From 707515aa8360ae2620824934567fcff5b8bb348a Mon Sep 17 00:00:00 2001 From: Steven Kearnes Date: Sun, 3 May 2026 22:08:06 -0400 Subject: [PATCH 1/4] Drop editor in favor of ord-app The Flask-based editor under ord_interface/editor/ has been replaced by the standalone ord-app (https://app.open-reaction-database.org). This removes the editor and everything that existed only to support it. Co-Authored-By: Claude Opus 4.7 (1M context) --- .github/workflows/run_tests.yml | 7 +- README.md | 6 +- app/src/views/contribute/DatasetsView.vue | 86 - app/src/views/contribute/EnumerateView.vue | 138 - app/src/views/contribute/MainContribute.vue | 146 - app/src/views/contribute/UploadView.vue | 102 - copilot/front-end/manifest.yml | 4 +- dump.rdb | Bin 88 -> 0 bytes ord_interface/Dockerfile | 37 +- ord_interface/about.html | 232 - ord_interface/build_test_database.sh | 6 - ord_interface/docker-compose.yml | 2 - ord_interface/editor/README.md | 141 - ord_interface/editor/build.sh | 71 - ord_interface/editor/css/reaction.css | 288 - .../empty.pbtxt | 3 - .../full.pbtxt | 636 - .../ord-nielsen-example.pbtxt | 20061 ---------------- ord_interface/editor/html/dataset.html | 255 - ord_interface/editor/html/datasets.html | 346 - ord_interface/editor/html/login.html | 63 - ord_interface/editor/html/reaction.html | 1225 - ord_interface/editor/html/submissions.html | 65 - ord_interface/editor/html/template.html | 341 - .../editor/img/template-editor-how.png | Bin 43549 -> 0 bytes ord_interface/editor/js/amounts.js | 211 - ord_interface/editor/js/codes.js | 88 - ord_interface/editor/js/compounds.js | 615 - ord_interface/editor/js/conditions.js | 142 - ord_interface/editor/js/crudes.js | 119 - ord_interface/editor/js/data.js | 158 - ord_interface/editor/js/dataset.js | 299 - ord_interface/editor/js/electro.js | 209 - ord_interface/editor/js/enums.js | 62 - ord_interface/editor/js/flow.js | 86 - ord_interface/editor/js/identifiers.js | 115 - ord_interface/editor/js/illumination.js | 82 - ord_interface/editor/js/inputs.js | 284 - ord_interface/editor/js/notes.js | 109 - ord_interface/editor/js/observations.js | 112 - ord_interface/editor/js/outcomes.js | 326 - ord_interface/editor/js/pressure.js | 176 - ord_interface/editor/js/products.js | 633 - ord_interface/editor/js/provenance.js | 196 - ord_interface/editor/js/reaction.js | 349 - ord_interface/editor/js/setups.js | 246 - ord_interface/editor/js/stirring.js | 92 - ord_interface/editor/js/temperature.js | 161 - ord_interface/editor/js/test.js | 109 - ord_interface/editor/js/uploads.js | 175 - ord_interface/editor/js/utils.js | 850 - ord_interface/editor/js/workups.js | 419 - ord_interface/editor/py/migrate.py | 58 - ord_interface/editor/py/serve.py | 991 - ord_interface/editor/py/serve_test.py | 406 - .../editor/py/testdata/nielsen_fig1.csv | 81 - .../py/testdata/nielsen_fig1_dataset.pbtxt | 20035 --------------- .../py/testdata/nielsen_fig1_template.pbtxt | 230 - ord_interface/editor/schema.sql | 58 - ord_interface/interface.py | 37 - ord_interface/nginx.conf | 16 - ord_interface/run_tests.sh | 7 +- ord_interface/start_app.sh | 9 - setup.py | 2 - 64 files changed, 6 insertions(+), 52608 deletions(-) delete mode 100644 app/src/views/contribute/DatasetsView.vue delete mode 100644 app/src/views/contribute/EnumerateView.vue delete mode 100644 app/src/views/contribute/MainContribute.vue delete mode 100644 app/src/views/contribute/UploadView.vue delete mode 100644 dump.rdb delete mode 100644 ord_interface/about.html delete mode 100644 ord_interface/editor/README.md delete mode 100755 ord_interface/editor/build.sh delete mode 100644 ord_interface/editor/css/reaction.css delete mode 100644 ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/empty.pbtxt delete mode 100644 ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt delete mode 100644 ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/ord-nielsen-example.pbtxt delete mode 100644 ord_interface/editor/html/dataset.html delete mode 100644 ord_interface/editor/html/datasets.html delete mode 100644 ord_interface/editor/html/login.html delete mode 100644 ord_interface/editor/html/reaction.html delete mode 100644 ord_interface/editor/html/submissions.html delete mode 100644 ord_interface/editor/html/template.html delete mode 100644 ord_interface/editor/img/template-editor-how.png delete mode 100644 ord_interface/editor/js/amounts.js delete mode 100644 ord_interface/editor/js/codes.js delete mode 100644 ord_interface/editor/js/compounds.js delete mode 100644 ord_interface/editor/js/conditions.js delete mode 100644 ord_interface/editor/js/crudes.js delete mode 100644 ord_interface/editor/js/data.js delete mode 100644 ord_interface/editor/js/dataset.js delete mode 100644 ord_interface/editor/js/electro.js delete mode 100644 ord_interface/editor/js/enums.js delete mode 100644 ord_interface/editor/js/flow.js delete mode 100644 ord_interface/editor/js/identifiers.js delete mode 100644 ord_interface/editor/js/illumination.js delete mode 100644 ord_interface/editor/js/inputs.js delete mode 100644 ord_interface/editor/js/notes.js delete mode 100644 ord_interface/editor/js/observations.js delete mode 100644 ord_interface/editor/js/outcomes.js delete mode 100644 ord_interface/editor/js/pressure.js delete mode 100644 ord_interface/editor/js/products.js delete mode 100644 ord_interface/editor/js/provenance.js delete mode 100644 ord_interface/editor/js/reaction.js delete mode 100644 ord_interface/editor/js/setups.js delete mode 100644 ord_interface/editor/js/stirring.js delete mode 100644 ord_interface/editor/js/temperature.js delete mode 100644 ord_interface/editor/js/test.js delete mode 100644 ord_interface/editor/js/uploads.js delete mode 100644 ord_interface/editor/js/utils.js delete mode 100644 ord_interface/editor/js/workups.js delete mode 100755 ord_interface/editor/py/migrate.py delete mode 100644 ord_interface/editor/py/serve.py delete mode 100644 ord_interface/editor/py/serve_test.py delete mode 100644 ord_interface/editor/py/testdata/nielsen_fig1.csv delete mode 100644 ord_interface/editor/py/testdata/nielsen_fig1_dataset.pbtxt delete mode 100644 ord_interface/editor/py/testdata/nielsen_fig1_template.pbtxt delete mode 100644 ord_interface/editor/schema.sql delete mode 100644 ord_interface/interface.py diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 5d8b6291..41020061 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -55,7 +55,7 @@ jobs: shell: bash -l {0} run: | coverage erase - pytest -vv --cov=ord_interface --durations=20 --ignore=ord_interface/editor + pytest -vv --cov=ord_interface --durations=20 coverage xml - uses: codecov/codecov-action@v1 @@ -64,7 +64,6 @@ jobs: matrix: python-version: ["3.10", "3.11", "3.12"] # NOTE(skearnes): Docker is not supported on macOS GitLab runners. - # NOTE(skearnes): ubuntu-latest AppArmor doesn't play nicely with puppeteer. runs-on: ubuntu-22.04 steps: - uses: actions/checkout@v4 @@ -81,10 +80,6 @@ jobs: python -m pip install --upgrade pip python -m pip install wheel python -m pip install .[tests] - - name: Install non-python test dependencies - run: | - cd "${GITHUB_WORKSPACE}/ord_interface" - npm install puppeteer - name: Run tests run: | cd "${GITHUB_WORKSPACE}/ord_interface" diff --git a/README.md b/README.md index 04d69832..993897b9 100644 --- a/README.md +++ b/README.md @@ -13,9 +13,8 @@ Web interface and api for the Open Reaction Database - **/browse** - Main browse page of the different reaction sets - **/reaction-view** - Display of a single reaction from search results - **/search** - Search interface and results -- **/ord_interface** - Contains the Flask app API and legacy interface - - **/client** - endpoints for the browse and search functionality - - **/editor** - endpoints for the reaction submission functionality +- **/ord_interface** - Contains the FastAPI server + - **/api** - endpoints for the browse and search functionality - **/visualization** - helper functions for reaction and molecule visuals ## Key Caveats / Constraints @@ -49,7 +48,6 @@ pip install -e '.[tests]' # you will need Docker installed on your computer first cd ord_interface ./build_test_database.sh -# If you are running on Apple silicon, append `--build-arg="ARCH=aarch_64"` to the next command. docker build --file Dockerfile -t openreactiondatabase/ord-interface .. docker compose up ``` diff --git a/app/src/views/contribute/DatasetsView.vue b/app/src/views/contribute/DatasetsView.vue deleted file mode 100644 index 5dc612ec..00000000 --- a/app/src/views/contribute/DatasetsView.vue +++ /dev/null @@ -1,86 +0,0 @@ - - - - - - - \ No newline at end of file diff --git a/app/src/views/contribute/EnumerateView.vue b/app/src/views/contribute/EnumerateView.vue deleted file mode 100644 index 333f434f..00000000 --- a/app/src/views/contribute/EnumerateView.vue +++ /dev/null @@ -1,138 +0,0 @@ - - - - - - - \ No newline at end of file diff --git a/app/src/views/contribute/MainContribute.vue b/app/src/views/contribute/MainContribute.vue deleted file mode 100644 index 79eeec5e..00000000 --- a/app/src/views/contribute/MainContribute.vue +++ /dev/null @@ -1,146 +0,0 @@ - - - - - - - \ No newline at end of file diff --git a/app/src/views/contribute/UploadView.vue b/app/src/views/contribute/UploadView.vue deleted file mode 100644 index 0d000444..00000000 --- a/app/src/views/contribute/UploadView.vue +++ /dev/null @@ -1,102 +0,0 @@ - - - - - - - \ No newline at end of file diff --git a/copilot/front-end/manifest.yml b/copilot/front-end/manifest.yml index c75d486a..9d2ff955 100644 --- a/copilot/front-end/manifest.yml +++ b/copilot/front-end/manifest.yml @@ -27,7 +27,7 @@ http: path: '/' # You can specify a custom health check path. The default is "/". healthcheck: - path: '/editor/healthcheck' + path: '/' success_codes: '200,302' # Configuration for your containers and service. @@ -50,8 +50,6 @@ count: # Number of tasks that should be running in your service. response_time: 2s secrets: - GH_CLIENT_ID: /copilot/ord-editor/secrets/GH_CLIENT_ID - GH_CLIENT_SECRET: /copilot/ord-editor/secrets/GH_CLIENT_SECRET POSTGRES_HOST: /copilot/ord-interface/secrets/POSTGRES_HOST POSTGRES_USER: /copilot/ord-interface/secrets/POSTGRES_USER POSTGRES_PASSWORD: /copilot/ord-interface/secrets/POSTGRES_PASSWORD diff --git a/dump.rdb b/dump.rdb deleted file mode 100644 index 5782721c3419eaede62dc89f92cb75983d63b2e3..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 88 zcmWG?b@2=~FfcUy#aWb^l3A= - - - - - - Open Reaction Database - About - - - - - - - - - -
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About

