Criteria (django-criteria)

Plugin to manage creation and management of criteria index

Search is a Django app to run Elastic search queries.

Quick start

1. Installation:

   pip install -e git://github.com/D-I-L/django-criteria.git#egg=criteria
   

2. If you need to start a Django project:

   django-admin startproject [project_name]
   

3. Add "criteria" to your INSTALLED_APPS in settings.py:

   INSTALLED_APPS = (
       ...
       'criteria',
   )
   

4. Update the Elastic settings in the settings.py:

   'GENE_CRITERIA': {
                 'name': 'pydgin_imb_criteria_gene',
                 'idx_type': {
                     'IS_GENE_IN_MHC': {'type': 'is_gene_in_mhc',  'auth_public': True},
                     'CAND_GENE_IN_STUDY': {'type': 'cand_gene_in_study',  'auth_public': True},
                     'CAND_GENE_IN_REGION': {'type': 'cand_gene_in_region',  'auth_public': True},
                     'GENE_IN_REGION': {'type': 'gene_in_region',  'auth_public': True},
                 },
                 'auth_public': True
             },
             'MARKER_CRITERIA': {
                 'name': 'pydgin_imb_criteria_marker',
                 'idx_type': {
                     'IS_MARKER_IN_MHC': {'type': 'is_marker_in_mhc',  'auth_public': True},
                     'IS_AN_INDEX_SNP': {'type': 'is_an_index_snp',  'auth_public': True},
                     'MARKER_IS_GWAS_SIGNIFICANT_STUDY': {'type': 'marker_is_gwas_significant_in_study',  'auth_public': True},
                     'RSQ_WITH_INDEX_SNP': {'type': 'rsq_with_index_snp',  'auth_public': True},
                     'MARKER_IS_GWAS_SIGNIFICANT_IC': {'type': 'marker_is_gwas_significant_in_ic',  'auth_public': True},
                 },
                 'auth_public': True
             },
             'REGION_CRITERIA': {
                 'name': 'pydgin_imb_criteria_region',
                 'idx_type': {
                     'IS_REGION_IN_MHC': {'type': 'is_region_in_mhc',  'auth_public': True},
                     'IS_REGION_FOR_DISEASE': {'type': 'is_region_for_disease',  'auth_public': True},
                 },
                 'auth_public': True
             },
             'STUDY_CRITERIA': {
                 'name': 'pydgin_imb_criteria_study',
                 'idx_type': {
                     'STUDY_FOR_DISEASE': {'type': 'study_for_disease',  'auth_public': True},
                 },
                 'auth_public': True
             },
   

5. Tests can be run as follows:

   ./manage.py test criteria.test
   

Create Mapping and Loading Data into Elastic

All the criterias are defined in criteria.ini, each section for one criteria. Criteria indexes are derived from the source indexes. So make sure that the source indexes exists and you are pointing to the right source index keys as defined in elastic_settings.

[cand_gene_in_study] desc: Candidate Gene for a Study feature: gene link_to_feature: study source_idx: STUDY source_idx_type: STUDY source_fields : study_id,genes,diseases,authors test_id: ENSG00000136634 text:A <strong>candidate gene in a study</strong> is defined as a gene cited in the principal paper of one of our curated studies. Following the link will take you to the study.

Help:

./manage.py criteria_index --help

Show (list the criterias, without creating them):

./manage.py criteria_index --feature gene --show (Output: ['is_gene_in_mhc', 'cand_gene_in_study', 'cand_gene_in_region', 'gene_in_region'])

./manage.py criteria_index --feature region --show (Output: ['is_region_in_mhc', 'is_region_for_disease'])

./manage.py criteria_index --feature marker --show (Output: ['is_marker_in_mhc', 'is_an_index_snp', 'marker_is_gwas_significant_in_study', 'marker_is_gwas_significant_in_ic', 'rsq_with_index_snp'])

./manage.py criteria_index --feature region --show (Output: ['is_region_in_mhc', 'is_region_for_disease'])

Run all criterias for feature gene (in normal mode):

./manage.py criteria_index --feature gene

Run all criterias for feature gene (in test mode):

./manage.py criteria_index --feature gene --test

Run one criteria for feature gene:

./manage.py criteria_index --feature gene --criteria cand_gene_in_study

Run one criteria for feature marker:

./manage.py criteria_index --feature marker --criteria is_an_index_snp