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-rwxr-xr-xwqflask/utility/__init__.py12
-rwxr-xr-xwqflask/wqflask/show_trait/DataEditingPage.py264
2 files changed, 156 insertions, 120 deletions
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index e69de29b..206d0d1c 100755
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -0,0 +1,12 @@
+class Bunch(object):
+ """Make the configuration a little cleaner"""
+ def __init__(self, config_string = "", **kw):
+ if config_string:
+ td = yaml.load(config_string)
+ self.__dict__.update(td)
+ else:
+ self.__dict__ = kw
+
+ def __repr__(self):
+ return yaml.dump(self.__dict__, default_flow_style=False)
+
diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index d186889b..e431fd76 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -12,7 +12,7 @@ from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
from base import webqtlCaseData
-from utility import webqtlUtil, Plot
+from utility import webqtlUtil, Plot, Bunch
from base.webqtlTrait import webqtlTrait
from dbFunction import webqtlDatabaseFunction
from base.templatePage import templatePage
@@ -1467,9 +1467,6 @@ class DataEditingPage(templatePage):
all_samples_ordered = fd.f1list + fd.samplelist
else:
all_samples_ordered = fd.f1list + fd.parlist + fd.samplelist
-
- attribute_ids = []
- attribute_names = []
#ZS: Id values for this trait's extra attributes;
#used to create "Exclude" dropdown and query for attribute values and create
@@ -1479,6 +1476,8 @@ class DataEditingPage(templatePage):
CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId
group by CaseAttributeXRef.CaseAttributeId""",
(str(this_trait.db.id),))
+
+
for this_attr_name in attribute_names:
# Todo: Needs testing still!
@@ -1491,36 +1490,28 @@ class DataEditingPage(templatePage):
distinct_values = self.cursor.fetchall()
this_trait_samples = set(this_trait.data.keys())
- #ZS - Checks if there are any samples in this_trait_samples that aren't in all_samples_ordered
- #Will need to be used in the future to determine whether to create one or two tables are created (probably)
- #other_samples_exist = this_trait_samples - set(all_samples_ordered)
- #mainForm = None # Just trying to get things working
+ primary_sample_names = all_samples_ordered
- primary_samplelist = all_samples_ordered
-
- print("primary_samplelist is:", pf(primary_samplelist))
+ print("primary_samplelist is:", pf(primary_sample_names))
primary_samples = SampleList(self.cursor,
- fd=fd,
- variance_data_page=variance_data_page,
- samplelist=primary_samplelist,
- #mainForm=mainForm,
- this_trait=this_trait,
- attribute_ids=attribute_ids,
- attribute_names=attribute_names,
- samples='primary',
- header="%s Only" % (fd.RISet))
-
-
- other_samples = []
+ fd=fd,
+ variance_data_page=variance_data_page,
+ sample_names=primary_sample_names,
+ this_trait=this_trait,
+ samples='primary',
+ header="%s Only" % (fd.RISet))
+
+
+ other_sample_names = []
for sample in this_trait.data.keys():
print("hjk - sample is:", sample)
if sample not in all_samples_ordered:
all_samples_ordered.append(sample)
- other_samples.append(sample)
+ other_sample_names.append(sample)
- if other_samples:
+ if other_sample_names:
unappended_par_f1 = fd.f1list + fd.parlist
par_f1_samples = ["_2nd_" + sample for sample in unappended_par_f1]
@@ -1528,31 +1519,24 @@ class DataEditingPage(templatePage):
other_samples = par_f1_samples + other_samples
other_samples = SampleList(self.cursor,
- fd=fd,
- variance_data_page=variance_data_page,
- samplelist=other_samples,
- #mainForm=mainForm,
- this_trait=this_trait,
- attribute_ids=attribute_ids,
- attribute_names=attribute_names,
- samples='other',
- header="Non-%s" % (fd.RISet))