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- The Open Reaction Database (ORD) is an open-access schema and infrastructure for structuring and - sharing organic reaction data, including a centralized data repository. The ORD schema supports - conventional and emerging technologies, from benchtop reactions to automated high-throughput - experiments and flow chemistry. Our vision is that a consistent data representation and - infrastructure to support data sharing will enable downstream applications that will greatly improve - the state of the art with respect to computer-aided synthesis planning, reaction prediction, and - other predictive chemistry tasks. -

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- Since our initial meeting in October 2019, the database has grown to include more than 2M reactions - (including a large dataset of reactions extracted from USPTO sources) and received contributions - from academic and industrial users, both from published and unpublished work. Some of our current - efforts include: -

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  • Improving user interfaces and providing support to contributors on GitHub and via email.
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  • - Working with companies to incorporate the ORD schema into their reaction informatics - infrastructure, including the development of "translators" between the ORD schema and electronic - lab notebooks (ELNs). -
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  • - Engaging with journals and other stakeholders to drive adoption of the ORD schema as a FAIR data structure for sharing reaction - data across academia, government, and industry. -
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- Please reach out to help@open-reaction-database.org for help preparing a contribution or to discuss - using the ORD in your company or lab. -

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Publications and Media

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Journal Articles
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  • - Kearnes SM, Maser MR, Wleklinski M, Kast A, Doyle AG, Dreher SD, Hawkins JM, Jensen KF, Coley - CW. The Open Reaction Database. J Am Chem Soc 2021, 143(45), 18820-18826. (JACS) -
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  • - Mercado R, Kearnes SM, Coley C. Data Sharing in Chemistry: Lessons Learned and a Case for - Mandating Structured Reaction Data. J Chem Inf Model 2023, 63(14), 4253-4265. (JCIM) -
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News
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  • - A new database for machine-learning research (C&EN, - 22 November 2021) -
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  • - Yield-predicting AI needs chemists to stop ignoring failed experiments (Chemistry - World, 12 May 2022) -
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  • - Chemists debate machine learning's future in synthesis planning and ask for open data (C&EN, - 18 May 2022) -
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  • - For chemists, the AI revolution has yet to happen (Nature, 17 May 2023) -
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Leadership

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Governing Committee
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  • Connor Coley (MIT, C-CAS)
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  • Abby Doyle (UCLA, C-CAS)
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  • Spencer Dreher (Merck)
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  • Klavs Jensen (MIT)
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  • Steven Kearnes (Genesis Therapeutics)
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Advisory Board
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  • Alán Aspuru-Guzik (Toronto, MADNESS)
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  • Timothy Cernak (Michigan, Entos)
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  • Lucy Colwell (Cambridge, SynTech, Google)
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  • Werngard Czechtizky (AstraZeneca)
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  • JW Feng
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  • Matthew Gaunt (Cambridge, SynTech)
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  • Alex Godfrey
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  • Mimi Hii (A*STAR, Imperial, ROAR)
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  • Greg Landrum (T5 Informatics)
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  • Fabio Lima (Novartis)
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  • Christos Nicolaou (Novo Nordisk)
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  • Sarah Reisman (Caltech)
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  • Francesco Rianjongdee
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  • Matthew Sigman (Utah, C-CAS)
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  • Jay Stevens (BMS)
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  • Sarah Trice
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  • Huimin Zhao (UIUC, MMLI)
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Support

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We gratefully acknowledge support from:

