", - "pino-pretty": "^10.2.0", - "prettier": "^3.0.0", - "typescript": "~5.1", - "youch": "^3.2.3", - "youch-terminal": "^2.2.2" + "eslint-plugin-prettier": "^5.0.1", + "pino-pretty": "^10.3.0", + "prettier": "^3.1.1", + "typescript": "~5.3", + "youch": "^3.3.3", + "youch-terminal": "^2.2.3" } }, "node_modules/@aashutoshrathi/word-wrap": { @@ -100,9 +100,9 @@ } }, "node_modules/@adonisjs/assembler": { - "version": "5.9.5", - "resolved": "https://registry.npmjs.org/@adonisjs/assembler/-/assembler-5.9.5.tgz", - "integrity": "sha512-wCtQRZ4KoIZkzi+ux5NrDUDNASRomytRZ7AZBdw8Hi3LlEOeac4T8+47y7gXwJFKH2nnGoiIwnXGIgJyolXEfQ==", + "version": "5.9.6", + "resolved": "https://registry.npmjs.org/@adonisjs/assembler/-/assembler-5.9.6.tgz", + "integrity": "sha512-8CLAX8vlsfsYmtoBxI8YfyZyNZwtUB0FiplEbd8hmo5iv1/52SU2LEU1R6gPk4hkJbqHx22aS8UeZoogPqnmwg==", "dev": true, "dependencies": { "@adonisjs/application": "^5.2.5", @@ -123,6 +123,9 @@ "picomatch": "^2.3.1", "slash": "^3.0.0" }, + "engines": { + "node": ">=14.0.0" + }, "peerDependencies": { "@adonisjs/core": "^5.1.0" } @@ -545,18 +548,18 @@ } }, "node_modules/@eslint-community/regexpp": { - "version": "4.5.1", - "resolved": "https://registry.npmjs.org/@eslint-community/regexpp/-/regexpp-4.5.1.tgz", - "integrity": 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"requires": { "kleur": "^4.1.5", diff --git a/package.json b/package.json index f26c76c..d8830f8 100644 --- a/package.json +++ b/package.json @@ -42,28 +42,28 @@ "printWidth": 100 }, "devDependencies": { - "@adonisjs/assembler": "^5.9.5", + "@adonisjs/assembler": "^5.9.6", "@japa/preset-adonis": "^1.2.0", - "@japa/runner": "^2.5.1", + "@japa/runner": "^3.1.0", "adonis-preset-ts": "^2.1.0", - "eslint": "^8.45.0", - "eslint-config-prettier": "^8.9.0", + "eslint": "^8.55.0", + "eslint-config-prettier": "^9.1.0", "eslint-plugin-adonis": "^2.1.1", - "eslint-plugin-prettier": "^5.0.0", - "pino-pretty": "^10.2.0", - "prettier": "^3.0.0", - "typescript": "~5.1", - "youch": "^3.2.3", - "youch-terminal": "^2.2.2" + "eslint-plugin-prettier": "^5.0.1", + "pino-pretty": "^10.3.0", + "prettier": "^3.1.1", + "typescript": "~5.3", + "youch": "^3.3.3", + "youch-terminal": "^2.2.3" }, "dependencies": { "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", "nmr-load-save": "^0.23.8", - "playwright": "^1.39.0", + "playwright": "^1.40.1", "proxy-addr": "^2.0.7", - "reflect-metadata": "^0.1.13", + "reflect-metadata": "^0.2.0", "source-map-support": "^0.5.21" } } From 97bbc2d4d2a5f31cadcd5ce01d7c1f51df86c716 Mon Sep 17 00:00:00 2001 From: hamed musallam Date: Thu, 14 Dec 2023 12:37:31 +0100 Subject: [PATCH 10/11] feat: update nmr-load-save to version 0.23.11 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index d8830f8..418292c 100644 --- a/package.json +++ b/package.json @@ -60,7 +60,7 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.23.8", + "nmr-load-save": "^0.23.11", "playwright": "^1.40.1", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.2.0", From cdefe1453d0958ad6f539dc4a186f0db91d6c509 Mon Sep 17 00:00:00 2001 From: hamed musallam Date: Thu, 7 Mar 2024 13:44:20 +0100 Subject: [PATCH 11/11] feat: update nmr-load-save to version 0.27.3 --- package-lock.json | 492 ++++++++++++++++++++++++++++------------------ package.json | 4 +- 2 files changed, 300 insertions(+), 196 deletions(-) diff --git a/package-lock.json b/package-lock.json index defd5a4..ada1f3e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,7 +11,7 @@ "@adonisjs/core": "^5.9.0", "@adonisjs/repl": "^3.1.11", "adonis5-swagger": "^1.4.1", - "nmr-load-save": "^0.23.2", + "nmr-load-save": "^0.27.3", "playwright": "^1.39.0", "proxy-addr": "^2.0.7", "reflect-metadata": "^0.1.13", @@ -1263,14 +1263,14 @@ "integrity": "sha512-wOuvG1SN4Us4rez+tylwwwCV1psiNVOkJeM3AUWUNWg/jDQY2+HE/444y5gc+jBmRqASOm2Oeh5c1axHobwRKQ==" }, "node_modules/@types/lodash": { - "version": "4.14.195", - "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.14.195.tgz", - "integrity": "sha512-Hwx9EUgdwf2GLarOjQp5ZH8ZmblzcbTBC2wtQWNKARBSxM9ezRIAUpeDTgoQRAFB0+8CNWXVA9+MaSOzOF3nPg==" + "version": "4.14.202", + "resolved": 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