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-rw-r--r--gn2/wqflask/show_trait/SampleList.py223
1 files changed, 223 insertions, 0 deletions
diff --git a/gn2/wqflask/show_trait/SampleList.py b/gn2/wqflask/show_trait/SampleList.py
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+++ b/gn2/wqflask/show_trait/SampleList.py
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+import re
+import itertools
+
+from gn2.wqflask.database import database_connection
+from gn2.base import webqtlCaseData, webqtlConfig
+from pprint import pformat as pf
+
+from gn2.utility import Plot
+from gn2.utility import Bunch
+from gn2.utility.tools import get_setting
+
+class SampleList:
+ def __init__(self,
+ dataset,
+ sample_names,
+ this_trait,
+ sample_group_type="primary",
+ header="Samples"):
+
+ self.dataset = dataset
+ self.this_trait = this_trait
+ self.sample_group_type = sample_group_type # primary or other
+ self.header = header
+
+ self.sample_list = [] # The actual list
+ self.sample_attribute_values = {}
+
+ self.get_attributes()
+
+ if self.this_trait and self.dataset:
+ self.get_extra_attribute_values()
+
+ for counter, sample_name in enumerate(sample_names, 1):
+ sample_name = sample_name.replace("_2nd_", "")
+
+ # self.this_trait will be a list if it is a Temp trait
+ if isinstance(self.this_trait, list):
+ sample = webqtlCaseData.webqtlCaseData(name=sample_name)
+ if counter <= len(self.this_trait):
+ if isinstance(self.this_trait[counter - 1], (bytes, bytearray)):
+ if (self.this_trait[counter - 1].decode("utf-8").lower() != 'x'):
+ sample = webqtlCaseData.webqtlCaseData(
+ name=sample_name,
+ value=float(self.this_trait[counter - 1]))
+ else:
+ if (self.this_trait[counter - 1].lower() != 'x'):
+ sample = webqtlCaseData.webqtlCaseData(
+ name=sample_name,
+ value=float(self.this_trait[counter - 1]))
+ else:
+ # If there's no value for the sample/strain,
+ # create the sample object (so samples with no value
+ # are still displayed in the table)
+ try:
+ sample = self.this_trait.data[sample_name]
+ except KeyError:
+ sample = webqtlCaseData.webqtlCaseData(name=sample_name)
+
+ sample.extra_info = {}
+ if (self.dataset.group.name == 'AXBXA'
+ and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')):
+ sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
+ sample.extra_info['css_class'] = "fs12"
+
+ sample.this_id = str(counter)
+
+ # For extra attribute columns; currently only used by
+ # several datasets
+ if self.sample_attribute_values:
+ sample.extra_attributes = self.sample_attribute_values.get(
+ sample_name, {})
+
+ # Add a url so RRID case attributes can be displayed as links
+ if '36' in sample.extra_attributes:
+ rrid_string = str(sample.extra_attributes['36'])
+ if self.dataset.group.species == "mouse":
+ if len(rrid_string.split(":")) > 1:
+ the_rrid = rrid_string.split(":")[1]
+ sample.extra_attributes['36'] = [
+ rrid_string]
+ sample.extra_attributes['36'].append(
+ webqtlConfig.RRID_MOUSE_URL % the_rrid)
+ elif self.dataset.group.species == "rat":
+ if len(rrid_string):
+ the_rrid = rrid_string.split("_")[1]
+ sample.extra_attributes['36'] = [
+ rrid_string]
+ sample.extra_attributes['36'].append(
+ webqtlConfig.RRID_RAT_URL % the_rrid)
+
+ self.sample_list.append(sample)
+
+ self.se_exists = any(sample.variance for sample in self.sample_list)
+ self.num_cases_exists = False
+ if (any(sample.num_cases for sample in self.sample_list) and
+ any((sample.num_cases and sample.num_cases != "1") for sample in self.sample_list)):
+ self.num_cases_exists = True
+
+ first_attr_col = self.get_first_attr_col()
+ for sample in self.sample_list:
+ sample.first_attr_col = first_attr_col
+
+ self.do_outliers()
+
+ def __repr__(self):
+ return "<SampleList> --> %s" % (pf(self.__dict__))
+