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  • Google
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  • Relay Therapeutics
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  • Schmidt Futures
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  • University of Notre Dame
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- © Copyright 2023 Open Reaction Database Project Authors -
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- - - diff --git a/ord_interface/build_test_database.sh b/ord_interface/build_test_database.sh index 728267ec..af4969e4 100755 --- a/ord_interface/build_test_database.sh +++ b/ord_interface/build_test_database.sh @@ -33,12 +33,6 @@ while [ $? -ne 0 ]; do done set -e -# Editor. -cd editor -psql -p 5432 -h localhost -U postgres -f schema.sql -python py/migrate.py -cd .. - # Client. psql -p 5432 -h localhost -U postgres -c 'CREATE DATABASE ord;' python client/build_database.py diff --git a/ord_interface/docker-compose.yml b/ord_interface/docker-compose.yml index f3ed14c8..1a540e23 100644 --- a/ord_interface/docker-compose.yml +++ b/ord_interface/docker-compose.yml @@ -26,8 +26,6 @@ services: - POSTGRES_USER=postgres - POSTGRES_PASSWORD=postgres - POSTGRES_DATABASE=ord - - GH_CLIENT_ID=${GH_CLIENT_ID} - - GH_CLIENT_SECRET=${GH_CLIENT_SECRET} image: "openreactiondatabase/ord-interface:latest" ports: - "8080:8080" diff --git a/ord_interface/editor/README.md b/ord_interface/editor/README.md deleted file mode 100644 index 355abc4b..00000000 --- a/ord_interface/editor/README.md +++ /dev/null @@ -1,141 +0,0 @@ -# Reaction Editor - -A [web app](https://editor.open-reaction-database.org/datasets) for browsing, -modifying, and creating submissions to the Open Reaction Database. - -## Getting Started - -``` -$ export ORD_EDITOR_POSTGRES_PASSWORD=######## -$ export ORD_EDITOR_MOUNT=$HOME/ord-editor-postgres -$ docker build -t openreactiondatabase/ord-editor . -$ docker-compose up -``` -That builds the editor, launches it in a container, and points it at a second -container running Postgres where the editor keeps its state. You can see the -editor at [http://localhost:5001/](http://localhost:5001). - -The first time you do this runs, you must initialize the Postgres schema. -``` -psql -p 5432 -h localhost -U postgres -f schema.sql -``` -You may also want to import some data to get started. The migration script -slurps the contents of the db/ directory. -``` -export PGPASSWORD=######## -./py/migrate.py -``` - -## How it Works - -When you load a reaction in the editor, the editor reads the entire dataset -from the server and maps the content of the chosen reaction onto the DOM. When -you save, it reverses the process. Javascript functions called "load..." go -from reaction to DOM, and functions called "unload..." do the reverse. - -Some fields like images are too big to go in the DOM. These fields have type -"bytes". When a bytes field is loaded, the load function creates a random token -for it, puts the token in the DOM element, and saves the bytes data in a table. -The unload function reads back the token and uses it to restore the bytes data. - -You modify a bytes field by uploading a file. Since Javascript does not have -access to files, the model in this case is different. When you save, the bytes -field in the reaction is assigned its token and the file is uploaded in a -separate connection with the same token. The server merges the reaction and its -upload after both are available. - -Really large datasets need to pass both ways on the network every time you save -them, including all their images. - -## Development - -You can get lightweight iterations by compiling and running the editor outside -Docker. - -First install and run Postgres, or start its Docker image with the -"docker-compose" command above. Then set up the editor dependencies below. When -that's done, you can start the editor in a debug mode where modifications to -python or JS can be deployed quickly. -``` -$ make -$ export POSTGRES_PASSWORD=######## -$ export FLASK_ENV=development -$ ./serve.sh --port=5001 -``` -This starts service at [http://localhost:5001/](http://localhost:5001/). - -### Dependencies - -There are several. - -#### ORD-Schema Environment - -You must clone -[https://github.com/Open-Reaction-Database/ord-schema/](ord-schema) to provide -the proto definitions. This repo assumes that both repos share a common parent -directory: -``` - - \-ord-schema - \-ord-editor -``` - -Activate Conda and install the setup.py modules by following the top-level -[instructions](https://github.com/Open-Reaction-Database/ord-schema/blob/main/README.md). - -#### Closure JS Library - -Unpack closure-library in this directory so that Closure can find it too. -``` -$ url=https://github.com/google/closure-library/archive/v20200517.tar.gz -$ wget $url -O - | tar zxf - -``` -The editor has been tested with [Closure -v20200517](https://github.com/google/closure-library/releases/). - -#### Protobuf JS Runtime - -Unpack the archive in the editor directory so the Closure compiler can find it. -``` -$ url=https://github.com/protocolbuffers/protobuf/releases/download/v3.14.0/protobuf-js-3.14.0.tar.gz -$ wget $url -O - | tar zxf - -``` -At the time of writing, [version -3.14.0](https://github.com/protocolbuffers/protobuf/releases/tag/v3.14.0) -matches the protoc compiler in pip's protoc-wheel-0 distribution referenced -from ../requirements.txt. - -#### Ketcher - -Ketcher draws molecule diagrams. First install Node.js and npm -([instructions](https://nodejs.org/en/download/)). Then, in this directory, -``` -$ git clone git@github.com:Open-Reaction-Database/ketcher.git -$ cd ketcher -$ npm install && npm run build -``` - -## Testing and Validation - -There is an end-to-end test that reads a densely populated dataset into the -editor, writes it back out again, and asserts that the proto is unchanged. - -Start the editor as described above and then -``` -$ make test -``` - -The test depends on [Node.js](https://nodejs.org/en/download/) and the -Puppeteer headless Chrome package. -``` -$ npm i puppeteer -``` - -There is also an Abseil test. Start the editor as described above and then -``` -$ export POSTGRES_PASSWORD=######## -python ./py/serve_test.py -``` -Note that this test exercises python code in the test process, not the editor's -Docker container. This test may behave differently from the editor as it -appears in a browser if the two become out of sync. diff --git a/ord_interface/editor/build.sh b/ord_interface/editor/build.sh deleted file mode 100755 index 94991ce1..00000000 --- a/ord_interface/editor/build.sh +++ /dev/null @@ -1,71 +0,0 @@ -#!/bin/bash -# Copyright 2022 Open Reaction Database Project Authors -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -# https://vaneyckt.io/posts/safer_bash_scripts_with_set_euxo_pipefail/ -set -Eeuxo pipefail - -rm -rf gen # Clean up from previous run. -mkdir -p gen/js/ord gen/js/proto/ord -# Compile JS proto wrappers. -# https://github.com/google/closure-library/releases/ -CLOSURE=closure-library-20200517 -# https://raw.githubusercontent.com/google/closure-compiler/master/contrib/externs/jquery-3.3.js -JQUERY_EXTERNS=externs/jquery-3.3.js -# https://github.com/protocolbuffers/protobuf/releases -PROTOBUF=protobuf-3.14.0 -echo "protoc: $(which protoc) $(protoc --version)" -for source in /app/ord-schema/proto/*.proto; do - protoc \ - --experimental_allow_proto3_optional \ - --js_out=binary:gen/js/proto/ord \ - --proto_path=/app \ - "${source}" -done -# Build dataset.js -java -jar node_modules/google-closure-compiler-java/compiler.jar \ - js/*.js \ - gen/js/proto/ord/*.js \ - "${PROTOBUF}"/js/*.js \ - "${PROTOBUF}"/js/binary/*.js \ - "${CLOSURE}"/closure/goog/*.js \ - "${CLOSURE}"/closure/goog/*/*.js \ - "${CLOSURE}"/closure/goog/labs/*/*.js \ - --externs="${JQUERY_EXTERNS}" \ - --entry_point=ord.dataset \ - --js_output_file=gen/js/ord/dataset.js \ - --dependency_mode=PRUNE \ - --jscomp_error="*" \ - --hide_warnings_for="${CLOSURE}" \ - --hide_warnings_for="${PROTOBUF}" \ - --hide_warnings_for=gen/js/proto/ord \ - || (rm -f gen/js/ord/dataset.js && false) -# Build