Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

1 files changed, 195 insertions, 0 deletions

diff --git a/gn2/base/data_set/datasetgroup.py b/gn2/base/data_set/datasetgroup.py
new file mode 100644
index 00000000..d124283f
--- /dev/null
+++ b/gn2/base/data_set/datasetgroup.py
@@ -0,0 +1,195 @@
+"Dataset Group class ..."
+
+import os
+import json
+
+
+from gn2.base import webqtlConfig
+from .markers import Markers, HumanMarkers
+from gn2.utility import webqtlUtil
+from gn2.utility import gen_geno_ob
+from gn2.db import webqtlDatabaseFunction
+from gn2.maintenance import get_group_samplelists
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import (
+    locate,
+    USE_REDIS,
+    flat_files,
+    get_setting,
+    flat_file_exists,
+    locate_ignore_error)
+
+class DatasetGroup:
+    """
+    Each group has multiple datasets; each species has multiple groups.
+
+    For example, Mouse has multiple groups (BXD, BXA, etc), and each group
+    has multiple datasets associated with it.
+
+    """
+
+    def __init__(self, dataset, name=None):
+        """This sets self.group and self.group_id"""
+        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+            if not name:
+                cursor.execute(dataset.query_for_group,
+                               (dataset.name,))
+            else:
+                cursor.execute(
+                    "SELECT InbredSet.Name, "
+                    "InbredSet.Id, "
+                    "InbredSet.GeneticType, "
+                    "InbredSet.InbredSetCode "
+                    "FROM InbredSet WHERE Name = %s",
+                    (name,))
+            results = cursor.fetchone()
+            if results:
+                (self.name, self.id, self.genetic_type, self.code) = results
+            else:
+                self.name = name or dataset.name
+        if self.name == 'BXD300':
+            self.name = "BXD"
+
+        self.f1list = None
+        self.parlist = None
+        self.get_f1_parent_strains()
+
+        self.mapping_id, self.mapping_names = self.get_mapping_methods()
+
+        self.species = webqtlDatabaseFunction.retrieve_species(self.name)
+
+        self.incparentsf1 = False
+        self.allsamples = None
+        self._datasets = None
+        self.genofile = None
+
+    def get_mapping_methods(self):
+        mapping_id = ()
+        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+            cursor.execute(
+                "SELECT MappingMethodId FROM "
+                "InbredSet WHERE Name= %s",
+                (self.name,))
+            results = cursor.fetchone()
+            if results and results[0]:
+                mapping_id = results[0]
+        if mapping_id == "1":
+            mapping_names = ["GEMMA", "QTLReaper", "R/qtl"]
+        elif mapping_id == "2":
+            mapping_names = ["GEMMA"]
+        elif mapping_id == "3":
+            mapping_names = ["R/qtl"]
+        elif mapping_id == "4":
+            mapping_names = ["GEMMA", "PLINK"]
+        else:
+            mapping_names = []
+
+        return mapping_id, mapping_names
+
+    def get_markers(self):
+        def check_plink_gemma():
+            if flat_file_exists("mapping"):
+                MAPPING_PATH = flat_files("mapping") + "/"
+                if os.path.isfile(MAPPING_PATH + self.name + ".bed"):
+                    return True
+            return False
+
+        if check_plink_gemma():
+            marker_class = HumanMarkers
+        else:
+            marker_class = Markers
+
+        if self.genofile:
+            self.markers = marker_class(self.genofile[:-5])
+        else:
+            self.markers = marker_class(self.name)
+
+    def get_f1_parent_strains(self):
+        try:
+            # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
+            f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
+        except KeyError:
+            f1 = f12 = maternal = paternal = None
+
+        if f1 and f12:
+            self.f1list = [f1, f12]
+        if maternal and paternal:
+            self.parlist = [maternal, paternal]
+
+    def get_study_samplelists(self):
+        study_sample_file = locate_ignore_error(
+            self.name + ".json", 'study_sample_lists')
+        try:
+            f = open(study_sample_file)
+        except:
+            return []
+        study_samples = json.load(f)
+        return study_samples
+
+    def get_genofiles(self):
+        jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name)
+        try:
+            f = open(jsonfile)
+        except:
+            return None
+        jsondata = json.load(f)
+        return jsondata['genofile']
+
+    def get_samplelist(self, redis_conn):
+        result = None
+        key = "samplelist:v3:" + self.name
+        if USE_REDIS:
+            result = redis_conn.get(key)
+
+        if result is not None:
+            self.samplelist = json.loads(result)
+        else:
+            genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype')
+            if genotype_fn:
+                self.samplelist = get_group_samplelists.get_samplelist(
+                    "geno", genotype_fn)
+            else:
+                self.samplelist = None
+
+            if USE_REDIS:
+                redis_conn.set(key, json.dumps(self.samplelist))
+                redis_conn.expire(key, 60 * 5)
+
+    def all_samples_ordered(self):
+        result = []
+        lists = (self.parlist, self.f1list, self.samplelist)
+        [result.extend(l) for l in lists if l]
+        return result
+
+    def read_genotype_file(self, use_reaper=False):
+        '''Read genotype from .geno file instead of database'''
+        # genotype_1 is Dataset Object without parents and f1
+        # genotype_2 is Dataset Object with parents and f1 (not for intercross)
+
+        # reaper barfs on unicode filenames, so here we ensure it's a string
+        if self.genofile:
+            if "RData" in self.genofile:  # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
+                full_filename = str(
+                    locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
+            else:
+                full_filename = str(locate(self.genofile, 'genotype'))
+        else:
+            full_filename = str(locate(self.name + '.geno', 'genotype'))
+        genotype_1 = gen_geno_ob.genotype(full_filename)
+
+        if genotype_1.type == "group" and self.parlist:
+            genotype_2 = genotype_1.add(
+                Mat=self.parlist[0], Pat=self.parlist[1])  # , F1=_f1)
+        else:
+            genotype_2 = genotype_1
+
+        # determine default genotype object
+        if self.incparentsf1 and genotype_1.type != "intercross":
+            genotype = genotype_2
+        else:
+            self.incparentsf1 = 0
+            genotype = genotype_1
+
+        self.samplelist = list(genotype.prgy)
+
+        return genotype