Bump ord-schema version

.github/workflows/cleanup.yml

@@ -17,8 +17,7 @@ name: Lint
 on: [pull_request, push]
 
 env:
-  # ord-schema is versioned to avoid breaking ord-editor.
-  ORD_SCHEMA_TAG: v0.1.1
+  ORD_SCHEMA_TAG: v0.2.3
 
 jobs:
   check_licenses:
@@ -51,6 +50,7 @@ jobs:
       - name: yapf
         run: |
           cd "${GITHUB_WORKSPACE}/ord-editor"
+          pip install -r requirements.txt
           pip install yapf
           yapf --parallel --recursive --exclude="*_pb2.py" --quiet .
       - name: Install ord-schema
@@ -102,8 +102,8 @@ jobs:
           cd "${GITHUB_WORKSPACE}/ord-editor"
           pip install flask pylint yapf
           npm install google-protobuf puppeteer
-          wget https://github.com/protocolbuffers/protobuf/releases/download/v3.13.0/protobuf-js-3.13.0.tar.gz
-          tar -xzf protobuf-js-3.13.0.tar.gz
+          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
           wget https://github.com/google/closure-library/archive/v20200517.tar.gz
           tar -xzf v20200517.tar.gz
           git clone https://github.com/Open-Reaction-Database/ketcher.git

.github/workflows/run_tests.yml

@@ -32,4 +32,4 @@ jobs:
         pip install psycopg2-binary
         npm install puppeteer
         export ORD_EDITOR_POSTGRES_PASSWORD=test
-        ./run_editor_tests.sh
+        ./run_tests.sh

Dockerfile

@@ -26,11 +26,12 @@
 
 FROM continuumio/miniconda3
 
-RUN apt-get update && apt-get install -y \
-    build-essential \
-    procps \
-    unzip \
- && rm -rf /var/lib/apt/lists/*
+# default-jre is required for running the closure compiler linter.
+# https://github.com/geerlingguy/ansible-role-java/issues/64#issuecomment-597132394
+RUN mkdir /usr/share/man/man1/
+RUN apt-get update \
+ && apt-get install -y build-essential default-jre procps unzip \
+ && apt-get clean
 
 RUN conda install -c rdkit \
     flask \
@@ -53,23 +54,30 @@ RUN cd ketcher \
 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/v3.13.0/protobuf-js-3.13.0.tar.gz \
- && tar -xzf protobuf-js-3.13.0.tar.gz \
- && rm protobuf-js-3.13.0.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
+
+# Dependencies for testing.
+RUN npm install google-closure-compiler
 
 # Install ord-schema.
 WORKDIR ..
 RUN git clone https://github.com/Open-Reaction-Database/ord-schema.git
 WORKDIR ord-schema
-# NOTE(kearnes): ord-schema is versioned to avoid breaking ord-editor.
-ARG ORD_SCHEMA_TAG=v0.1.1
+ARG ORD_SCHEMA_TAG=v0.2.3
 RUN git fetch --tags && git checkout "${ORD_SCHEMA_TAG}"
 RUN pip install -r requirements.txt
 RUN python setup.py install
 
-# COPY the local state.
+# Install editor dependencies.
 WORKDIR ../ord-editor
+COPY requirements.txt ./
+RUN pip install -r requirements.txt
+
+# COPY the local state.
 COPY Makefile schema.sql ./
+COPY actions/ actions/
 COPY css/ css/
 COPY db/ db/
 COPY html/ html/

Makefile

@@ -2,7 +2,7 @@
 closure = closure-library-20200517
 
 # https://github.com/protocolbuffers/protobuf/releases
-protobuf = protobuf-3.13.0
+protobuf = protobuf-3.14.0
 
 # Check that the present ketcher code is compatible.
 ketcher-req = v0.1.0+ord

README.md

@@ -97,11 +97,11 @@ v20200517](https://github.com/google/closure-library/releases/).
 
