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-rw-r--r--wqflask/base/data_set.py17
-rw-r--r--wqflask/base/trait.py103
2 files changed, 107 insertions, 13 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 918932fa..06e02b02 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -271,7 +271,8 @@ class DatasetGroup(object):
self.f1list = None
self.parlist = None
self.get_f1_parent_strains()
- #logger.debug("parents/f1s: {}:{}".format(self.parlist, self.f1list))
+
+ self.accession_id = self.get_accession_id()
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
@@ -280,6 +281,20 @@ class DatasetGroup(object):
self._datasets = None
self.genofile = None
+ def get_accession_id(self):
+ results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
+ InbredSet.Name = %s and
+ PublishFreeze.InbredSetId = InbredSet.Id and
+ InfoFiles.InfoPageName = PublishFreeze.Name and
+ PublishFreeze.public > 0 and
+ PublishFreeze.confidentiality < 1 order by
+ PublishFreeze.CreateTime desc""", (self.name)).fetchone()
+
+ if results != None:
+ return str(results[0])
+ else:
+ return "None"
+
def get_specified_markers(self, markers = []):
self.markers = HumanMarkers(self.name, markers)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 276c624a..8788d983 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -91,16 +91,27 @@ class GeneralTrait(object):
additive=self.additive
)
elif self.dataset.type == "Publish":
- return dict(name=self.name,
- dataset=self.dataset.name,
- description=self.description_display,
- authors=self.authors,
- pubmed_text=self.pubmed_text,
- pubmed_link=self.pubmed_link,
- lrs_score=self.LRS_score_repr,
- lrs_location=self.LRS_location_repr,
- additive=self.additive
- )
+ if self.pubmed_id:
+ return dict(name=self.name,
+ dataset=self.dataset.name,
+ description=self.description_display,
+ authors=self.authors,
+ pubmed_text=self.pubmed_text,
+ pubmed_link=self.pubmed_link,
+ lrs_score=self.LRS_score_repr,
+ lrs_location=self.LRS_location_repr,
+ additive=self.additive
+ )
+ else:
+ return dict(name=self.name,
+ dataset=self.dataset.name,
+ description=self.description_display,
+ authors=self.authors,
+ pubmed_text=self.pubmed_text,
+ lrs_score=self.LRS_score_repr,
+ lrs_location=self.LRS_location_repr,
+ additive=self.additive
+ )
elif self.dataset.type == "Geno":
return dict(name=self.name,
dataset=self.dataset.name,
@@ -109,6 +120,62 @@ class GeneralTrait(object):
else:
return dict()
+ def jsonable_table_row(self, index, search_type):
+ """Return a list suitable for json and intended to be displayed in a table
+
+ Actual turning into json doesn't happen here though"""
+
+ if self.dataset.type == "ProbeSet":
+ if self.mean == "":
+ mean = "N/A"
+ else:
+ mean = "%.3f" % round(float(self.additive), 2)
+ if self.additive == "":
+ additive = "N/A"
+ else:
+ additive = "%.3f" % round(float(self.additive), 2)
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="{{ data_hmac(\'{}:{}\'.format(' + str(self.name) + ',' + self.dataset.name + ')) }}">',
+ index,
+ '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>',
+ self.symbol,
+ self.description_display,
+ self.location_repr,
+ mean,
+ self.LRS_score_repr,
+ self.LRS_location_repr,
+ additive]
+ elif self.dataset.type == "Publish":
+ if self.additive == "":
+ additive = "N/A"
+ else:
+ additive = "%.2f" % round(float(self.additive), 2)
+ if self.pubmed_id:
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="{{ data_hmac(\'{}:{}\'.format(' + str(self.name) + ',' + self.dataset.name + ')) }}">',
+ index,
+ '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>',
+ self.description_display,
+ self.authors,
+ '<a href="' + self.pubmed_link + '">' + self.pubmed_text + '</href>',
+ self.LRS_score_repr,
+ self.LRS_location_repr,
+ additive]
+ else:
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="{{ data_hmac(\'{}:{}\'.format(' + str(self.name) + ',' + self.dataset.name + ')) }}">',
+ index,
+ '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>',
+ self.description_display,
+ self.authors,
+ self.pubmed_text,
+ self.LRS_score_repr,
+ self.LRS_location_repr,
+ additive]
+ elif self.dataset.type == "Geno":
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="{{ data_hmac(\'{}:{}\'.format(' + str(self.name) + ',' + self.dataset.name + ')) }}">',
+ index,
+ '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>',
+ self.location_repr]
+ else:
+ return dict()
def get_name(self):
stringy = ""
@@ -418,7 +485,7 @@ class GeneralTrait(object):
self.description_display = description_display
#XZ: trait_location_value is used for sorting
- trait_location_repr = 'N/A'
+ self.location_repr = 'N/A'
trait_location_value = 1000000
if self.chr and self.mb:
@@ -438,6 +505,18 @@ class GeneralTrait(object):
self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
self.location_value = trait_location_value
+ elif self.dataset.type == "Geno":
+ self.location_repr = 'N/A'
+ trait_location_value = 1000000
+
+ if self.chr and self.mb:
+ #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
+ #This is so we can convert the location to a number used for sorting
+ trait_location_value = convert_location_to_value(self.chr, self.mb)
+
+ #ZS: Put this in function currently called "convert_location_to_value"
+ self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
+ self.location_value = trait_location_value
if get_qtl_info:
#LRS and its location
@@ -459,7 +538,7 @@ class GeneralTrait(object):
logger.sql(query)
trait_qtl = g.db.execute(query).fetchone()
if trait_qtl:
- self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl
+ self.locus, self.lrs, self.pvalue, self.mean, self.additive = trait_qtl
if self.locus:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 18:15:13 +0000