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-rwxr-xr-xwqflask/wqflask/do_search.py44
-rwxr-xr-xwqflask/wqflask/search_results.py15
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_select_menu.js10
-rwxr-xr-xwqflask/wqflask/templates/index_page.html46
4 files changed, 68 insertions, 47 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index fc8db204..02e73bb0 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -534,7 +534,14 @@ class LrsSearch(DoSearch):
DoSearch.search_types['LRS'] = 'LrsSearch'
def get_from_clause(self):
- if self.search_operator == "=":
+ #If the user typed, for example "Chr4", the "Chr" substring needs to be removed so that all search elements can be converted to floats
+ if len(self.search_term) > 2 and "Chr" in self.search_term[2]:
+ chr_num = self.search_term[2].replace("Chr", "")
+ self.search_term[2] = chr_num
+
+ self.search_term = [float(value) for value in self.search_term]
+
+ if len(self.search_term) > 2:
from_clause = ", Geno"
else:
from_clause = ""
@@ -542,41 +549,36 @@ class LrsSearch(DoSearch):
return from_clause
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.lrs_min, self.lrs_max = self.search_term[:2]
+ lrs_min, 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),
+ where_clause = """ %sXRef.LRS > %s and
+ %sXRef.LRS < %s """ % self.mescape(self.dataset.type,
+ min(lrs_min, lrs_max),
self.dataset.type,
- max(self.lrs_min, self.lrs_max))
+ max(lrs_min, lrs_max))
if len(self.search_term) > 2:
- self.chr_num = self.search_term[2]
- self.sub_clause += """ Geno.Chr = %s and """ % (self.chr_num)
+ chr_num = self.search_term[2]
+ where_clause += """ and Geno.Chr = %s """ % (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))
-
- #%s.Chr = Geno.Chr
- where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and
+ mb_low, mb_high = self.search_term[3:]
+ where_clause += """ and Geno.Mb > %s and
+ Geno.Mb < %s
+ """ % self.mescape(min(mb_low, mb_high),
+ max(mb_low, mb_high))
+
+ where_clause += """ and %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 """ % self.mescape(self.dataset.type,
+ where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type,
self.search_operator,
self.search_term[0])
- where_clause = self.sub_clause
return where_clause
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index b48c9583..01d65278 100755
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -77,10 +77,15 @@ class SearchResultPage(object):
self.trait_type = kw['trait_type']
self.quick_search()
else:
+ print("kw is:", kw)
+ if kw['search_terms_or']:
+ self.and_or = "or"
+ self.search_terms = kw['search_terms_or']
+ else:
+ self.and_or = "and"
+ self.search_terms = kw['search_terms_and']
self.search_term_exists = True
self.results = []
- print("kw is:", kw)
- self.search_terms = kw['search_terms']
if kw['type'] == "Phenotypes":
dataset_type = "Publish"
elif kw['type'] == "Genotypes":
@@ -237,10 +242,14 @@ class SearchResultPage(object):
where_clause = the_search.get_where_clause()
combined_where_clause += "(" + where_clause + ")"
if (i+1) < len(self.search_terms):
- combined_where_clause += "AND"
+ if self.and_or == "and":
+ combined_where_clause += "AND"
+ else:
+ combined_where_clause += "OR"
else:
self.search_term_exists = False
if self.search_term_exists:
+ combined_where_clause = "(" + combined_where_clause + ")"
final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause)
results = the_search.execute(final_query)
self.results.extend(results)
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
index 5bd54359..fb9fdcf3 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
@@ -134,10 +134,12 @@ $(function() {
return _results;
};
check_search_term = function() {
- var search_term;
- search_term = $('#tfor').val();
- console.log("search_term:", search_term);
- if (search_term === "") {
+ var or_search_term, and_search_term;
+ or_search_term = $('#or_search').val();
+ and_search_term = $('#and_search').val();
+ console.log("or_search_term:", or_search_term);
+ console.log("and_search_term:", and_search_term);
+ if (or_search_term === "" && and_search_term === "") {
alert("Please enter one or more search terms or search equations.");
return false;
}
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 150a71f1..3d5ddde4 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -76,10 +76,10 @@
<!-- GET ANY SEARCH -->
<div class="form-group">
- <label for="tfor" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Search for:</label>
+ <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
<div class="col-xs-10 controls">
<div class="col-xs-8">
- <textarea name="search_terms" rows="2" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="tfor"></textarea>
+ <textarea name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
</div>
</div>
</div>
@@ -87,19 +87,33 @@
<!-- GET ANY HELP -->
<div class="form-group">
<label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
+ <div class="col-xs-10 controls">
+ <div class="col-xs-12 controls">
+ Enter terms, genes, ID numbers in the <b>Search</b> field.<br>
+ Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br>
+ Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>.
+ </div>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
+ <div class="col-xs-10 controls">
+ <div class="col-xs-8">
+ <textarea name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
+ </div>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
<div class="col-xs-10 controls">
<div class="col-xs-2 controls" style="width: 100px !important;">
<input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
</div>
- <div class="col-xs-9 controls">
- Enter terms, genes, ID numbers in the <b>Search</b> field
- Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*)
- Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>
- </div>
</div>
</div>
-
<!-- SEARCH, MAKE DEFAULT -->
<div class="form-group">
@@ -116,21 +130,15 @@
<h2>Advanced commands</h2>
</div>
- <p>GeneNetwork supports a variety of advanced searches.</p>
-
- <p>To try them out copy these examples into the search field:</p>
+ <p>You can also use advanced commands. Copy these simple examples into the Get Any or Combined search fields:</p>
<ul>
- <!--<li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
+ <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
chromosome 1 between 25 and 30 Mb.</li>
<li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a>
- linkage between 23 and 46.</li>-->
-
- <li><b>MEAN=(15 16)</b> finds highly expressed genes (15 to 16 log2 units).</li>
-
- <li><b>LRS=(23 46)</b> finds genes with peak <a href="http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a> linkage between 23 and 46.</li>
+ linkage between 23 and 46.</li>
<li><b>RIF=mitochondrial</b> searches RNA databases for <a href="http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank">
GeneRIF</a> links.</li>
@@ -146,12 +154,12 @@
<li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b>
finds synapse-associated genes with <a href="http://www.genenetwork.org/glossary.html#E" target="_blank">
cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores
- between 9 and 999.</li>
+ between 9 and 999.</li>-->
<li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E" target="_blank">
trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
- scores between 9 and 999.</li>-->
+ scores between 9 and 999.</li>
</ul>
</section>
</div>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 16:14:12 +0000