monarch-initiative/hpo-plain-index

Name: hpo-plain-index

Owner: Monarch Initiative

Description: Generates a solr index of plain language terms in the HPO and their grouping classes

Created: 2018-02-25 18:21:35.0

Updated: 2018-03-01 16:09:04.0

Pushed: 2018-03-01 18:43:02.0

Homepage: null

Size: 60

Language: Python

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README

HPO Plain Language Indexer

Builds a solr index of HPO plain language synonyms, including phenotype and anatomy groupings to enable faceting. For example:

"id": "HP:0000464",
"exact_synonym": [
  "Abnormality of the neck"
],
"phenotype_closure": [
  "HP:0000464",
  "HP:0000152",
  "HP:0000118"
],
"phenotype_closure_label": [
  "Abnormality of the neck",
  "Abnormality of head or neck",
  "Phenotypic abnormality"
],
"anatomy_closure": [
  "UBERON_0007811",
  "UBERON_0000153",
  "UBERON_0013702"
],
"anatomy_closure_label": [
  "craniocervical region",
  "anterior region of body",
  "body proper"
]

Building and running with Docker Compose

Build and initialize:

docker-compose up -d

(Wait 30 seconds) Run the integration tests:

docker-compose run loader integration-tests

Run the unit tests:

docker-compose run loader test

Load the data (takes ~10 minutes):

docker-compose run loader load-index

Archive and copy index to local filesystem

docker-compose exec solr bash -c 'cd /opt/solr/server/solr && tar cfv hpo-pl.tar hpo-pl/'
docker cp solr-hpo:/opt/solr/server/solr/hpo-pl.tar ./