+ def do_outliers(self):
+ values = [sample.value for sample in self.sample_list
+ if sample.value is not None]
+ upper_bound, lower_bound = Plot.find_outliers(values)
+
+ for sample in self.sample_list:
+ if sample.value:
+ if upper_bound and sample.value > upper_bound:
+ sample.outlier = True
+ elif lower_bound and sample.value < lower_bound:
+ sample.outlier = True
+ else:
+ sample.outlier = False
+
+ def get_attributes(self):
+ """Finds which extra attributes apply to this dataset"""
+
+ # Get attribute names and distinct values for each attribute
+ with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+ cursor.execute(
+ "SELECT DISTINCT CaseAttribute.CaseAttributeId, "
+ "CaseAttribute.Name, CaseAttribute.Description, "
+ "CaseAttributeXRefNew.Value FROM "
+ "CaseAttribute, CaseAttributeXRefNew WHERE "
+ "CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.CaseAttributeId "
+ "AND CaseAttributeXRefNew.InbredSetId = %s "
+ "ORDER BY CaseAttribute.CaseAttributeId", (str(self.dataset.group.id),)
+ )
+
+ self.attributes = {}
+ for attr, values in itertools.groupby(
+ cursor.fetchall(), lambda row: (row[0], row[1], row[2])
+ ):
+ key, name, description = attr
+ self.attributes[key] = Bunch()
+ self.attributes[key].id = key
+ self.attributes[key].name = name
+ self.attributes[key].description = description
+ self.attributes[key].distinct_values = [
+ item[3] for item in values]
+ self.attributes[key].distinct_values = natural_sort(
+ self.attributes[key].distinct_values)
+ all_numbers = True
+ for value in self.attributes[key].distinct_values:
+ try:
+ val_as_float = float(value)
+ except:
+ all_numbers = False
+ break
+
+ if all_numbers:
+ self.attributes[key].alignment = "right"
+ else:
+ self.attributes[key].alignment = "left"
+
+ def get_extra_attribute_values(self):
+ if self.attributes:
+ with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+ cursor.execute(
+ "SELECT Strain.Name AS SampleName, "
+ "CaseAttributeId AS Id, "
+ "CaseAttributeXRefNew.Value FROM Strain, "
+ "StrainXRef, InbredSet, CaseAttributeXRefNew "
+ "WHERE StrainXRef.StrainId = Strain.Id "
+ "AND InbredSet.Id = StrainXRef.InbredSetId "
+ "AND CaseAttributeXRefNew.StrainId = Strain.Id "
+ "AND InbredSet.Id = CaseAttributeXRefNew.InbredSetId "
+ "AND CaseAttributeXRefNew.InbredSetId = %s "
+ "ORDER BY SampleName", (self.dataset.group.id,)
+ )
+
+ for sample_name, items in itertools.groupby(
+ cursor.fetchall(), lambda row: row[0]
+ ):
+ attribute_values = {}
+ # Make a list of attr IDs without values (that have values for other samples)
+ valueless_attr_ids = [self.attributes[key].id for key in self.attributes.keys()]
+ for item in items:
+ sample_name, _id, value = item
+ valueless_attr_ids.remove(_id)
+ attribute_value = value
+
+ # If it's an int, turn it into one for sorting
+ # (for example, 101 would be lower than 80 if
+ # they're strings instead of ints)
+ try:
+ attribute_value = int(attribute_value)
+ except ValueError:
+ pass
+
+ attribute_values[str(_id)] = attribute_value
+ for attr_id in valueless_attr_ids:
+ attribute_values[str(attr_id)] = ""
+
+ self.sample_attribute_values[sample_name] = attribute_values
+
+ def get_first_attr_col(self):
+ first_attr_col = 4
+ if self.se_exists:
+ first_attr_col += 2
+ if self.num_cases_exists:
+ first_attr_col += 1
+
+ return first_attr_col
+
+
+def natural_sort(a_list, key=lambda s: s):
+ """
+ Sort the list into natural alphanumeric order.
+ """
+ def get_alphanum_key_func(key):
+ def convert(text): return int(text) if text.isdigit() else text
+ return lambda s: [convert(c) for c in re.split('([0-9]+)', key(s))]
+ sort_key = get_alphanum_key_func(key)
+ sorted_list = sorted(a_list, key=sort_key)
+ return sorted_list
generated by cgit v1.2.3 (git 2.46.2) at 2025-02-17 00:15:09 +0000