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-rw-r--r--wqflask/scripts/index.py142
1 files changed, 71 insertions, 71 deletions
diff --git a/wqflask/scripts/index.py b/wqflask/scripts/index.py
index f59a8788..c871db43 100644
--- a/wqflask/scripts/index.py
+++ b/wqflask/scripts/index.py
@@ -30,47 +30,47 @@ def write_document(db, idterm, doctype, doc):
# pylint: disable=missing-function-docstring
def main():
- with database_connection() as conn, conn.cursor(MonadicDictCursor) as cursor:
- # FIXME: Some Max LRS values in the DB are wrongly listed as
- # 0.000, but shouldn't be displayed. Make them NULLs in the
- # database.
- cursor.execute("""
- SELECT ProbeSet.Name AS name,
- ProbeSet.Symbol AS symbol,
- ProbeSet.description AS description,
- ProbeSet.Chr AS chr,
- ProbeSet.Mb AS mb,
- ProbeSet.alias AS alias,
- ProbeSet.GenbankId AS genbankid,
- ProbeSet.UniGeneId AS unigeneid,
- ProbeSet.Probe_Target_Description AS probe_target_description,
- ProbeSetFreeze.Name AS dataset,
- ProbeSetFreeze.FullName AS dataset_fullname,
- ProbeSetFreeze.Id AS dataset_id,
- Species.Name AS species,
- InbredSet.Name AS `group`,
- Tissue.Name AS tissue,
- ProbeSetXRef.Mean AS mean,
- ProbeSetXRef.LRS AS lrs,
- ProbeSetXRef.additive AS additive,
- Geno.Chr as geno_chr,
- Geno.Mb as geno_mb
- FROM Species
- INNER JOIN InbredSet ON InbredSet.SpeciesId = Species.Id
- INNER JOIN ProbeFreeze ON ProbeFreeze.InbredSetId = InbredSet.Id
- INNER JOIN Tissue ON ProbeFreeze.TissueId = Tissue.Id
- INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
- INNER JOIN ProbeSetXRef ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
- INNER JOIN ProbeSet ON ProbeSet.Id = ProbeSetXRef.ProbeSetId
- LEFT JOIN Geno ON ProbeSetXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id
- WHERE ProbeSetFreeze.confidentiality < 1 AND ProbeSetFreeze.public > 0
- """)
- termgenerator = xapian.TermGenerator()
- termgenerator.set_stemmer(xapian.Stem("en"))
- indexer = partial(index_text, termgenerator)
-
- # pylint: disable=invalid-name
- with xapian_writable_database() as db:
+ termgenerator = xapian.TermGenerator()
+ termgenerator.set_stemmer(xapian.Stem("en"))
+ indexer = partial(index_text, termgenerator)
+
+ # FIXME: Some Max LRS values in the DB are wrongly listed as
+ # 0.000, but shouldn't be displayed. Make them NULLs in the
+ # database.
+ # pylint: disable=invalid-name
+ with xapian_writable_database() as db:
+ with database_connection() as conn, conn.cursor(MonadicDictCursor) as cursor:
+ cursor.execute("""
+ SELECT ProbeSet.Name AS name,
+ ProbeSet.Symbol AS symbol,
+ ProbeSet.description AS description,
+ ProbeSet.Chr AS chr,
+ ProbeSet.Mb AS mb,
+ ProbeSet.alias AS alias,
+ ProbeSet.GenbankId AS genbankid,
+ ProbeSet.UniGeneId AS unigeneid,
+ ProbeSet.Probe_Target_Description AS probe_target_description,
+ ProbeSetFreeze.Name AS dataset,
+ ProbeSetFreeze.FullName AS dataset_fullname,
+ ProbeSetFreeze.Id AS dataset_id,
+ Species.Name AS species,
+ InbredSet.Name AS `group`,
+ Tissue.Name AS tissue,
+ ProbeSetXRef.Mean AS mean,
+ ProbeSetXRef.LRS AS lrs,
+ ProbeSetXRef.additive AS additive,
+ Geno.Chr as geno_chr,
+ Geno.Mb as geno_mb
+ FROM Species
+ INNER JOIN InbredSet ON InbredSet.SpeciesId = Species.Id
+ INNER JOIN ProbeFreeze ON ProbeFreeze.InbredSetId = InbredSet.Id
