diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6d83de43..636a4506 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -52,7 +52,7 @@ jobs: shell: bash -l {0} run: | uv run coverage erase - uv run pytest -vv --cov=ord_interface --durations=20 --ignore=ord_interface/editor + uv run pytest -vv --cov=ord_interface --durations=20 uv run coverage report test_app: @@ -60,25 +60,19 @@ jobs: matrix: python-version: ["3.11", "3.12", "3.13", "3.14"] # 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 + runs-on: ubuntu-latest steps: - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 - uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: true python-version: ${{ matrix.python-version }} - - uses: actions/setup-node@820762786026740c76f36085b0efc47a31fe5020 # v7.0.0 - name: actions-setup-redis uses: shogo82148/actions-setup-redis@59cda539fd5cc9be4c42bb07e4b28156951f37d6 # v1.55.0 - name: Set up Docker Buildx uses: docker/setup-buildx-action@bb05f3f5519dd87d3ba754cc423b652a5edd6d2c # v4.2.0 - name: Install ord-interface run: uv sync --frozen - - name: Install non-python test dependencies - run: | - cd "${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 ed6e5a8f..8731b262 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,6 @@ Web interface and FastAPI server for the [Open Reaction Database](https://open-r - `api/` — FastAPI server (search, view, queries) - `client/` — utilities for building the Postgres + rdkit-cartridge database - `visualization/` — Jinja filters and helpers for rendering reactions and molecules - - `editor/` — legacy reaction-submission UI (being removed) The React frontend talks to the FastAPI server, so both processes need to be running for the UI to work. On Windows, use WSL. @@ -47,7 +46,6 @@ rest of the steps. ```shell cd ord_interface ./build_test_database.sh -# Apple silicon: append `--build-arg="ARCH=aarch_64"`. docker build --file Dockerfile -t openreactiondatabase/ord-interface .. docker compose up ``` diff --git a/ord_interface/Dockerfile b/ord_interface/Dockerfile index 1b167459..dd362ff4 100644 --- a/ord_interface/Dockerfile +++ b/ord_interface/Dockerfile @@ -18,14 +18,9 @@ FROM python:3.11 -# default-jre is required for running the closure compiler linter. -# For this next line, see: -# https://github.com/geerlingguy/ansible-role-java/issues/64#issuecomment-597132394 -RUN mkdir -p /usr/share/man/man1/ RUN apt-get update \ && apt-get install -y \ build-essential \ - default-jre \ nginx \ npm \ procps \ @@ -33,31 +28,11 @@ RUN apt-get update \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* -# Fetch and build editor dependencies. +# Fetch the Ketcher distribution served by the SPA. # NOTE(kearnes): Do this before COPYing the local state so it can be cached. WORKDIR /app/ord-interface/ord_interface RUN wget https://github.com/epam/ketcher/releases/download/v2.5.1/ketcher-standalone-2.5.1.zip \ && unzip ketcher-standalone-2.5.1.zip -WORKDIR /app/ord-interface/ord_interface/editor -RUN wget https://github.com/google/closure-library/archive/v20200517.tar.gz \ - && tar -xzf v20200517.tar.gz \ - && rm v20200517.tar.gz -RUN wget https://github.com/protocolbuffers/protobuf/releases/download/v3.14.0/protobuf-js-3.14.0.tar.gz \ - && tar -xzf protobuf-js-3.14.0.tar.gz \ - && rm protobuf-js-3.14.0.tar.gz -ARG ARCH=x86_64 -RUN wget https://github.com/protocolbuffers/protobuf/releases/download/v3.14.0/protoc-3.14.0-linux-${ARCH}.zip \ - && unzip protoc-3.14.0-linux-${ARCH}.zip -ENV PATH="/app/ord-interface/ord_interface/editor/bin:${PATH}" -RUN wget https://raw.githubusercontent.com/google/closure-compiler/master/contrib/externs/jquery-3.3.js \ - && mkdir -p externs \ - && mv jquery-3.3.js externs -RUN npm install google-closure-compiler@20220803 -WORKDIR /app -RUN wget https://github.com/open-reaction-database/ord-schema/archive/refs/tags/v0.3.93.zip \ - && unzip v0.3.93.zip \ - && rm v0.3.93.zip \ - && mv ord-schema-0.3.93 ord-schema # Install dependencies. WORKDIR /app/ord-interface @@ -68,12 +43,6 @@ ENV UV_PROJECT_ENVIRONMENT=/usr/local \ COPY pyproject.toml uv.lock README.md ./ RUN uv sync --frozen --no-dev --no-install-project -# Copy the local state. -COPY ord_interface/editor/js/ ord_interface/editor/js/ -COPY ord_interface/editor/build.sh ord_interface/editor -WORKDIR /app/ord-interface/ord_interface/editor -RUN ./build.sh -WORKDIR /app/ord-interface # Build the SPA (React + TypeScript + Vite). COPY app/ app/ WORKDIR /app/ord-interface/app @@ -88,10 +57,7 @@ RUN cp -r /app/ord-interface/ord_interface/standalone/ /app/ord-interface/app/pu && npm run build \ && mv dist/ /app/ord-interface/spa WORKDIR /app/ord-interface -# Copy the rest of the editor files. -COPY ord_interface/editor/ ord_interface/editor/ # Now copy everything else. -COPY ord_interface/interface.py ord_interface/ COPY ord_interface/api/ ord_interface/api/ COPY ord_interface/visualization/ ord_interface/visualization/ RUN uv sync --frozen --no-dev diff --git a/ord_interface/api/main.py b/ord_interface/api/main.py index 94ed1eeb..4fa1f6d2 100644 --- a/ord_interface/api/main.py +++ b/ord_interface/api/main.py @@ -15,7 +15,6 @@ """Open Reaction Database API.""" import os -import re from contextlib import asynccontextmanager from fastapi import FastAPI @@ -33,8 +32,7 @@ async def lifespan(*args, **kwargs): from testing.postgresql import Postgresql with Postgresql() as postgres: - url = re.sub("postgresql://", "postgresql+psycopg://", postgres.url()) - setup_test_postgres(url) + setup_test_postgres(postgres.url()) os.environ["ORD_INTERFACE_POSTGRES"] = postgres.url() yield else: diff --git a/ord_interface/api/testing.py b/ord_interface/api/testing.py index a7f9da5c..6c364cf1 100644 --- a/ord_interface/api/testing.py +++ b/ord_interface/api/testing.py @@ -20,12 +20,18 @@ from ord_schema.message_helpers import load_message from ord_schema.orm.database import add_dataset, prepare_database, update_derived_data from ord_schema.proto import dataset_pb2 -from sqlalchemy import create_engine +from sqlalchemy import create_engine, make_url from sqlalchemy.orm import Session def setup_test_postgres(url: str) -> None: - """Adds test data to a postgres database.""" + """Adds test data to a postgres database. + + Args: + url: Postgres connection URL. Any driver it names is replaced with + psycopg (v3), the only Postgres driver we install; SQLAlchemy would + otherwise reach for psycopg2 on a bare ``postgresql://`` URL. + """ datasets = [ load_message(filename, dataset_pb2.Dataset) for filename in glob( @@ -33,7 +39,9 @@ def setup_test_postgres(url: str) -> None: ) ] assert datasets - engine = create_engine(url, future=True) + engine = create_engine( + make_url(url).set(drivername="postgresql+psycopg"), future=True + ) rdkit_cartridge = prepare_database(engine) with Session(engine) as session: for dataset in datasets: 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 - 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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 -
- -
- -
-
- - - - - diff --git a/ord_interface/editor/html/datasets.html b/ord_interface/editor/html/datasets.html deleted file mode 100644 index dd295cda..00000000 --- a/ord_interface/editor/html/datasets.html +++ /dev/null @@ -1,365 +0,0 @@ - - - - - - - - Open Reaction Database - Interactive Editor - - - - - - - - - - - - - - - -
- -
-
-
-
{{ user_name }}
- {% if client_id %} -
-
Guest - Mode -
-
- - 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 - . -

-
-
- - - - - - \ 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 91e4c8a9..00000000 --- a/ord_interface/editor/html/login.html +++ /dev/null @@ -1,89 +0,0 @@ - - - - - Login - - - - -
- Notice: The ORD editor will be deactivated after July 31, 2026. - Please download any datasets you wish to keep before that date. -
- The new editor is available at https://app.open-reaction-database.org/ - (learn more). -
- Questions? Contact help@open-reaction-database.org. -
-
-
- - 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. -

- - - -
- 
-
- - - diff --git a/ord_interface/editor/img/template-editor-how.png b/ord_interface/editor/img/template-editor-how.png deleted file mode 100644 index 02b01aab..00000000 Binary files a/ord_interface/editor/img/template-editor-how.png and /dev/null differ diff --git a/ord_interface/editor/js/amounts.js b/ord_interface/editor/js/amounts.js deleted file mode 100644 index 84d74722..00000000 --- a/ord_interface/editor/js/amounts.js +++ /dev/null @@ -1,211 +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. - */ - -goog.module('ord.amounts'); -goog.module.declareLegacyNamespace(); -exports = { - init, - load, - unload, -}; - -const utils = goog.require('ord.utils'); - -const Amount = goog.require('proto.ord.Amount'); -const Mass = goog.require('proto.ord.Mass'); -const MassUnit = goog.require('proto.ord.Mass.MassUnit'); -const Moles = goog.require('proto.ord.Moles'); -const MolesUnit = goog.require('proto.ord.Moles.MolesUnit'); -const Volume = goog.require('proto.ord.Volume'); -const VolumeUnit = goog.require('proto.ord.Volume.VolumeUnit'); - -/** - * Initializes the selector for an Amount section. - * @param {!jQuery} node The parent div containing the Amount section. - */ -function init(node) { - const select = $('select.amount_units', node); - select.append(''); - if (select.hasClass('mass')) { - select.append(''); - for (let key in MassUnit) { - if (key === 'UNSPECIFIED') { - continue; - } - const option = $(''); - for (let key in MolesUnit) { - if (key === 'UNSPECIFIED') { - continue; - } - const option = $(''); - for (let key in VolumeUnit) { - if (key === 'UNSPECIFIED') { - continue; - } - const option = $('