-
+ fd=fd,
+ variance_data_page=variance_data_page,
+ sample_names=other_sample_names,
+ this_trait=this_trait,
+ samples='other',
+ header="Non-%s" % (fd.RISet))
+
+ self.sample_groups = (primary_samples, other_samples)
+ else:
+ self.sample_groups = (primary_samples,)
#TODO: Figure out why this if statement is written this way - Zach
- if (other_samples or (fd.f1list and this_trait.data.has_key(fd.f1list[0]))
+ if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0]))
or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))):
print("hjs")
fd.allsamplelist = all_samples_ordered
-
-
- #self.primary_samples = dict(header = "%s Only" % (fd.RISet),
- # samples = primary_samples,)
- #
- #self.other_samples = dict(header = "Non-%s" % (fd.RISet),
- # samples = other_samples,)
- self.sample_groups = (primary_samples, other_samples)
+
class SampleList(list):
@@ -1560,56 +1544,35 @@ class SampleList(list):
cursor,
fd,
variance_data_page,
- samplelist,
+ sample_names,
this_trait,
- attribute_ids,
- attribute_names,
samples,
header):
self.header = header
-
- if attribute_ids == None:
- attribute_ids = []
-
- if attribute_names == None:
- attribute_names = []
-
- #XZ, Aug 23, 2010: I commented the code related to the display of animal case
- #sampleInfo = this_trait.has_key('sampleInfo') and this_trait.sampleInfo
- print("in create_sample_objects")
- #table_body = []
- ################### Only used to find upperBound and lowerBound
- #vals = []
- #for sampleNameOrig in samplelist:
- # sampleName = sampleNameOrig.replace("_2nd_", "")
- # print("pen: %s - %s" % (sampleNameOrig, sampleName))
- # try:
- # thisval = this_trait.data[sampleName].value
- # thisvar = this_trait.data[sampleName].variance
- # thisValFull = [sampleName, thisval, thisvar]
- #
- # vals.append(thisValFull)
- # except KeyError:
- # print("**x** Skipping:", sampleName)
- #
- #upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers.
-
+
+
+ self.calc_attributes()
- #the_samples = []
+ for counter, sample_name in enumerate(sample_names, 1):
+ sample_name = sample_name.replace("_2nd_", "")
- for counter, sampleNameOrig in enumerate(samplelist, 1):
- sampleName = sampleNameOrig.replace("_2nd_", "")
- sampleNameAdd = ''
- if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'):
- sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank")
-
+ #ZS - 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 = this_trait.data[sampleName]
+ sample = this_trait.data[sample_name]
except KeyError:
- print("No sample %s, let's create it now" % sampleName)
- sample = webqtlCaseData.webqtlCaseData(sampleName)
+ print("No sample %s, let's create it now" % sample_name)
+ sample = webqtlCaseData.webqtlCaseData(sample_name)
+
+ #sampleNameAdd = ''
+ #if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'):
+ # sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank")
+ sample.extra_info = {}
+ if fd.RISet == '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"
+
print("zyt - sampleNameOrig:", sampleNameOrig)
print(" type of sample:", type(sample))
@@ -1620,42 +1583,7 @@ class SampleList(list):
#### For extra attribute columns; currently only used by two human datasets - Zach
if this_trait and this_trait.db and this_trait.db.type == 'ProbeSet':
- if len(attribute_ids) > 0:
-
- #ZS: Get StrainId value for the next query
- cursor.execute("""SELECT Strain.Id
- FROM Strain, StrainXRef, InbredSetd
- WHERE Strain.Name = '%s' and
- StrainXRef.StrainId = Strain.Id and
- InbredSet.Id = StrainXRef.InbredSetId and
- InbredSet.Name = '%s'""" % (sampleName, fd.RISet))
-
- sample_id = cursor.fetchone()[0]
-
- attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column).
