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-rwxr-xr-xwqflask/wqflask/do_search.py192
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py1
-rwxr-xr-xwqflask/wqflask/search_results.py77
-rw-r--r--wqflask/wqflask/static/new/javascript/scatter-matrix.js4
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait.coffee4
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait.js4
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait_statistics_new.html2
-rwxr-xr-xwqflask/wqflask/views.py2
9 files changed, 230 insertions, 58 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 29f3de98..31dc11b5 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -38,7 +38,6 @@ class DoSearch(object):
query = self.normalize_spaces(query)
print("in do_search query is:", pf(query))
results = g.db.execute(query, no_parameters=True).fetchall()
- #results = self.cursor.fetchall()
return results
#def escape(self, stringy):
@@ -139,11 +138,8 @@ class MrnaAssaySearch(DoSearch):
return query
- def run(self):
- """Generates and runs a simple search of an mRNA expression dataset"""
-
- print("Running ProbeSetSearch")
- query = self.base_query + """WHERE (MATCH (ProbeSet.Name,
+ def get_where_clause(self):
+ where_clause = """(MATCH (ProbeSet.Name,
ProbeSet.description,
ProbeSet.symbol,
alias,
@@ -156,6 +152,37 @@ class MrnaAssaySearch(DoSearch):
""" % (escape(self.search_term[0]),
escape(str(self.dataset.id)))
+ return where_clause
+
+ def run_combined(self, from_clause, where_clause):
+ """Generates and runs a combined search of an mRNA expression dataset"""
+
+ print("Running ProbeSetSearch")
+ #query = self.base_query + from_clause + " WHERE " + where_clause
+
+ from_clause = self.normalize_spaces(from_clause)
+
+ query = (self.base_query +
+ """%s
+ WHERE %s
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetXRef.ProbeSetFreezeId = %s
+ """ % (escape(from_clause),
+ where_clause,
+ escape(str(self.dataset.id))))
+
+ print("final query is:", pf(query))
+
+
+ return self.execute(query)
+
+ def run(self):
+ """Generates and runs a simple search of an mRNA expression dataset"""
+
+ print("Running ProbeSetSearch")
+ where_clause = self.get_where_clause()
+ query = self.base_query + "WHERE " + where_clause
+
#print("final query is:", pf(query))
return self.execute(query)
@@ -433,12 +460,15 @@ class LrsSearch(MrnaAssaySearch):
DoSearch.search_types['LRS'] = 'LrsSearch'
- def run(self):
+ def get_from_clause(self):
+ if self.search_operator == "=":
+ return ", Geno"
+ else:
+ return ""
+ def get_where_clause(self):
self.search_term = [float(value) for value in self.search_term]
- self.from_clause = ", Geno"
-
if self.search_operator == "=":
assert isinstance(self.search_term, (list, tuple))
self.lrs_min, self.lrs_max = self.search_term[:2]
@@ -451,7 +481,7 @@ class LrsSearch(MrnaAssaySearch):
if len(self.search_term) > 2:
self.chr_num = self.search_term[2]
- self.sub_clause += """ Geno.Chr = %s and """ % (escape(self.chr_num))
+ self.sub_clause += """ Geno.Chr = %s and """ % (self.chr_num)
if len(self.search_term) == 5:
self.mb_low, self.mb_high = self.search_term[3:]
self.sub_clause += """ Geno.Mb > %s and
@@ -459,21 +489,71 @@ class LrsSearch(MrnaAssaySearch):
""" % self.mescape(min(self.mb_low, self.mb_high),
max(self.mb_low, self.mb_high))
print("self.sub_clause is:", pf(self.sub_clause))
+
+ #%s.Chr = Geno.Chr
+ where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and
+ Geno.SpeciesId = %s
+ """ % self.mescape(self.dataset.type,
+ self.species_id)
else:
# Deal with >, <, >=, and <=
print("self.search_term is:", self.search_term)
- self.sub_clause = """ %sXRef.LRS %s %s and """ % self.mescape(self.dataset.type,
+ self.sub_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type,
self.search_operator,
self.search_term[0])
+ where_clause = self.sub_clause
+
- self.where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and
- Geno.SpeciesId = %s and
- %s.Chr = Geno.Chr
- """ % self.mescape(self.dataset.type,
- self.species_id,
- self.dataset.type)
+ return where_clause
- print("where_clause is:", pf(self.where_clause))
