Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

3 files changed, 291 insertions, 18 deletions

diff --git a/scripts/maintenance/datastructure.py b/scripts/maintenance/datastructure.py
new file mode 100755
index 00000000..9f3e8b1e
--- /dev/null
+++ b/scripts/maintenance/datastructure.py
@@ -0,0 +1,177 @@
+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 get_nextorderid_strainxref(inbredsetid):
+    cursor, con = utilities.get_cursor()
+    sql = """
+        SELECT StrainXRef.`OrderId`
+        FROM StrainXRef
+        WHERE StrainXRef.`InbredSetId`=%s
+        ORDER BY StrainXRef.`OrderId` DESC
+        LIMIT 1
+        """
+    cursor.execute(sql, (inbredsetid))
+    re = cursor.fetchone()
+    if re:
+        orderid = re[0] + 1
+    else:
+        orderid = 1
+    return orderid
+
+def insert_strain(inbredsetid, strainname):
+    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))
+
+def insert_strainxref(inbredsetid, strainid):
+    orderid = get_nextorderid_strainxref(inbredsetid)
+    cursor, con = utilities.get_cursor()
+    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_strainxref(inbredsetid, strainid):
+    cursor, con = utilities.get_cursor()
+    sql = """
+        SELECT StrainXRef.`StrainId`
+        FROM StrainXRef
+        WHERE StrainXRef.`InbredSetId`=%s
+        AND StrainXRef.`StrainId`=%s
+        """
+    cursor.execute(sql, (inbredsetid, strainid))
+    return cursor.fetchone()
+
+def get_strain_sure(inbredsetid, strainname, updatestrainxref=None):
+    strain = get_strain(inbredsetid, strainname)
+    if not strain:
+        insert_strain(inbredsetid, strainname)
+        strain = get_strain(inbredsetid, strainname)
+    strainxref = get_strainxref(inbredsetid, strain[0])
+    if not strainxref and updatestrainxref:
+        insert_strainxref(inbredsetid, strain[0])
+    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
diff --git a/scripts/maintenance/load_phenotypes.py b/scripts/maintenance/load_phenotypes.py
index 759d2eec..aa02d0cd 100755
--- a/scripts/maintenance/load_phenotypes.py
+++ b/scripts/maintenance/load_phenotypes.py
@@ -1,3 +1,11 @@
+# Load Python3 environment with GN2 utilities:
+#
+#   source /usr/local/guix-profiles/gn-latest-20210512/etc/profile
+#
+# and run
+#
+#   python load_phenotypes.py [args...] 
+
 import sys
 import csv
 