- for attribute_id in attribute_ids:
-
- #ZS: Add extra case attribute values (if any)
- cursor.execute("""SELECT Value
- FROM CaseAttributeXRef
- WHERE ProbeSetFreezeId = '%s' AND
- StrainId = '%s' AND
- CaseAttributeId = '%s'
- group by CaseAttributeXRef.CaseAttributeId""" % (this_trait.db.id, sample_id, str(attribute_id)))
-
- attributeValue = cursor.fetchone()[0] #Trait-specific attributes, if any
-
- #ZS: 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:
- attributeValue = int(attributeValue)
- except:
- pass
-
- span_Id = samples+"_attribute"+str(attr_counter)+"_sample"+str(i+1)
- attr_container = HT.Span(attributeValue, Id=span_Id)
- attr_className = str(attributeValue) + " " + className
- table_row.append(HT.TD(attr_container, align='right', Class=attr_className))
- attr_counter += 1
+ self.get_extra_attribute_values(attribute_ids, this_trait, sample_name)
self.append(sample)
#table_body.append(table_row)
@@ -1679,3 +1607,99 @@ class SampleList(list):
sample.outlier = True
else:
sample.outlier = False
+
+ def calc_attributes(self):
+ """Finds which extra attributes apply to this dataset"""
+
+
+ #ZS: Id and name values for this trait's extra attributes
+ self.cursor.execute('''SELECT CaseAttribute.Id, CaseAttribute.Name
+ FROM CaseAttribute, CaseAttributeXRef
+ WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND
+ CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId
+ group by CaseAttributeXRef.CaseAttributeId''',
+ (str(this_trait.db.id),))
+
+ #self.attributes = {key, value in self.cursor.fetchall()}
+ #self.attributes = OrderedDict(self.attributes.iteritems())
+
+ self.attributes = {}
+ for key, value in self.cursor.fetchall():
+ self.attributes[key] = Bunch()
+ self.attributes[key].name = value
+
+ self.cursor.execute('''SELECT DISTINCT CaseAttributeXRef.Value
+ FROM CaseAttribute, CaseAttributeXRef
+ WHERE CaseAttribute.Name = %s AND
+ CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,))
+
+ self.attributes[key].distinct_values = self.cursor.fetchall()
+
+
+ try:
+
+ exclude_menu = HT.Select(name="exclude_menu")
+ dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden)
+
+ for attribute in self.cursor.fetchall():
+ attribute_ids.append(attribute[0])
+ attribute_names.append(attribute[1])
+ for this_attr_name in attribute_names:
+ exclude_menu.append((this_attr_name.capitalize(), this_attr_name))
+ self.cursor.execute("""SELECT DISTINCT CaseAttributeXRef.Value
+ FROM CaseAttribute, CaseAttributeXRef
+ WHERE CaseAttribute.Name = '%s' AND
+ CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id""" % (this_attr_name))
+ try:
+ distinct_values = self.cursor.fetchall()
+ attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus
+ attr_value_menu = HT.Select(name=this_attr_name)
+ attr_value_menu.append(("None", "show_all"))
+ for value in distinct_values:
+ attr_value_menu.append((str(value[0]), value[0]))
+ attr_value_menu_div.append(attr_value_menu)
+ dropdown_menus.append(attr_value_menu_div)
+ except:
+ pass
+ except:
+ pass
+
+
+ def get_extra_attribute_values(self):
+
+ if len(attribute_ids) > 0:
+
+ #ZS: Get StrainId value for the next query
+ cursor.execute("""SELECT Strain.Id
+ FROM Strain, StrainXRef, InbredSetd
+ WHERE Strain.Name = '%s' and
+ StrainXRef.StrainId = Strain.Id and
+ InbredSet.Id = StrainXRef.InbredSetId and
+ InbredSet.Name = '%s'""" % (sampleName, fd.RISet))
+
+ sample_id = cursor.fetchone()[0]
+
+ attr_counter = 1 # This is needed so the javascript can know which attribute type to associate this value with for the exported excel sheet (each attribute type being a column).
+ for attribute_id in attribute_ids:
+
+ #ZS: Add extra case attribute values (if any)
+ cursor.execute("""SELECT Value
+ FROM CaseAttributeXRef
+ WHERE ProbeSetFreezeId = '%s' AND
+ StrainId = '%s' AND
+ CaseAttributeId = '%s'
+ group by CaseAttributeXRef.CaseAttributeId""" % (this_trait.db.id, sample_id, str(attribute_id)))
+
+ attributeValue = cursor.fetchone()[0] #Trait-specific attributes, if any
+
+ #ZS: 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:
+ attributeValue = int(attributeValue)
+ except ValueError:
+ pass
+
+ span_Id = samples+"_attribute"+str(attr_counter)+"_sample"+str(i+1)
+ attr_container = HT.Span(attributeValue, Id=span_Id)
+ attr_className = str(attributeValue) + " " + className
+ table_row.append(HT.TD(attr_container, align='right', Class=attr_className))
+ attr_counter += 1
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 11:24:37 +0000