Merge pull request #3 from EnzymeML/Peacock68-patch-1

Peacock68 patch 1

.github/workflows/gen.yml

@@ -0,0 +1,50 @@
+name: MD-Models Pipeline
+
+on:
+  push:
+    paths:
+      - "specifications/*.md"
+  workflow_dispatch:
+
+jobs:
+  generate:
+    name: Generate Pipeline
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up Rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+
+      - name: Install MD-Models
+        run: cargo install --git https://github.com/JR-1991/md-models.git
+
+      - name: Run the generation pipeline
+        run: md-models pipeline -i gen.toml
+
+      - name: "Push generated code/schemes"
+        shell: "bash"
+        run: |
+          if [[ `git status --porcelain` ]]; then
+              git add --all
+              git config --global user.name 'MD-Models Bot'
+              git config --global user.email '[email protected]'
+              git commit -am "Model update"
+              git push
+          else
+            echo "Nothing changed!"
+          fi
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - uses: actions/cache@v2
+        with:
+          path: .cache
+          key: ${{ github.ref }}
+      - run: pip install mkdocs-material jupyter nbconvert mkdocs-jupyter
+      - run: mkdocs gh-deploy --force

database-example/README.md

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+# Setting up a PostgreSQL database and STRENDA-DB Light
+
+The following example demonstrates how to set up a PostgreSQL database using Docker and sdRDM-DB. Here we will make use of the `create_tables` functionality to build the necessary tables for the database.
+
+## Docker installation
+
+To install Docker, follow the instructions provided in the [official documentation](https://docs.docker.com/get-docker/).
+
+## Database setup
+
+This example includes a `docker-compose` recipe to spawn a new instance of a PostgreSQL database. For this, run the following command:
+
+```bash
+mkdir data
+sudo docker-compose up -d
+```
+
+_(The `sudo` command may only be necessary for linux dists)_
+
+## Create tables
+
+Once the database is up and running, you can create the tables by running the following command:
+
+```bash
+python3 create_tables.py
+```
+
+_Output_
+
+```bash
+🎉 Connected
+
+🚀 Creating tables for data model ../specifications/STRENDADB_light_20240904_fix.md
+│
+├── Table __model_meta__ not existing. Adding to DB!
+├── Added table model 'DATA_MODEL' to __model_meta__ table
+├── Added table model 'Publication' to __model_meta__ table
+├── Added table model 'Author' to __model_meta__ table
+├── Added table model 'Experiment' to __model_meta__ table
+├── Added table model 'ProteinDescription' to __model_meta__ table
+├── Added table model 'ProteinSource' to __model_meta__ table
+├── Added table model 'SequenceModifications' to __model_meta__ table
+├── Added table model 'PosttranslationalModifications' to __model_meta__ table
+├── Added table model 'ProteinReaction' to __model_meta__ table
+├── Added table model 'Dataset' to __model_meta__ table
+├── Added table model 'AssayConditions' to __model_meta__ table
+├── Added table model 'SmallAssayComponents' to __model_meta__ table
+├── Added table model 'MacromolecularComponents' to __model_meta__ table
+├── Added table model 'RoleOfComponent' to __model_meta__ table
+├── Added table model 'CompoundClassification' to __model_meta__ table
+├── Added table model 'ResultsSet' to __model_meta__ table
+├── Added table model 'InitialKineticsParameters' to __model_meta__ table
+├── Added table model 'Activation' to __model_meta__ table
+├── Added table model 'Inhibition' to __model_meta__ table
+├── Created table 'Publication'
+├── Created table 'Author'
+├── Created table 'Experiment'
+├── Created table 'ProteinDescription'
+├── Created table 'ProteinSource'
+├── Created table 'SequenceModifications'
+├── Created table 'PosttranslationalModifications'
+├── Created table 'ProteinReaction'
+├── Created table 'Dataset'
+├── Created table 'AssayConditions'
+├── Created table 'SmallAssayComponents'
+├── Created table 'MacromolecularComponents'
+├── Created table 'RoleOfComponent'
+├── Created table 'CompoundClassification'
+├── Created table 'ResultsSet'
+├── Created table 'InitialKineticsParameters'
+├── Created table 'Activation'
+├── Created table 'Inhibition'
+├── Added primary key 'id' to table Publication
+├── Added primary key 'id' to table Author
+├── Added primary key 'id' to table Experiment
+├── Added primary key 'id' to table ProteinDescription
+├── Added primary key 'id' to table ProteinSource
+├── Added primary key 'id' to table SequenceModifications
+├── Added primary key 'id' to table PosttranslationalModifications
+├── Added primary key 'id' to table ProteinReaction
+├── Added primary key 'id' to table Dataset
+├── Added primary key 'id' to table AssayConditions
+├── Added primary key 'id' to table SmallAssayComponents
+├── Added primary key 'id' to table MacromolecularComponents
+├── Added primary key 'id' to table RoleOfComponent
+├── Added primary key 'id' to table CompoundClassification
+├── Added primary key 'id' to table ResultsSet
+├── Added primary key 'id' to table InitialKineticsParameters
+├── Added primary key 'id' to table Activation
+├── Added primary key 'id' to table Inhibition
+├── Added join table 'Publication_author_Author'
+├── Added join table 'Publication_experiment_Experiment'
+├── Added foreign key 'protein_assay__fk' to table 'Experiment'
+├── Added foreign key 'protein_sequence__fk' to table 'ProteinDescription'
+├── Added foreign key 'posttranslational_modifications__fk' to table 'ProteinDescription'
+├── Added foreign key 'protein_source__fk' to table 'ProteinDescription'
+├── Added foreign key 'reaction__fk' to table 'ProteinDescription'
+├── Added join table 'ProteinDescription_protein_characterization_Dataset'
+├── Added join table 'Dataset_assay_conditions_AssayConditions'
+├── Added join table 'Dataset_results_set_ResultsSet'
+├── Added foreign key 'small_assay_components__fk' to table 'AssayConditions'
+├── Added foreign key 'macromolecular_components__fk' to table 'AssayConditions'
+├── Added foreign key 'role__fk' to table 'MacromolecularComponents'
+├── Added foreign key 'initial_kinetic_parameters__fk' to table 'ResultsSet'
+├── Added foreign key 'activation__fk' to table 'ResultsSet'
+├── Added foreign key 'inhibition__fk' to table 'ResultsSet'
+│
+╰── 🎉 Created all tables for data model ../specifications/STRENDADB_light_20240904_fix.md
+```
+
+## Working with the database
+
+In the Jupyter notebook `UseDatabase.ipynb`, you can find an example of how to interact with the database using the `sdrdm-db` library.