+ def get_final_query(self):
+ self.from_clause = self.get_from_clause()
+ self.where_clause = self.get_where_clause()
+ self.query = self.compile_final_query(self.from_clause, self.where_clause)
+
+ return self.query
+
+ def run(self):
+
+ self.from_clause = self.get_from_clause()
+
+ #self.search_term = [float(value) for value in self.search_term]
+ #
+ #if self.search_operator == "=":
+ # assert isinstance(self.search_term, (list, tuple))
+ # self.lrs_min, self.lrs_max = self.search_term[:2]
+ #
+ # self.sub_clause = """ %sXRef.LRS > %s and
+ # %sXRef.LRS < %s and """ % self.mescape(self.dataset.type,
+ # min(self.lrs_min, self.lrs_max),
+ # self.dataset.type,
+ # max(self.lrs_min, self.lrs_max))
+ #
+ # if len(self.search_term) > 2:
+ # self.chr_num = self.search_term[2]
+ # self.sub_clause += """ Geno.Chr = %s and """ % (escape(self.chr_num))
+ # if len(self.search_term) == 5:
+ # self.mb_low, self.mb_high = self.search_term[3:]
+ # self.sub_clause += """ Geno.Mb > %s and
+ # Geno.Mb < %s and
+ # """ % self.mescape(min(self.mb_low, self.mb_high),
+ # max(self.mb_low, self.mb_high))
+ # print("self.sub_clause is:", pf(self.sub_clause))
+ #else:
+ # # Deal with >, <, >=, and <=
+ # print("self.search_term is:", self.search_term)
+ # self.sub_clause = """ %sXRef.LRS %s %s and """ % self.mescape(self.dataset.type,
+ # self.search_operator,
+ # self.search_term[0])
+ #
+ #self.where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and
+ # Geno.SpeciesId = %s and
+ # %s.Chr = Geno.Chr
+ # """ % self.mescape(self.dataset.type,
+ # self.species_id,
+ # self.dataset.type)
+
+ self.where_clause = self.get_where_clause()
self.query = self.compile_final_query(self.from_clause, self.where_clause)
@@ -586,25 +666,54 @@ class MeanSearch(MrnaAssaySearch):
DoSearch.search_types['MEAN'] = "MeanSearch"
- def run(self):
-
+ def get_where_clause(self):
self.search_term = [float(value) for value in self.search_term]
if self.search_operator == "=":
assert isinstance(self.search_term, (list, tuple))
self.mean_min, self.mean_max = self.search_term[:2]
- self.where_clause = """ %sXRef.mean > %s and
+ where_clause = """ %sXRef.mean > %s and
%sXRef.mean < %s """ % self.mescape(self.dataset.type,
min(self.mean_min, self.mean_max),
self.dataset.type,
max(self.mean_min, self.mean_max))
else:
# Deal with >, <, >=, and <=
- self.where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type,
+ where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type,
self.search_operator,
- self.search_term[0])
+ self.search_term[0])
+
+ return where_clause
+ def get_final_query(self):
+ self.where_clause = self.get_where_clause()
+ print("where_clause is:", pf(self.where_clause))
+
+ self.query = self.compile_final_query(where_clause = self.where_clause)
+
+ return self.query
+
+ def run(self):
+
+ #self.search_term = [float(value) for value in self.search_term]
+ #
+ #if self.search_operator == "=":
+ # assert isinstance(self.search_term, (list, tuple))
+ # self.mean_min, self.mean_max = self.search_term[:2]
+ #
+ # self.where_clause = """ %sXRef.mean > %s and
+ # %sXRef.mean < %s """ % self.mescape(self.dataset.type,
+ # min(self.mean_min, self.mean_max),
+ # self.dataset.type,
+ # max(self.mean_min, self.mean_max))
+ #else:
+ # # Deal with >, <, >=, and <=
+ # self.where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type,
+ # self.search_operator,
+ # self.search_term[0])
+
+ self.where_clause = self.get_where_clause()
print("where_clause is:", pf(self.where_clause))
self.query = self.compile_final_query(where_clause = self.where_clause)
@@ -616,14 +725,11 @@ class RangeSearch(MrnaAssaySearch):
DoSearch.search_types['RANGE'] = "RangeSearch"
- def run(self):
-
- self.search_term = [float(value) for value in self.search_term]
-
+ def get_where_clause(self):
if self.search_operator == "=":
assert isinstance(self.search_term, (list, tuple))
self.range_min, self.range_max = self.search_term[:2]
- self.where_clause = """ (SELECT Pow(2, max(value) -min(value))
+ where_clause = """ (SELECT Pow(2, max(value) -min(value))
FROM ProbeSetData
WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s AND
(SELECT Pow(2, max(value) -min(value))
@@ -633,12 +739,38 @@ class RangeSearch(MrnaAssaySearch):
max(self.range_min, self.range_max))
else:
# Deal with >, <, >=, and <=
- self.where_clause = """ (SELECT Pow(2, max(value) -min(value))
+ where_clause = """ (SELECT Pow(2, max(value) -min(value))
FROM ProbeSetData
WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s
""" % (escape(self.search_term[0]))
- print("where_clause is:", pf(self.where_clause))
+ print("where_clause is:", pf(where_clause))
+
+ return where_clause
+
+ def run(self):
+
+ #self.search_term = [float(value) for value in self.search_term]
+ #
+ #if self.search_operator == "=":
+ # assert isinstance(self.search_term, (list, tuple))
+ # self.range_min, self.range_max = self.search_term[:2]
+ # self.where_clause = """ (SELECT Pow(2, max(value) -min(value))
+ # FROM ProbeSetData
+ # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s AND
+ # (SELECT Pow(2, max(value) -min(value))
+ # FROM ProbeSetData
+ # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) < %s
+ # """ % self.mescape(min(self.range_min, self.range_max),
+ # max(self.range_min, self.range_max))
+ #else:
+ # # Deal with >, <, >=, and <=
+ # self.where_clause = """ (SELECT Pow(2, max(value) -min(value))
+ # FROM ProbeSetData
+ # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s
+ # """ % (escape(self.search_term[0]))
+
+ self.where_clause = self.get_where_clause()
self.query = self.compile_final_query(where_clause = self.where_clause)
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 60221c05..fa680f5f 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -720,6 +720,7 @@ class MarkerRegression(object):
#def gen_human_results(self, pheno_vector, tempdata):
def gen_human_results(self, pheno_vector, key, temp_uuid):
file_base = os.path.join(webqtlConfig.PYLMM_PATH, self.dataset.group.name)
+ print("file_base:", file_base)
plink_input = input.plink(file_base, type='b')
input_file_name = os.path.join(webqtlConfig.SNP_PATH, self.dataset.group.name + ".snps.gz")
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index c6521106..a2958108 100755
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -221,26 +221,63 @@ class SearchResultPage(object):
self.search_terms = parser.parse(self.search_terms)
print("After parsing:", self.search_terms)
- for a_search in self.search_terms:
- print("[kodak] item is:", pf(a_search))
- search_term = a_search['search_term']
- search_operator = a_search['separator']
- if a_search['key']:
- search_type = a_search['key'].upper()
- else:
- # We fall back to the dataset type as the key to get the right object
- search_type = self.dataset.type
+ if len(self.search_terms) > 1:
+ combined_from_clause = ""
+ combined_where_clause = ""
+ for i, a_search in enumerate(self.search_terms):
+ print("[kodak] item is:", pf(a_search))
+ search_term = a_search['search_term']
+ search_operator = a_search['separator']
+ if a_search['key']:
+ search_type = a_search['key'].upper()
+ else:
+ # We fall back to the dataset type as the key to get the right object
+ search_type = self.dataset.type
+
+ print("search_type is:", pf(search_type))
+
+ search_ob = do_search.DoSearch.get_search(search_type)
+ search_class = getattr(do_search, search_ob)
+ the_search = search_class(search_term,
+ search_operator,
+ self.dataset,
+ )
+
+ #search_query = the_search.get_final_query()
+
+ get_from_clause = getattr(the_search, "get_from_clause", None)
+ if callable(get_from_clause):
+ from_clause = the_search.get_from_clause()
+ combined_from_clause += from_clause
+ where_clause = the_search.get_where_clause()
+ combined_where_clause += "(" + where_clause + ")"
+ if (i+1) < len(self.search_terms):
+ combined_where_clause += "AND"
+
+ results = the_search.run_combined(combined_from_clause, combined_where_clause)
+ self.results.extend(results)
+
+ else:
+ for a_search in self.search_terms:
+ print("[kodak] item is:", pf(a_search))
+ search_term = a_search['search_term']
+ search_operator = a_search['separator']
+ if a_search['key']:
+ search_type = a_search['key'].upper()
