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ADDING_DATA.md

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Example

  • Adding Opentargets DRUG-TARGET data to the test data
  • For this example we are using the config files in test/config/ e.g. test/config/data_integration.yml and test/config/db_schema.yml. In practice you would create new versios of these and put them in config/
  • In production, changes should not be made to the test directory.

1. Create new branch

git checkout -b dev-$USER

2. Create .env file

Copy example.env to .env and edit

3. If necessary, create the source data

  • this can be done on a remote server, just need to add SERVER_NAME name to .env
  • need to copy the created data to the specified DATA_DIR using the function copy_source_data()

Example:

python -m test.scripts.source.get_opentargets

4. Edit data_integration.yml

For example, uncomment the following sections in test/config/data_integration.yml and check the filenames in files: match the name of the source data, e.g. today's date.

  • Node
  drug-ot:
    name: Drug
    files:
      drug-target: opentargets/open_targets_2020-10-19.csv
    script: nodes.drug.opentargets
    source: Opentargets-2020-10-19
  • Relationship
  ot-drug-target:
    name: OPENTARGETS_DRUG_TO_TARGET
    files:
      drug-target: opentargets/open_targets_2020-10-19.csv
    script: rels.opentargets_drug_target
    source: Opentargets-2020-08-24

5. Edit db_schema.yml

  • Node
  Drug:
    properties:
      id:
        type: string
      label:
        type: string
      molecule_type:
        type: string
    required:
      - label
      - id
    index: label
    meta:
      _id: id
      _name: label
  • Relationship
  OPENTARGETS_DRUG_TO_TARGET:
    properties:
      source:
        type: Drug
      target:
        type: Gene
      action_type:
        type: string
      phase:
        type: string
    required:
      - source
      - target 
      - phase
      - action_type

6. Write a load script for both node and relationship

Note, if just testing out the demo data, this step can be skipped.

  • if new node type make a new directory, e.g. mkdir workflow/scripts/nodes/drug
  • all property values for both nodes and relationships should have no spaces

To access source files specified in data_integration.yml use the key/value pairs, e.g.

FILE = get_source(meta_id,1)

To process the final dataframe

create_import(df=df, meta_id=meta_id)

To add constraints, e.g. Neo4j property indexes

constraintCommands = ["CREATE index on :Drug(label);"]
create_constraints(constraintCommands, meta_id)

7. Test the build for new data only

python -m test.scripts.processing.nodes.drug.opentargets -n drug-ot
python -m test.scripts.processing.rels.opentargets_drug_target -n ot-drug-target
  • can also use local data, e.g. not in DATA_DIR
python -m test.scripts.processing.nodes.drug.opentargets -n drug-ot -r /path/to/local/data

8. Look at the profiling output

open test/results/graph_data/0.0.1/nodes/drug-ot/drug-ot.profile.html

9. Test the entire build

snakemake -r check_new_data -j 10

10. Commit code to new branch and check the result of Github actions

https://github.com/elswob/neo4j-build-pipeline/actions