+ INNER JOIN Tissue ON ProbeFreeze.TissueId = Tissue.Id
+ INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
+ INNER JOIN ProbeSetXRef ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
+ INNER JOIN ProbeSet ON ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ LEFT JOIN Geno ON ProbeSetXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id
+ WHERE ProbeSetFreeze.confidentiality < 1 AND ProbeSetFreeze.public > 0
+ """)
for trait in cursor.fetchall():
doc = xapian.Document()
termgenerator.set_document(doc)
@@ -87,36 +87,36 @@ def main():
doc.set_data(json.dumps(trait.data))
write_document(db, trait["name"].bind(lambda name: f"Q{name}"), "gene", doc)
- cursor.execute("""
- SELECT Species.Name AS species,
- InbredSet.Name AS `group`,
- PublishFreeze.Name AS dataset,
- PublishFreeze.FullName AS dataset_fullname,
- PublishXRef.Id AS name,
- COALESCE(Phenotype.Post_publication_abbreviation, Phenotype.Pre_publication_abbreviation) AS abbreviation,
- COALESCE(Phenotype.Post_publication_description, Phenotype.Pre_publication_description) AS description,
- Phenotype.Lab_code,
- Publication.Abstract,
- Publication.Title,
- Publication.Authors AS authors,
- Publication.Year AS year,
- Publication.PubMed_ID AS pubmed_id,
- PublishXRef.LRS as lrs,
- PublishXRef.additive,
- InbredSet.InbredSetCode AS inbredsetcode,
- PublishXRef.mean,
- PublishFreeze.Id AS dataset_id,
- Geno.Chr as geno_chr,
- Geno.Mb as geno_mb
- FROM Species
- INNER JOIN InbredSet ON InbredSet.SpeciesId = Species.Id
- INNER JOIN PublishFreeze ON PublishFreeze.InbredSetId = InbredSet.Id
- INNER JOIN PublishXRef ON PublishXRef.InbredSetId = InbredSet.Id
- INNER JOIN Phenotype ON PublishXRef.PhenotypeId = Phenotype.Id
- INNER JOIN Publication ON PublishXRef.PublicationId = Publication.Id
- LEFT JOIN Geno ON PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id
- """)
- with xapian_writable_database() as db:
+ with database_connection() as conn, conn.cursor(MonadicDictCursor) as cursor:
+ cursor.execute("""
+ SELECT Species.Name AS species,
+ InbredSet.Name AS `group`,
+ PublishFreeze.Name AS dataset,
+ PublishFreeze.FullName AS dataset_fullname,
+ PublishXRef.Id AS name,
+ COALESCE(Phenotype.Post_publication_abbreviation, Phenotype.Pre_publication_abbreviation) AS abbreviation,
+ COALESCE(Phenotype.Post_publication_description, Phenotype.Pre_publication_description) AS description,
+ Phenotype.Lab_code,
+ Publication.Abstract,
+ Publication.Title,
+ Publication.Authors AS authors,
+ Publication.Year AS year,
+ Publication.PubMed_ID AS pubmed_id,
+ PublishXRef.LRS as lrs,
+ PublishXRef.additive,
+ InbredSet.InbredSetCode AS inbredsetcode,
+ PublishXRef.mean,
+ PublishFreeze.Id AS dataset_id,
+ Geno.Chr as geno_chr,
+ Geno.Mb as geno_mb
+ FROM Species
+ INNER JOIN InbredSet ON InbredSet.SpeciesId = Species.Id
+ INNER JOIN PublishFreeze ON PublishFreeze.InbredSetId = InbredSet.Id
+ INNER JOIN PublishXRef ON PublishXRef.InbredSetId = InbredSet.Id
+ INNER JOIN Phenotype ON PublishXRef.PhenotypeId = Phenotype.Id
+ INNER JOIN Publication ON PublishXRef.PublicationId = Publication.Id
+ LEFT JOIN Geno ON PublishXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id
+ """)
for i, trait in enumerate(cursor.fetchall()):
doc = xapian.Document()
termgenerator.set_document(doc)