+ else:
+ # We fall back to the dataset type as the key to get the right object
+ search_type = self.dataset.type
- print("search_type is:", pf(search_type))
-
- search_ob = do_search.DoSearch.get_search(search_type)
- search_class = getattr(do_search, search_ob)
- print("search_class is: ", pf(search_class))
- the_search = search_class(search_term,
- search_operator,
- self.dataset,
- )
- self.results.extend(the_search.run())
- #print("in the search results are:", self.results)
+ print("search_type is:", pf(search_type))
+
+ search_ob = do_search.DoSearch.get_search(search_type)
+ search_class = getattr(do_search, search_ob)
+ print("search_class is: ", pf(search_class))
+ the_search = search_class(search_term,
+ search_operator,
+ self.dataset,
+ )
+ self.results.extend(the_search.run())
+ #print("in the search results are:", self.results)
self.header_fields = the_search.header_fields
diff --git a/wqflask/wqflask/static/new/javascript/scatter-matrix.js b/wqflask/wqflask/static/new/javascript/scatter-matrix.js
index 38fd276e..38cdc75b 100644
--- a/wqflask/wqflask/static/new/javascript/scatter-matrix.js
+++ b/wqflask/wqflask/static/new/javascript/scatter-matrix.js
@@ -56,9 +56,11 @@ ScatterMatrix.prototype.render = function () {
var container = d3.select('#scatterplot_container').append('div')
.attr('class', 'scatter-matrix-container');
var control = container.append('div')
- .attr('class', 'scatter-matrix-control');
+ .attr('class', 'scatter-matrix-control')
+ .style({'float':'left'})
var svg = container.append('div')
.attr('class', 'scatter-matrix-svg')
+ .style({'float':'right'})
.html('<em>Loading data...</em>');
this.onData(function() {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 2cdad5ee..d05ccbf7 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -95,12 +95,12 @@ $ ->
new Box_Plot(all_samples)
d3.select("#select_compare_trait").on("click", =>
- $('.qtlcharts').empty()
+ $('.scatter-matrix-container').remove()
open_trait_selection()
)
d3.select("#clear_compare_trait").on("click", =>
- $('.qtlcharts').empty()
+ $('.scatter-matrix-container').remove()
)
open_trait_selection = () ->
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 40bc3d0a..159dafcb 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -91,13 +91,13 @@ $(function() {
});
d3.select("#select_compare_trait").on("click", (function(_this) {
return function() {
- $('.qtlcharts').empty();
+ $('.scatter-matrix-container').remove();
return open_trait_selection();
};
})(this));
d3.select("#clear_compare_trait").on("click", (function(_this) {
return function() {
- return $('.qtlcharts').empty();
+ return $('.scatter-matrix-container').remove();
};
})(this));
open_trait_selection = function() {
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 6f5fe237..d6c7b18e 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -84,7 +84,7 @@
<div class="mapping_method_fields form-group">
<label for="mapping_permutations" class="col-xs-1 control-label">Permutations</label>
<div style="margin-left: 20px;" class="col-xs-2 controls">
- <input name="num_perm_pylmm" value="2000" type="text" class="form-control">
+ <input name="num_perm_pylmm" value="0" type="text" class="form-control">
</div>
</div>
<div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html
index 9ce60c0b..f2ebbbef 100755
--- a/wqflask/wqflask/templates/show_trait_statistics_new.html
+++ b/wqflask/wqflask/templates/show_trait_statistics_new.html
@@ -121,7 +121,7 @@
</div>-->
<div class="tab-pane" id="scatterplot_matrix">
- <div class="btn-group">
+ <div style="margin-bottom:40px;" class="btn-group">
<button type="button" class="btn btn-default" id="select_compare_trait">
<i class="icon-th-large"></i> Select Traits
</button>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index cdf93147..9110c5a1 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -293,7 +293,7 @@ def marker_regression_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- version = "v4"
+ version = "v3"
key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
print("key is:", pf(key))
with Bench("Loading cache"):