reaction.js -java -jar node_modules/google-closure-compiler-java/compiler.jar \ - js/*.js \ - gen/js/proto/ord/*.js \ - "${PROTOBUF}"/js/*.js \ - "${PROTOBUF}"/js/binary/*.js \ - "${CLOSURE}"/closure/goog/*.js \ - "${CLOSURE}"/closure/goog/*/*.js \ - "${CLOSURE}"/closure/goog/labs/*/*.js \ - --externs="${JQUERY_EXTERNS}" \ - --entry_point=ord.reaction \ - --js_output_file=gen/js/ord/reaction.js \ - --dependency_mode=PRUNE \ - --jscomp_error="*" \ - --hide_warnings_for="${CLOSURE}" \ - --hide_warnings_for="${PROTOBUF}" \ - --hide_warnings_for=gen/js/proto/ord \ - || (rm -f gen/js/ord/reaction.js && false) diff --git a/ord_interface/editor/css/reaction.css b/ord_interface/editor/css/reaction.css deleted file mode 100644 index c2d59bfd..00000000 --- a/ord_interface/editor/css/reaction.css +++ /dev/null @@ -1,288 +0,0 @@ -/** - * Copyright 2020 Open Reaction Database Project Authors - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -:root { - --body-width: 968px; -} - -body { - padding: 100px 20px 20px; - width: var(--body-width); - margin: auto; -} -#pageLoad { - text-align: center; -} -#sections { - margin-left: 168px; - width: 800px; -} -.edittext, .selector, .optional_bool, .selector_style { - margin: 2px; - display: inline-block; -} -.edittext { - padding: 0 2px; -} -button { - font-size: small; - border: 1px solid black; - vertical-align: middle; -} -.button-lg { - font-size: medium; -} -.edittext { - width: 200px; - height: auto; - min-height: 20px; - border: 1px solid #c0c0c0; - white-space: pre-wrap; -} -.shorttext { - width: 75px; -} -.veryshorttext { - width: 25px; -} -.paratext { - height: 100px; - width: 400px; - max-height: 200px; - overflow-y: scroll; - word-break: break-all; - vertical-align: bottom; -} -.longtext { - width: 400px; - max-height: 75px; - overflow-y: scroll; - vertical-align: bottom; -} -.invalid { - border: 2px solid red; -} -.validate_status, .validate_message, .validate_warning_status, .validate_warning_message { - padding: 2px 4px; - margin: 2px; - display: inline-block; -} -.validate { - display: inline-block; - font-size: medium; - vertical-align: middle; -} -.validate_status { - color: #ff4444; - display: none; -} -.validate_warning_status { - color: #ffbb33; - display: none; -} -.validate_message, .validate_warning_message { - position: absolute; - z-index: 2; - visibility: hidden; - max-width: 500px; -} -.validate_message { - background-color: pink; -} -.validate_warning_message { - background-color: #FAFAD2; -} -.spacer { - height: 24px; -} -fieldset { - margin-top: 24px; - margin-inline-start: 2px; - margin-inline-end: 2px; - padding-block-start: 0.35em; - padding-inline-start: 0.75em; - padding-inline-end: 0.75em; - padding-block-end: 0.625em; - min-inline-size: min-content; - border-width: 2px; -} -#header { - background: white; - border: black 1px; - border-style: none none solid none; - padding: 10px 0; - position: fixed; - top: 0; - width: var(--body-width); - z-index: 1; -} -.section { - scroll-margin-top: 120px; - margin-top: 48px; -} -#nav { - margin-top: 10px; - margin-right: 26px; - position: fixed; - width: 150px; -} -.navSection { - padding: 8px; - margin-bottom: 4px; - cursor: pointer; -} -.inputNavSection { - padding: 8px; - margin-bottom: 4px; - cursor: pointer; - font-size: 90%; - border-width: 0 0 0 10px; - border-style: solid; - border-color: white; - background-clip: padding-box; -} -.navSection:hover, .inputNavSection:hover { - background-color: lightblue; -} -.data_uploader .adder { - width: 208px; - display: inline-block; - padding-left: 2px; - position: relative; -} -.data_uploader_text { - display: inline-block; - border: 1px solid #c0c0c0; - height: 21px; -} -.data_uploader_chooser_file { - opacity: 0; - position: absolute; - width: 100px; -} -.data_uploader_file_name { - min-width: 99px; - overflow-x: visible; - vertical-align: bottom -} -.data_uploader_file_retrieve { - width: 100px; - border: none; - cursor: pointer; - color:blue; - text-decoration:underline; -} -.input_name_label { - padding-right: 4px; -} -/* Default hidden fields */ -.amount_includes_solutes, -.amount_includes_solutes_label, -#automation_platform, -.limiting_reactant, -.component_compound_preparation_reaction_id { - display: none; -} - -.amount_includes_solutes_label { - padding-left: 4px; - padding-top: 4px; -} - -#ketcher-iframe { - width: 800px; - height: 432px; - border-width: 0; -} - -/* Extra custom stylings for Ketcher. */ -#ketcher-spinner { - position: absolute; - z-index: 1; - top: 0; - bottom: 0; - left: 0; - right: 0; - overflow: auto; - margin: auto; - width: 50px; - height: 50px; -} -#process { - display: none; -} -#identity { - float: right; - align-items: center; -} -#identity img { - height: 24px; - width: 24px; - margin-right: 8px; - border-radius: 12px; -} -#login { - padding: 10px; - border-style: solid; - border-color: lightgray; - border-radius: 30px; - cursor: pointer; - width: fit-content; - display: flex; -} -#login:hover { - border-color: black; -} -.s2 { - border: none; -} -.s3 { - border-style: none none none solid; - border-color: #e6e6e6; -} -.s4 { - border-style: none none none solid; - border-color: #d6d6d6; -} -.s5 { - border-style: none none none solid; - border-color: #c6c6c6; -} -.product_measurement_section { - padding-top: 20px; -} -#reaction_id { - display: inline-block; - font-family: monospace; - font-size: large; -} -.spacer { - width: 10px; -} -.remove, .text_upload, .help { - border: none; - background-color: unset; - font-size: medium; -} -.reaction_identifier_value { - width: auto; - min-width: 200px; - max-width: 800px; -} -.optional { - display: block; - margin: 8px 0; -} diff --git a/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/empty.pbtxt b/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/empty.pbtxt deleted file mode 100644 index 6d028678..00000000 --- a/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/empty.pbtxt +++ /dev/null @@ -1,3 +0,0 @@ -reactions { - reaction_id: "test" -} diff --git a/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt b/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt deleted file mode 100644 index 0ede50e0..00000000 --- a/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt +++ /dev/null @@ -1,636 +0,0 @@ -name: "1" -description: "2" -reactions { - identifiers { - type: REACTION_TYPE - details: "2" - value: "1" - } - identifiers { - type: REACTION_SMILES - details: "3" - value: "123\n" - } - inputs { - key: "4" - value { - components { - identifiers { - type: SMILES - details: "6" - value: "5" - } - amount { - volume { - value: 7.0 - precision: 8.0 - units: LITER - } - volume_includes_solutes: true - } - reaction_role: REACTANT - is_limiting: true - preparations { - type: REPURIFIED - details: "9" - reaction_id: "9.5" - } - source { - vendor: "10" - catalog_id: "11" - lot: "12" - } - features { - key: "13" - value { - float_value: 14.0 - description: "15" - format: "txt" - } - } - } - crude_components { - reaction_id: "15.25" - includes_workup: true - has_derived_amount: false - amount { - volume { - value: 15.5 - precision: 15.75 - units: MICROLITER - } - } - } - addition_order: 16 - addition_time { - value: 19.0 - precision: 20.0 - units: HOUR - } - addition_speed { - type: ALL_AT_ONCE - details: "17" - } - addition_duration { - value: 21.0 - precision: 22.0 - units: MINUTE - } - flow_rate { - value: 23.0 - precision: 24.0 - units: MICROLITER_PER_MINUTE - } - addition_device { - type: SYRINGE - details: "18" - } - addition_temperature { - value: 23.0 - precision: 24.0 - units: FAHRENHEIT - } - } - } - inputs { - key: "5" - value { - addition_order: 93 - addition_time { - value: 96.0 - precision: 97.0 - units: MINUTE - } - addition_speed { - type: DROPWISE - details: "94" - } - addition_duration { - value: 98.0 - precision: 99.0 - units: SECOND - } - flow_rate { - value: 100.0 - precision: 101.0 - units: MICROLITER_PER_MINUTE - } - addition_device { - type: CANNULA - details: "95" - } - addition_temperature { - value: 100.0 - precision: 101.0 - units: CELSIUS - } - } - } - setup { - vessel { - type: ROUND_BOTTOM_FLASK - details: "25" - material { - type: POLYPROPYLENE - details: "26" - } - preparations { - type: EVACUATED_BACKFILLED - details: "31" - } - attachments { - type: CAP - details: "32" - } - volume { - value: 27.0 - precision: 28.0 - units: MILLILITER - } - } - is_automated: true - automation_platform: "29" - automation_code { - key: "33" - value { - integer_value: 34 - description: "35" - format: "36" - } - } - environment { - type: FUME_HOOD - details: "30" - } - } - conditions { - temperature { - control { - type: DRY_ALUMINUM_PLATE - details: "37" - } - setpoint { - value: 38.0 - precision: 39.0 - units: KELVIN - } - measurements { - type: THERMOCOUPLE_INTERNAL - details: "44" - time { - value: 42.0 - precision: 43.0 - units: HOUR - } - temperature { - value: 40.0 - precision: 41.0 - units: CELSIUS - } - } - } - pressure { - control { - type: PRESSURIZED - details: "45" - } - setpoint { - value: 46.0 - precision: 47.0 - units: ATMOSPHERE - } - atmosphere { - type: CARBON_MONOXIDE - details: "48" - } - measurements { - type: PRESSURE_TRANSDUCER - details: "53" - time { - value: 51.0 - precision: 52.0 - units: SECOND - } - pressure { - value: 49.0 - precision: 50.0 - units: PASCAL - } - } - } - stirring { - type: OVERHEAD_MIXER - details: "54" - rate { - type: MEDIUM - details: "55" - rpm: 56 - } - } - illumination { - type: DEUTERIUM_LAMP - details: "57" - peak_wavelength { - value: 58.0 - precision: 59.0 - units: NANOMETER - } - color: "62" - distance_to_vessel { - value: 60.0 - precision: 61.0 - units: FOOT - } - } - electrochemistry { - type: CONSTANT_VOLTAGE - details: "63" - current { - value: 64.0 - precision: 65.0 - units: MILLIAMPERE - } - voltage { - value: 66.0 - precision: 67.0 - units: VOLT - } - anode_material: "68" - cathode_material: "69" - electrode_separation { - value: 70.0 - precision: 71.0 - units: MILLIMETER - } - cell { - type: DIVIDED_CELL - details: "72" - } - } - flow { - type: PLUG_FLOW_REACTOR - details: "73" - pump_type: "74" - tubing { - type: COPPER - details: "75" - diameter { - value: 76.0 - precision: 77.0 - units: MILLIMETER - } - } - } - reflux: true - ph: 78.0 - conditions_are_dynamic: false - details: "79" - } - notes { - is_heterogeneous: true - forms_precipitate: false - offgasses: true - is_sensitive_to_moisture: false - is_sensitive_to_light: true - safety_notes: "80" - procedure_details: "81" - } - observations { - time { - value: 82.0 - precision: 83.0 - units: SECOND - } - comment: "87" - image { - url: "84" - description: "85" - format: "86" - } - } - workups { - type: FILTRATION - details: "92" - duration { - value: 90.0 - precision: 91.0 - units: HOUR - } - input { - addition_order: 93 - addition_time { - value: 96.0 - precision: 97.0 - units: MINUTE - } - addition_speed { - type: DROPWISE - details: "94" - } - addition_duration { - value: 98.0 - precision: 99.0 - units: SECOND - } - flow_rate { - value: 100.0 - precision: 101.0 - units: MICROLITER_PER_MINUTE - } - addition_device { - type: CANNULA - details: "95" - } - addition_temperature { - value: 100.0 - precision: 101.0 - units: KELVIN - } - } - amount { - volume { - value: 123.0 - precision: 0.5 - units: MILLILITER - } - } - temperature { - control { - type: OIL_BATH - details: "104" - } - setpoint { - value: 102.0 - precision: 103.0 - units: FAHRENHEIT - } - measurements { - type: INFRARED - details: "109" - time { - value: 105.0 - precision: 106.0 - units: HOUR - } - temperature { - value: 107.0 - precision: 108.0 - units: CELSIUS - } - } - } - keep_phase: "88" - stirring { - type: OVERHEAD_MIXER - details: "110" - rate { - type: HIGH - details: "111" - rpm: 112 - } - } - target_ph: 89.0 - is_automated: true - } - outcomes { - reaction_time { - value: 113.0 - precision: 114.0 - units: SECOND - } - conversion { - value: 115.0 - precision: 116.0 - } - products { - identifiers { - type: IUPAC_NAME - details: "116.2" - value: "116.1" - } - identifiers { - type: NAME - details: "Name of this compound" - value: "DMSO" - } - identifiers { - type: SMILES - details: "NAME resolved by the PubChem API" - value: "CS(C)=O" - } - is_desired_product: true - measurements { - analysis_key: "analysis1" - type: YIELD - details: "analysis1_details" - uses_internal_standard: true - is_normalized: true - uses_authentic_standard: false - percentage { - value: 117.0 - precision: 118.0 - } - mass_spec_details { - type: EIC - eic_masses: 1.2 - eic_masses: 3.4 - eic_masses: 5.6 - } - selectivity { - type: ZE - details: "123" - } - } - measurements { - analysis_key: "analysis1" - type: PURITY - details: "analysis details here" - uses_internal_standard: true - is_normalized: false - uses_authentic_standard: true - authentic_standard { - identifiers { - type: NAME - details: "Name of this compound" - value: "DBU" - } - identifiers { - type: SMILES - details: "NAME resolved by the PubChem API" - value: "C1CCC2=NCCCN2CC1" - } - reaction_role: AUTHENTIC_STANDARD - } - percentage { - value: 119.0 - precision: 120.0 - } - } - measurements { - analysis_key: "analysis1" - type: AMOUNT - details: "more details here" - uses_internal_standard: false - is_normalized: true - uses_authentic_standard: false - amount { - mass { - value: 116.25 - precision: 116.375 - units: GRAM - } - } - } - measurements { - type: YIELD - details: "explicit zero yield" - percentage { - value: 0.0 - } - } - measurements { - type: PURITY - details: "even more details" - percentage { - value: 987.6 - precision: 543.2 - } - wavelength { - value: 24.0 - precision: 34.0 - units: NANOMETER - } - } - measurements { - type: SELECTIVITY - details: "try a string value" - string_value: "this is a string" - } - measurements { - analysis_key: "analysis1" - type: CUSTOM - details: "all the fields are present" - uses_internal_standard: false - is_normalized: false - uses_authentic_standard: false - retention_time { - value: 1.0 - precision: 2.0 - units: MINUTE - } - mass_spec_details { - type: TIC - details: "mass spec details" - tic_minimum_mz: 1.23 - tic_maximum_mz: 4.56 - eic_masses: 1.0 - eic_masses: 3.0 - eic_masses: 4.0 - eic_masses: -34.0 - eic_masses: 3.0 - } - selectivity { - type: EE - details: "very selective" - } - wavelength { - value: 3.0 - precision: 4.0 - units: WAVENUMBER - } - } - isolated_color: "124" - texture { - type: POWDER - details: "125" - } - features { - key: "116.5" - value { - float_value: 116.625 - description: "116.7" - } - } - reaction_role: PRODUCT - } - analyses { - key: "analysis1" - value { - type: NMR_13C - details: "132" - chmo_id: 131 - is_of_isolated_species: true - data { - key: "135" - value { - url: "136" - description: "137" - format: "138" - } - } - data { - key: "139" - value { - float_value: 140.0 - description: "141" - format: "142" - } - } - data { - key: "byte_data" - value { - bytes_value: "bytestring" - } - } - instrument_manufacturer: "133" - instrument_last_calibrated { - value: "134" - } - } - } - } - provenance { - experimenter { - username: "144" - name: "143" - orcid: "145" - organization: "146" - email: "foo@example.com" - } - city: "147" - experiment_start { - value: "148" - } - doi: "149" - patent: "150" - publication_url: "151" - record_created { - time { - value: "152" - } - person { - username: "153" - name: "154" - orcid: "155" - organization: "156" - email: "foo@example.com" - } - details: "157" - } - record_modified { - time { - value: "158" - } - person { - username: "159" - name: "160" - orcid: "161" - organization: "162" - email: "foo@example.com" - } - details: "163" - } - } - reaction_id: "full reaction" -} -dataset_id: "3" diff --git a/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/ord-nielsen-example.pbtxt b/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/ord-nielsen-example.pbtxt deleted file mode 100644 index beafad67..00000000 --- a/ord_interface/editor/db/680b0d9fe649417cb092d790907bd5a5/ord-nielsen-example.pbtxt +++ /dev/null @@ -1,20061 +0,0 @@ -name: "Deoxyfluorination screen" -description: "Reactions from Figure 1 of DOI: 10.1021/jacs.8b01523" -reactions { - identifiers { - type: REACTION_TYPE - value: "deoxyfluorination" - } - inputs { - key: "KNOWN FAILURE; see https://github.com/open-reaction-database/ord-schema/issues/672" - value { - components { - identifiers { - type: NAME - value: "titanium(V) ethoxide" - } - identifiers { - type: SMILES - value: "[O-]CC.