<commit_before># Bag upload queries
precompute.query.1 = SELECT a1_.id as a3_, a2_.value as a4_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = true)

precompute.query.2 = SELECT a1_.id as a3_, a2_.value as a4_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = false)

precompute.query.3 = SELECT a1_.id AS a3_, a2_.value AS a4_, a5_.shortName as a6_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_, org.intermine.model.bio.Organism AS a5_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = true AND a1_.organism CONTAINS a5_)

precompute.query.4 = SELECT a1_.id AS a3_, a2_.value AS a4_, a5_.shortName as a6_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_, org.intermine.model.bio.Organism AS a5_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = false AND a1_.organism CONTAINS a5_)

# gene/protein --> organism [used by some widgets]
precompute.query.5 = SELECT a1_.id as a3_, a2_.name AS a4_ FROM org.intermine.model.bio.Gene AS a1_, org.intermine.model.bio.Organism AS a2_ WHERE a1_.organism CONTAINS a2_

precompute.query.6 = SELECT a1_.id AS a3_, a2_.name AS a4_ FROM org.intermine.model.bio.Protein AS a1_, org.intermine.model.bio.Organism AS a2_ WHERE a1_.organism CONTAINS a2_

# chromosome distribution widget
precompute.query.7 = SELECT a2_.id as a4_, a1_.primaryIdentifier AS a5_, a2_.primaryIdentifier AS a6_,  a3_.name as a7_ FROM org.intermine.model.bio.Chromosome AS a1_, org.intermine.model.bio.LocatedSequenceFeature AS a2_, org.intermine.model.bio.Organism AS a3_ WHERE (a2_.chromosome CONTAINS a1_ AND a2_.organism CONTAINS a3_)
<commit_msg>precompute for genomic region search for metabolicmine<commit_after># Bag upload queries
precompute.query.1 = SELECT a1_.id as a3_, a2_.value as a4_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = true)

precompute.query.2 = SELECT a1_.id as a3_, a2_.value as a4_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = false)

precompute.query.3 = SELECT a1_.id AS a3_, a2_.value AS a4_, a5_.shortName as a6_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_, org.intermine.model.bio.Organism AS a5_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = true AND a1_.organism CONTAINS a5_)

precompute.query.4 = SELECT a1_.id AS a3_, a2_.value AS a4_, a5_.shortName as a6_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_, org.intermine.model.bio.Organism AS a5_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = false AND a1_.organism CONTAINS a5_)

# gene/protein --> organism [used by some widgets]
precompute.query.5 = SELECT a1_.id as a3_, a2_.name AS a4_ FROM org.intermine.model.bio.Gene AS a1_, org.intermine.model.bio.Organism AS a2_ WHERE a1_.organism CONTAINS a2_

precompute.query.6 = SELECT a1_.id AS a3_, a2_.name AS a4_ FROM org.intermine.model.bio.Protein AS a1_, org.intermine.model.bio.Organism AS a2_ WHERE a1_.organism CONTAINS a2_

# chromosome distribution widget
precompute.query.7 = SELECT a2_.id as a4_, a1_.primaryIdentifier AS a5_, a2_.primaryIdentifier AS a6_,  a3_.name as a7_ FROM org.intermine.model.bio.Chromosome AS a1_, org.intermine.model.bio.LocatedSequenceFeature AS a2_, org.intermine.model.bio.Organism AS a3_ WHERE (a2_.chromosome CONTAINS a1_ AND a2_.organism CONTAINS a3_)

# genomic region search
precompute.query.8 = SELECT a3_.shortName AS a1_, a4_.class AS a2_ FROM org.intermine.model.bio.Organism AS a3_, org.intermine.model.bio.SequenceFeature AS a4_ WHERE a4_.organism CONTAINS a3_

precompute.query.9 = SELECT a4_.class AS a1_, a5_.name AS a2_, a5_.description AS a3_ FROM org.intermine.model.bio.SequenceFeature AS a4_, org.intermine.model.bio.SOTerm AS a5_ WHERE a4_.sequenceOntologyTerm CONTAINS a5_
{'fraction_non_alphanumeric': 0.0898958080930458, 'fraction_numerical': 0.04555367094741943, 'mean_word_length': 4.578378378378378, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3870631', 'n_tokens_mistral': 1570, 'n_tokens_neox': 1515, 'n_words': 432}