 Unpack the archive in the editor directory so the Closure compiler can find it.
 ```
-$ url=https://github.com/protocolbuffers/protobuf/releases/download/v3.13.0/protobuf-js-3.13.0.tar.gz
+$ 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
-3.13.0](https://github.com/protocolbuffers/protobuf/releases/tag/v3.13.0)
+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.
 

actions/lint_js.sh

@@ -1,3 +1,4 @@
+#!/bin/bash
 # Copyright 2020 Open Reaction Database Project Authors
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -35,12 +36,12 @@ ENTRY_POINT="$1"
 java -jar node_modules/google-closure-compiler-java/compiler.jar \
     --entry_point "${ENTRY_POINT}" \
     --js 'closure-library-20200517/**.js' \
-    --js 'protobuf-3.13.0/js/**.js' \
+    --js 'protobuf-3.14.0/js/**.js' \
     --js 'gen/js/proto/ord/**.js'  \
     --js 'js/**.js' \
     --dependency_mode PRUNE \
     --checks_only \
     --jscomp_error lintChecks \
     --hide_warnings_for closure-library-20200517 \
-    --hide_warnings_for protobuf-3.13.0/js \
+    --hide_warnings_for protobuf-3.14.0/js \
     --hide_warnings_for gen/js/proto/ord

db/680b0d9fe649417cb092d790907bd5a5/full.pbtxt

@@ -48,10 +48,13 @@ reactions {
           details: "6"
           value: "5"
         }
-        volume {
-          value: 7.0
-          precision: 8.0
-          units: LITER
+        amount {
+          volume {
+            value: 7.0
+            precision: 8.0
+            units: LITER
+          }
+          volume_includes_solutes: true
         }
         reaction_role: REACTANT
         is_limiting: true
@@ -60,24 +63,29 @@ reactions {
           details: "9"
           reaction_id: "9.5"
         }
-        vendor_source: "10"
-        vendor_id: "11"
-        vendor_lot: "12"
+        source {
+          vendor: "10"
+          id: "11"
+          lot: "12"
+        }
         features {
-          name: "13"
-          float_value: 14.0
-          how_computed: "15"
+          key: "13"
+          value: {
+            float_value: 14.0
+            description: "15"
+          }
         }
-        volume_includes_solutes: true
       }
       crude_components {
         reaction_id: "15.25"
         includes_workup: true
         has_derived_amount: false
-        volume {
-          value: 15.5
-          precision: 15.75
-          units: MICROLITER
+        amount {
+          volume {
+            value: 15.5
+            precision: 15.75
+            units: MICROLITER
+          }
         }
       }
       addition_order: 16
@@ -298,7 +306,7 @@ reactions {
       format: "86"
     }
   }
-  workup {
+  workups {
     type: FILTRATION
     details: "92"
     duration {
@@ -371,10 +379,12 @@ reactions {
     }
     target_ph: 89.0
     is_automated: true
-    volume {
-      value: 123.0
-      precision: 0.5
-      units: MILLILITER
+    amount {
+      volume {
+        value: 123.0
+        precision: 0.5
+        units: MILLILITER
+      }
     }
   }
   outcomes {
@@ -388,43 +398,65 @@ reactions {
       precision: 116.0
     }
     products {
-      compound {
-        identifiers {
-          type: IUPAC_NAME
-          details: "116.2"
-          value: "116.1"
-        }
-        volume {
-          value: 116.25
-          precision: 116.375
-          units: MICROLITER
-        }
-        features {
-          name: "116.5"
+      identifiers {
+        type: IUPAC_NAME
+        details: "116.2"
+        value: "116.1"
+      }
+      features {
+        key: "116.5"
+        value: {
           float_value: 116.625
-          how_computed: "116.7"
+          description: "116.7"
         }
       }
       is_desired_product: true
-      compound_yield {
-        value: 117.0
-        precision: 118.0
-      }
-      purity {
-        value: 119.0
-        precision: 120.0
-      }
-      selectivity {
-        type: ZE
-        details: "123"
-        value: 121.0
-        precision: 122.0
-      }
-      analysis_identity: "analysis1"
-      analysis_yield: "analysis2"
-      analysis_yield: "analysis1"
-      analysis_purity: "analysis2"
-      analysis_selectivity: "analysis1"
+      measurements {
+        analysis_key: "analysis1"
+        type: YIELD
+        uses_internal_standard: 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
+        percentage {
+          value: 119.0
+          precision: 120.0
+        }
+      }
+      measurements {
+        analysis_key: "analysis1"
+        type: AMOUNT
+        amount {
+          mass {
+            value: 116.25
+            precision: 116.375
+            units: GRAM
+          }
+        }
+      }
+      measurements {
+        type: PURITY
+        percentage {
+          value: 987.6
+          precision: 543.2
+        }
+      }
       isolated_color: "124"
       texture {
         type: POWDER
@@ -437,23 +469,23 @@ reactions {
         type: NMR_13C
         chmo_id: 131
         details: "132"
-        processed_data {
+        data {
           key: "135"
           value {
             url: "136"
             description: "137"
             format: "138"
           }
         }
-        raw_data {
+        data {
           key: "139"
           value {
             float_value: 140.0
             description: "141"
             format: "142"
           }
         }
-        raw_data {
+        data {
           key: "byte_data"
           value {
             bytes_value: "bytestring"
@@ -463,13 +495,6 @@ reactions {
         instrument_last_calibrated {
           value: "134"
         }
-        uses_internal_standard: true
-        uses_authentic_standard: false
-      }
-    }
-    analyses {
-      key: "analysis2"
-      value {
       }
     }
   }