[Ti+5].[O-]CC.[O-]CC.[O-]CC.[O-]CC" - } - identifiers { - type: INCHI - value: "InChI=1S/5C2H5O.Ti/c5*1-2-3;/h5*2H2,1H3;/q5*-1;+5" - } - amount { - volume { - value: 3.58 - units: MILLILITER - } - } - reaction_role: CATALYST - } - } - } - inputs { - key: "alcohol in THF" - value { - components { - identifiers { - type: SMILES - value: "c1ccccc1CCC(O)C" - } - amount { - moles { - value: 0.1 - units: MILLIMOLE - } - } - reaction_role: REACTANT - is_limiting: true - } - components { - identifiers { - type: NAME - value: "THF" - } - identifiers { - type: SMILES - value: "C1CCCO1" - } - amount { - volume { - value: 125.0 - units: MICROLITER - } - } - reaction_role: SOLVENT - preparations { - type: DRIED - } - } - addition_order: 1 - } - } - inputs { - key: "base" - value { - components { - identifiers { - type: SMILES - value: "N\\2=C1\\N(CCCCC1)CCC/2" - } - identifiers { - type: NAME - value: "DBU" - } - amount { - moles { - value: 0.15 - units: MILLIMOLE - } - } - reaction_role: REAGENT - source { - vendor: "Millipore-Sigma" - } - } - addition_order: 3 - } - } - inputs { - key: "sulfonyl fluoride" - value { - components { - identifiers { - type: SMILES - value: "Clc1ccc(S(=O)(=O)F)cc1" - } - amount { - moles { - value: 0.11 - units: MILLIMOLE - } - } - reaction_role: REACTANT - } - components { - identifiers { - type: NAME - value: "THF" - } - identifiers { - type: SMILES - value: "C1CCCO1" - } - amount { - volume { - value: 125.0 - units: MICROLITER - } - } - reaction_role: SOLVENT - preparations { - type: DRIED - } - } - addition_order: 2 - } - } - setup { - vessel { - type: VIAL - material { - type: GLASS - } - attachments { - type: CAP - } - volume { - value: 1.0 - units: MILLILITER - } - } - is_automated: false - } - conditions { - temperature { - control { - type: AMBIENT - } - } - pressure { - control { - type: SEALED - } - atmosphere { - type: AIR - } - } - stirring { - type: STIR_BAR - rate { - type: HIGH - rpm: 600 - } - } - } - workups { - type: ADDITION - input { - components { - identifiers { - type: SMILES - value: "C1=CC=C2C(=C1)C=CC=C2F" - } - identifiers { - type: NAME - value: "1-fluoronaphthalene" - } - amount { - moles { - value: 0.1 - units: MILLIMOLE - } - } - reaction_role: INTERNAL_STANDARD - } - components { - identifiers { - type: NAME - value: "chloroform" - } - identifiers { - type: SMILES - value: "ClC(Cl)Cl" - } - amount { - volume { - value: 250.0 - units: MICROLITER - } - } - reaction_role: WORKUP - } - } - } - outcomes { - reaction_time { - value: 48.0 - units: HOUR - } - products { - identifiers { - type: SMILES - value: "c1ccccc1CCC(F)C" - } - is_desired_product: true - measurements { - analysis_key: "19f nmr of crude" - type: YIELD - uses_internal_standard: true - percentage { - value: 40.0 - precision: 4.8 - } - } - measurements { - analysis_key: "19f nmr of crude" - type: IDENTITY - } - } - analyses { - key: "19f nmr of crude" - value { - type: NMR_OTHER - details: "19F NMR using 1 equiv 1-fluoronaphthalene in 250 uL chloroform as internal standard" - 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Coley" - orcid: "0000-0002-8271-8723" - organization: "MIT" - email: "ccoley@mit.edu" - } - } - record_modified { - time { - value: "2021-02-25 08:49:31.467522" - } - person { - username: "skearnes" - email: "kearnes@google.com" - } - details: "Automatic migration from schema v0.2.15 to v0.3.0" - } - } - reaction_id: "test_reaction-78" -} -reactions { - identifiers { - type: REACTION_TYPE - value: "deoxyfluorination" - } - inputs { - key: "alcohol in THF" - value { - components { - identifiers { - type: SMILES - value: "O[C@H]1C[C@@H](C(OC)=O)N(C(OC(C)(C)C)=O)C1" - } - amount { - moles { - value: 0.1 - units: MILLIMOLE - } - } - reaction_role: REACTANT - is_limiting: true - } - components { - identifiers { - type: NAME - value: "THF" - } - identifiers { - type: SMILES - value: "C1CCCO1" - } - amount { - volume { - value: 125.0 - units: MICROLITER - } - } - reaction_role: SOLVENT - preparations { - type: DRIED - } - } - addition_order: 1 - } - } - inputs { - key: "base" - value { - components { - identifiers { - type: SMILES - value: "CC(C)(C)N=P(N1CCCC1)(N2CCCC2)N3CCCC3" - } - identifiers { - type: NAME - value: "BTPP" - } - amount { - moles { - value: 0.15 - units: MILLIMOLE - } - } - reaction_role: REAGENT - source { - vendor: "Millipore-Sigma" - } - } - addition_order: 3 - } - } - inputs { - key: "sulfonyl fluoride" - value { - components { - identifiers { - type: SMILES - value: "C(C(C(F)(F)S(=O)(=O)F)(F)F)(C(F)(F)F)(F)F" - } - amount { - moles { - value: 0.11 - units: MILLIMOLE - } - } - reaction_role: REACTANT - source { - vendor: "Acros" - } - } - components { - identifiers { - type: NAME - value: "THF" - } - identifiers { - type: SMILES - value: "C1CCCO1" - } - amount { - volume { - value: 125.0 - units: MICROLITER - } - } - reaction_role: SOLVENT - preparations { - type: DRIED - } - } - addition_order: 2 - } - } - setup { - vessel { - type: VIAL - material { - type: GLASS - } - attachments { - type: CAP - } - volume { - value: 1.0 - units: MILLILITER - } - } - is_automated: false - } - conditions { - temperature { - control { - type: AMBIENT - } - } - pressure { - control { - type: SEALED - } - atmosphere { - type: AIR - } - } - stirring { - type: STIR_BAR - rate { - type: HIGH - rpm: 600 - } - } - } - workups { - type: ADDITION - input { - components { - identifiers { - type: SMILES - value: "C1=CC=C2C(=C1)C=CC=C2F" - } - identifiers { - type: NAME - value: "1-fluoronaphthalene" - } - amount { - moles { - value: 0.1 - units: MILLIMOLE - } - } - reaction_role: INTERNAL_STANDARD - } - components { - identifiers { - type: NAME - value: "chloroform" - } - identifiers { - type: SMILES - value: "ClC(Cl)Cl" - } - amount { - volume { - value: 250.0 - units: MICROLITER - } - } - reaction_role: WORKUP - } - } - } - outcomes { - reaction_time { - value: 48.0 - units: HOUR - } - products { - identifiers { - type: SMILES - value: "F[C@H]1C[C@@H](C(OC)=O)N(C(OC(C)(C)C)=O)C1" - } - is_desired_product: true - measurements { - analysis_key: "19f nmr of crude" - type: YIELD - uses_internal_standard: true - percentage { - value: 58.0 - precision: 4.8 - } - } - measurements { - analysis_key: "19f nmr of crude" - type: IDENTITY - } - } - analyses { - key: "19f nmr of crude" - value { - type: NMR_OTHER - details: "19F NMR using 1 equiv 1-fluoronaphthalene in 250 uL chloroform as internal standard" - instrument_manufacturer: "Bruker" - } - } - } - provenance { - city: "Princeton, NJ" - doi: "10.1021/jacs.8b01523" - publication_url: "https://pubs.acs.org/doi/10.1021/jacs.8b01523" - record_created { - time { - value: "11/28/2020, 12:02:10" - } - person { - name: "Connor W. Coley" - orcid: "0000-0002-8271-8723" - organization: "MIT" - email: "ccoley@mit.edu" - } - } - record_modified { - time { - value: "2021-02-25 08:49:31.472679" - } - person { - username: "skearnes" - email: "kearnes@google.com" - } - details: "Automatic migration from schema v0.2.15 to v0.3.0" - } - } - reaction_id: "test_reaction-79" -} -dataset_id: "test_dataset" diff --git a/ord_interface/editor/html/dataset.html b/ord_interface/editor/html/dataset.html deleted file mode 100644 index 955d4016..00000000 --- a/ord_interface/editor/html/dataset.html +++ /dev/null @@ -1,255 +0,0 @@ - - - - - - - - - - - - - - {{ name }} Reactions - - - - - - - - - - -
- - - - - - - - - - - - - -
name -
-
ID -
-
description -
-
-
- -
-
- Reactions -
- -
- -
-
- -
-
- Reaction IDs -
- -
- -
-
- -
-
- © Copyright 2022 Open Reaction Database Project Authors -
-
- - - diff --git a/ord_interface/editor/html/datasets.html b/ord_interface/editor/html/datasets.html deleted file mode 100644 index d0e13c9a..00000000 --- a/ord_interface/editor/html/datasets.html +++ /dev/null @@ -1,346 +0,0 @@ - - - - - - - - Open Reaction Database - Interactive Editor - - - - - - - - - - - - - - - -
-
-
{{ user_name }}
- {% if client_id %} -
- -
- - Sign in with GitHub -
-
- - {% endif %} -
-
-
- -
- - - - -
-
-