@@ -9,35 +17,34 @@ def main(argv):
     config = utilities.get_config(argv[1])
     print("config:")
     for item in config.items('config'):
-        print(("\t%s" % (str(item))))
+        print("\t%s" % (str(item)))
     # var
     inbredsetid = config.get('config', 'inbredsetid')
-    print(("inbredsetid: %s" % inbredsetid))
+    print("inbredsetid: %s" % inbredsetid)
     species = datastructure.get_species(inbredsetid)
     speciesid = species[0]
-    print(("speciesid: %s" % speciesid))
+    print("speciesid: %s" % speciesid)
     dataid = datastructure.get_nextdataid_phenotype()
-    print(("next data id: %s" % dataid))
+    print("next data id: %s" % dataid)
     cursor, con = utilities.get_cursor()
     # datafile
     datafile = open(config.get('config', 'datafile'), 'r')
     phenotypedata = csv.reader(datafile, delimiter='\t', quotechar='"')
-    phenotypedata_head = next(phenotypedata)
-    print(("phenotypedata head:\n\t%s" % phenotypedata_head))
+    phenotypedata_head = phenotypedata.next()
+    print("phenotypedata head:\n\t%s" % phenotypedata_head)
     strainnames = phenotypedata_head[1:]
     strains = datastructure.get_strains_bynames(inbredsetid=inbredsetid, strainnames=strainnames, updatestrainxref="yes")
     # metafile
     metafile = open(config.get('config', 'metafile'), 'r')
     phenotypemeta = csv.reader(metafile, delimiter='\t', quotechar='"')
-    phenotypemeta_head = next(phenotypemeta)
-    print(("phenotypemeta head:\n\t%s" % phenotypemeta_head))
-    print()
+    phenotypemeta_head = phenotypemeta.next()
+    print("phenotypemeta head:\n\t%s" % phenotypemeta_head)
     # load
     for metarow in phenotypemeta:
         #
-        datarow_value = next(phenotypedata)
-        datarow_se = next(phenotypedata)
-        datarow_n = next(phenotypedata)
+        datarow_value = phenotypedata.next()
+        datarow_se = phenotypedata.next()
+        datarow_n = phenotypedata.next()
         # Phenotype
         sql = """
             INSERT INTO Phenotype
@@ -67,7 +74,7 @@ def main(argv):
             ))
         rowcount = cursor.rowcount
         phenotypeid = con.insert_id()
-        print(("INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid)))
+        print("INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid))
         # Publication
         publicationid = None # reset
         pubmed_id = utilities.to_db_string(metarow[0], None)
@@ -81,7 +88,7 @@ def main(argv):
             re = cursor.fetchone()
             if re:
                 publicationid = re[0]
-                print(("get Publication record: %d" % publicationid))
+                print("get Publication record: %d" % publicationid)
         if not publicationid:
             sql = """
                 INSERT INTO Publication
@@ -109,7 +116,7 @@ def main(argv):
                 ))
             rowcount = cursor.rowcount
             publicationid = con.insert_id()
-            print(("INSERT INTO Publication: %d record: %d" % (rowcount, publicationid)))
+            print("INSERT INTO Publication: %d record: %d" % (rowcount, publicationid))
         # data
         for index, strain in enumerate(strains):
             #
@@ -158,14 +165,14 @@ def main(argv):
         cursor.execute(sql, (inbredsetid, phenotypeid, publicationid, dataid, ""))
         rowcount = cursor.rowcount
         publishxrefid = con.insert_id()
-        print(("INSERT INTO PublishXRef: %d record: %d" % (rowcount, publishxrefid)))
+        print("INSERT INTO PublishXRef: %d record: %d" % (rowcount, publishxrefid))
         # for loop next
         dataid += 1
-        print()
+        print
     # release
     con.close()
 
 if __name__ == "__main__":
-    print(("command line arguments:\n\t%s" % sys.argv))
+    print("command line arguments:\n\t%s" % sys.argv)
     main(sys.argv)
     print("exit successfully")
diff --git a/scripts/maintenance/utilities.py b/scripts/maintenance/utilities.py
new file mode 100644
index 00000000..886410c2
--- /dev/null
+++ b/scripts/maintenance/utilities.py
@@ -0,0 +1,89 @@
+import MySQLdb
+import re
+import configparser
+
+def get_cursor():
+    host = 'tux.uthsc.edu'
+    user = 'webqtlout'
+    passwd = 'webqtlout'
+    db = 'db_webqtl'
+    con = MySQLdb.Connect(db=db, host=host, user=user, passwd=passwd)
+    cursor = con.cursor()
+    return cursor, con
+
+def clearspaces(s, default=None):
+    if s:
+        s = re.sub('\s+', ' ', s)
+        s = s.strip()
+        return s
+    else:
+        return default
+        
+def to_dic(keys, values):
+    dic = {}
+    for i in range(len(keys)):
+        key = keys[i]
+        value = values[i]
+        dic[key] = value
+    return dic
+
+def overlap(dic1, dic2):
+    keys = []
+    values1 = []
+    values2 = []
+    for key in dic1.keys():
+        if key in dic2:
+            value1 = dic1[key]
+            value2 = dic2[key]
+            if value1 and value2:
+                keys.append(key)
+                values1.append(value1)
+                values2.append(value2)
+    return keys, values1, values2
+
+def to_db_string(s, default):
+    if s:
+        s = s.strip()
+        if len(s) == 0:
+            return default
+        elif s == 'x':
+            return default
+        else:
+            return s
+    else:
+        return default
+
+def to_db_float(s, default):
+    if s:
+        s = s.strip()
+        if len(s) == 0:
+            return default
+        elif s == 'x':
+            return default
+        else:
+            try:
+                return float(s)
+            except:
+                return default
+    else:
+        return default
+        
+def to_db_int(s, default):
+    if s:
+        s = s.strip()
+        if len(s) == 0:
+            return default
+        elif s == 'x':
+            return default
+        else:
+            try:
+                return int(s)
+            except:
+                return default
+    else:
+        return default
+
+def get_config(configfile):
+    config = configparser.ConfigParser()
+    config.read(configfile)
+    return config