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-rw-r--r--wqflask/maintenance/dataset/datastructure.py155
1 files changed, 0 insertions, 155 deletions
diff --git a/wqflask/maintenance/dataset/datastructure.py b/wqflask/maintenance/dataset/datastructure.py
deleted file mode 100644
index 7139856f..00000000
--- a/wqflask/maintenance/dataset/datastructure.py
+++ /dev/null
@@ -1,155 +0,0 @@
-import utilities
-
-def get_probesetfreezes(inbredsetid):
- cursor, con = utilities.get_cursor()
- sql = """
- SELECT ProbeSetFreeze.`Id`, ProbeSetFreeze.`Name`, ProbeSetFreeze.`FullName`
- FROM ProbeSetFreeze, ProbeFreeze
- WHERE ProbeSetFreeze.`ProbeFreezeId`=ProbeFreeze.`Id`
- AND ProbeFreeze.`InbredSetId`=%s
- """
- cursor.execute(sql, (inbredsetid))
- return cursor.fetchall()
-
-def get_probesetfreeze(probesetfreezeid):
- cursor, con = utilities.get_cursor()
- sql = """
- SELECT ProbeSetFreeze.`Id`, ProbeSetFreeze.`Name`, ProbeSetFreeze.`FullName`
- FROM ProbeSetFreeze
- WHERE ProbeSetFreeze.`Id`=%s
- """
- cursor.execute(sql, (probesetfreezeid))
- return cursor.fetchone()
-
-def get_strains(inbredsetid):
- cursor, con = utilities.get_cursor()
- sql = """
- SELECT Strain.`Id`, Strain.`Name`
- FROM StrainXRef, Strain
- WHERE StrainXRef.`InbredSetId`=%s
- AND StrainXRef.`StrainId`=Strain.`Id`
- ORDER BY StrainXRef.`OrderId`
- """
- cursor.execute(sql, (inbredsetid))
- return cursor.fetchall()
-
-def get_inbredset(probesetfreezeid):
- cursor, con = utilities.get_cursor()
- sql = """
- SELECT InbredSet.`Id`, InbredSet.`Name`, InbredSet.`FullName`
- FROM InbredSet, ProbeFreeze, ProbeSetFreeze
- WHERE InbredSet.`Id`=ProbeFreeze.`InbredSetId`
- AND ProbeFreeze.`Id`=ProbeSetFreeze.`ProbeFreezeId`
- AND ProbeSetFreeze.`Id`=%s
- """
- cursor.execute(sql, (probesetfreezeid))
- return cursor.fetchone()
-
-def get_species(inbredsetid):
- cursor, con = utilities.get_cursor()
- sql = """
- SELECT Species.`Id`, Species.`Name`, Species.`MenuName`, Species.`FullName`
- FROM InbredSet, Species
- WHERE InbredSet.`Id`=%s
- AND InbredSet.`SpeciesId`=Species.`Id`
- """
- cursor.execute(sql, (inbredsetid))
- return cursor.fetchone()
-
-def get_genofreeze_byinbredsetid(inbredsetid):
- cursor, con = utilities.get_cursor()
- sql = """
- SELECT GenoFreeze.`Id`, GenoFreeze.`Name`, GenoFreeze.`FullName`, GenoFreeze.`InbredSetId`
- FROM GenoFreeze
- WHERE GenoFreeze.`InbredSetId`=%s
- """
- cursor.execute(sql, (inbredsetid))
- return cursor.fetchone()
-
-def get_nextdataid_genotype():
- cursor, con = utilities.get_cursor()
- sql = """
- SELECT GenoData.`Id`
- FROM GenoData
- ORDER BY GenoData.`Id` DESC
- LIMIT 1
- """
- cursor.execute(sql)
- re = cursor.fetchone()
- dataid = re[0]
- dataid += 1
- return dataid
-
-def get_nextdataid_phenotype():
- cursor, con = utilities.get_cursor()
- sql = """
- SELECT PublishData.`Id`
- FROM PublishData
- ORDER BY PublishData.`Id` DESC
- LIMIT 1
- """
- cursor.execute(sql)
- re = cursor.fetchone()
- dataid = re[0]
- dataid += 1
- return dataid
-
-def insert_strain(inbredsetid, strainname, updatestrainxref=None):
- speciesid = get_species(inbredsetid)[0]
- cursor, con = utilities.get_cursor()
- sql = """
- INSERT INTO Strain
- SET
- Strain.`Name`=%s,
- Strain.`Name2`=%s,
- Strain.`SpeciesId`=%s
- """
- cursor.execute(sql, (strainname, strainname, speciesid))
- strainid = con.insert_id()
- if updatestrainxref:
- sql = """
- SELECT StrainXRef.`OrderId`
- FROM StrainXRef
- where StrainXRef.`InbredSetId`=%s
- ORDER BY StrainXRef.`OrderId` DESC
- LIMIT 1
- """
- cursor.execute(sql, (inbredsetid))
- re = cursor.fetchone()
- orderid = re[0] + 1
- #
- sql = """
- INSERT INTO StrainXRef
- SET
- StrainXRef.`InbredSetId`=%s,
- StrainXRef.`StrainId`=%s,
- StrainXRef.`OrderId`=%s,
- StrainXRef.`Used_for_mapping`=%s,
- StrainXRef.`PedigreeStatus`=%s
- """
- cursor.execute(sql, (inbredsetid, strainid, orderid, "N", None))
-
-def get_strain(inbredsetid, strainname):
- speciesid = get_species(inbredsetid)[0]
- cursor, con = utilities.get_cursor()
- sql = """
- SELECT Strain.`Id`, Strain.`Name`
- FROM Strain
- WHERE Strain.`SpeciesId`=%s
- AND Strain.`Name` LIKE %s
- """
- cursor.execute(sql, (speciesid, strainname))
- return cursor.fetchone()
-
-def get_strain_sure(inbredsetid, strainname, updatestrainxref=None):
- strain = get_strain(inbredsetid, strainname)
- if not strain:
- insert_strain(inbredsetid, strainname, updatestrainxref)
- strain = get_strain(inbredsetid, strainname)
- return strain
-
-def get_strains_bynames(inbredsetid, strainnames, updatestrainxref=None):
- strains = []
- for strainname in strainnames:
- strains.append(get_strain_sure(inbredsetid, strainname, updatestrainxref))
- return strains