Getting started

-

Check out the tutorial - videos.

-

- Please send questions, comments, or issues to - help@open-reaction-database.org - or create a new issue on the - ord-interface GitHub - repository - . -

-
-
- -
-
- © Copyright 2022 Open Reaction Database Project Authors -
-
- - - - \ No newline at end of file diff --git a/ord_interface/editor/html/login.html b/ord_interface/editor/html/login.html deleted file mode 100644 index b22a464d..00000000 --- a/ord_interface/editor/html/login.html +++ /dev/null @@ -1,63 +0,0 @@ - - - - - Login - - - - -
-
- - Sign in with GitHub -
-
- - - diff --git a/ord_interface/editor/html/reaction.html b/ord_interface/editor/html/reaction.html deleted file mode 100644 index 639020e0..00000000 --- a/ord_interface/editor/html/reaction.html +++ /dev/null @@ -1,1225 +0,0 @@ - - - - - - - - - - - - - {{ reaction_id }} - - - - - - - - - - - - -
- -
-
-
- -
- - - Identifiers - - -
- -
- -
- - - Inputs - - -
- - - - - - - - - - - - - -
- - -
- -
- - - - Setup -
- - - - - - - - -
vessel
- details
material
- details
volume
- ±
-
-
automated
platform
environment
- details
-
- -
- -
- - - Vessel Preparations - -
- -
- -
-
- - - Vessel Attachments - -
- -
- -
-
- -
- - - Conditions -
- - - - - - -
reflux
pH
dynamic conditions - -
details - -
-
- - - Temperature -
- - - - -
control
- details
setpoint
- ±
-
-
-
- -
- -
-
- - - Stirring -
- - - - - -
method
- details
rate
- details
rpm
-
- - - - - - - - -
- -
- - - Notes -
- - - - - - - - - - - -
is heterogeneous
forms precipitate
is exothermic
offgasses
moisure sensitive
oxygen sensitive
light sensitive
safety notes
procedure details
-
- -
- - - Observations - - -
- -
- -
- -
- - - Workups - - -
- -
- -
- -
- - - Outcomes - - - -
- - - - - - - - - -
- -
- -
- - - Provenance - -
- -
- - - - - - - - - - - -
experimenter name
email
username
orcid
organization
city
experiment start
doi
patent
publication_url
-
-
-
- - - Record creation - - - - - - - - - - -
time -
- -
username
name
email
orcid
organization
details
-
-
-
- -
- -
-
- - - - - - - - - - - - - - - diff --git a/ord_interface/editor/html/submissions.html b/ord_interface/editor/html/submissions.html deleted file mode 100644 index c8679348..00000000 --- a/ord_interface/editor/html/submissions.html +++ /dev/null @@ -1,65 +0,0 @@ - - - - - -
-

Open pull requests

-
-sync - - - - - - - - - - {% for (number, title), names in pull_requests.items() %} - - - - - - {% endfor %} - -
NumberTitleDatasets
- {{ number }} - {{ title }} - {% for short_name, name in names %} - - {% endfor %} -
- - diff --git a/ord_interface/editor/html/template.html b/ord_interface/editor/html/template.html deleted file mode 100644 index 54fad4d1..00000000 --- a/ord_interface/editor/html/template.html +++ /dev/null @@ -1,341 +0,0 @@ - - - - - ORD Template Editor - - - - - -
- Create a template for a large factorial dataset. Read about templates at - - - https://docs.open-reaction-database.org/en/latest/guides/templates.html - -

- 1) Define a reaction in the Editor and export it using the "download" button. -

- 2) Import the reaction here using the "Choose File" button. -

- 3) Click on the fields that vary. You can give a name to each one if you like. -

- 4) Download your template using the "download" button on this page. -

- If you make a mistake, click the field's label (left of the name) to revert it. -

- - - -
- 
-
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    '); - for (let index = 0; index < errors.length; index++) { - const error = errors[index]; - const errorNode = $('
  • '); - errorNode.text(error); - $('ul', messageNode).append(errorNode); - } - } else { - statusNode.hide(); - messageNode.html(''); - messageNode.hide(); - } - const warningStatusNode = $('.validate_warning_status', validateNode); - const warningMessageNode = $('.validate_warning_message', validateNode); - if (warnings.length) { - warningStatusNode.show(); - warningStatusNode.text(' ' + warnings.length); - warningMessageNode.show(); - warningMessageNode.html('
      '); - for (let index = 0; index < warnings.length; index++) { - const warning = warnings[index]; - const warningNode = $('
    • '); - warningNode.text(warning); - $('ul', warningMessageNode).append(warningNode); - } - } else { - warningStatusNode.hide(); - warningMessageNode.html(''); - warningMessageNode.hide(); - } - }; - xhr.send(binary); -} - -/** - * Toggles the visibility of the 'validate' button for a given node. - * @param {!jQuery} target - */ -function toggleValidateMessage(target) { - switch (target.css('visibility')) { - case 'visible': - target.css('visibility', 'hidden'); - break; - case 'hidden': - target.css('visibility', 'visible'); - break; - } -} - -/** - * Downloads a dataset as a serialized Dataset proto. - * @param {string} fileName The name of the dataset to fetch. - * @return {!Promise} - */ -function getDataset(fileName) { - return new Promise(resolve => { - const xhr = new XMLHttpRequest(); - xhr.open('GET', session.root + 'dataset/proto/read/' + fileName); - xhr.responseType = 'arraybuffer'; - xhr.onload = function() { - asserts.assertInstanceof(xhr.response, ArrayBuffer); // Type hint. - const bytes = new Uint8Array(xhr.response); - const dataset = Dataset.deserializeBinary(bytes); - resolve(dataset); - }; - xhr.send(); - }); -} - -/** - * Uploads a serialized Dataset proto. - * @param {string} fileName The name of the new dataset. - * @param {!Dataset} dataset - */ -function putDataset(fileName, dataset) { - $('#save').text('saving'); - const xhr = new XMLHttpRequest(); - xhr.open('POST', session.root + 'dataset/proto/write/' + fileName); - const binary = dataset.serializeBinary(); - xhr.onload = clean; - xhr.send(binary); -} - -/** - * Compares a local Dataset to a Dataset on the server (used for testing). - * @param {string} fileName The name of a dataset on the server. - * @param {!Dataset} dataset A local Dataset. - * @return {!Promise} - */ -async function compareDataset(fileName, dataset) { - return new Promise((resolve, reject) => { - const xhr = new XMLHttpRequest(); - xhr.open('POST', session.root + 'dataset/proto/compare/' + fileName); - const binary = dataset.serializeBinary(); - xhr.onload = () => { - if (xhr.status === 200) { - resolve(); - } else { - reject(); - } - }; - xhr.onerror = reject; - xhr.send(binary); - }); -} - -/** - * Checks if the argument represents an empty protobuf message (that is, the - * argument's nested arrays only contains null or empty values), or is null or - * undefined. We use this check on both primitives and arrays/messages. - * NOTE: Unlike other primitive types, using a setter to set a oneof string - * field to “” causes the message to include the field and “”, which would be - * unwanted. So we instead claim that empty strings are empty messages. (Hence - * we don’t set _any_ empty string.) - * NOTE: In a submessage, setting a meaningful value (e.g. optional float to 0) - * will result in a non-null/undefined value in the submessage array. So, if - * the array of a submessage only contains null and undefined vals, we can - * assume that the message is truly “empty” (that is, doesn’t have anything - * meaningful that is set) and can be omitted when constructing the surrounding - * message. - * @param {!Message} obj The object to test. - * @return {boolean} Whether the message is empty. - * - * NOTE(kearnes): serializeBinary is not defined in the base class. - * @suppress {missingProperties} - */ -function isEmptyMessage(obj) { - const empty = new obj.constructor(); - // Compare binary encodings to cover optional fields. - return JSON.stringify(obj.serializeBinary()) === - JSON.stringify(empty.serializeBinary()); -} - -/** - * Supports unload() operations by filtering spurious selector matches due - * either to DOM templates or elements the user has removed undoably. - * @param {!jQuery} node The DOM node to test for spuriousness. - * @return {boolean} True means ignore this node. - */ -function isTemplateOrUndoBuffer(node) { - return !!(node.attr('id') || node.hasClass('undoable')); -} - -/** - * Unpacks a (value, units, precision) tuple into the given type. - * @param {string} prefix The prefix for element attributes. - * @param {TYPE} proto A protocol buffer with `value`, `precision`, - * and `units` fields. - * @param {?jQuery=} node The node containing the tuple. - * @return {TYPE} The updated protocol buffer. Note that the message - * is modified in-place. - * @template TYPE - */ -function readMetric(prefix, proto, node = null) { - const value = parseFloat($(prefix + '_value', node).text()); - if (!isNaN(value)) { - proto.setValue(value); - } - if (proto.setUnits) { - // proto.ord.Percentage doesn't have units. - const unitsNode = $(prefix + '_units', node); - const unitsName = unitsNode.attr('data-proto'); - const unitsEnum = nameToProto(asserts.assertString(unitsName)); - const units = getSelectorText(unitsNode[0]); - proto.setUnits(unitsEnum[units]); - } - const precision = parseFloat($(prefix + '_precision', node).text()); - if (!isNaN(precision)) { - proto.setPrecision(precision); - } - return proto; -} - -/** - * Unpacks a (value, units, precision) tuple into form elements. - * @param {string} prefix The prefix for element attributes. - * @param {?UnitMessage|?Percentage} proto A protocol buffer with - * `value`, `precision`, and `units` fields. (Percentage is allowed - * as a special case even though it doesn't have a `units` field.) - * @param {?jQuery=} node The target node for the tuple. - */ -function writeMetric(prefix, proto, node = null) { - if (!proto) { - return; - } - if (proto.hasValue()) { - $(prefix + '_value', node).text(proto.getValue()); - } - if (proto.getUnits) { - // proto.ord.Percentage doesn't have units. - setSelector($(prefix + '_units', node), proto.getUnits()); - } - if (proto.hasPrecision()) { - $(prefix + '_precision', node).text(proto.getPrecision()); - } -} - -/** - * Prompts the user to upload a file and sets the target node text with its - * contents. - * @param {!jQuery} identifierNode The node to update with the file contents. - * @param {string} valueClass The class containing `identifierNode`. - */ -function setTextFromFile(identifierNode, valueClass) { - const input = document.createElement('input'); - input.setAttribute('type', 'file'); - input.onchange = (event => { - const file = event.target.files[0]; - const reader = new FileReader(); - reader.readAsText(file); - reader.onload = readerEvent => { - const contents = readerEvent.target.result; - $('.' + valueClass, identifierNode).text(contents); - }; - }); - input.click(); -} - -/** - * Selects an