Created template for marek regression page and made the compute button direct

to it

added asbolute_import in data_set.py and trait.py

Made several minor changes and deleted commented out code in trait.py

9 files changed, 160 insertions, 215 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 612b9209..36d4acaf 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -16,11 +16,11 @@
 # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
 # at rwilliams@uthsc.edu and xzhou15@uthsc.edu
 #
-#
+#we
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import print_function, division
+from __future__ import absolute_import, print_function, division
 import os
 
 from flask import Flask, g
@@ -29,7 +29,7 @@ from htmlgen import HTMLgen2 as HT
 
 import reaper
 
-import webqtlConfig
+from base import webqtlConfig
 from base import species
 from dbFunction import webqtlDatabaseFunction
 from utility import webqtlUtil
@@ -50,6 +50,7 @@ def create_dataset(dataset_name):
         WHERE DBList.Name = '%s' and
               DBType.Id = DBList.DBTypeId
         """ % (escape(dataset_name))
+    print("query is: ", pf(query))
     dataset_type = g.db.execute(query).fetchone().Name
 
     #dataset_type = cursor.fetchone()[0]
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 8c9e3b10..241bf2ab 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,12 +1,12 @@
-from __future__ import division, print_function
+from __future__ import absolute_import, division, print_function
 
 import string
 
 from htmlgen import HTMLgen2 as HT
 
-import webqtlConfig
-from webqtlCaseData import webqtlCaseData
-from data_set import create_dataset
+from base import webqtlConfig
+from base.webqtlCaseData import webqtlCaseData
+from base.data_set import create_dataset
 from dbFunction import webqtlDatabaseFunction
 from utility import webqtlUtil
 
@@ -24,76 +24,28 @@ class GeneralTrait:
 
     def __init__(self, **kw):
         print("in GeneralTrait")
-        self.dataset = kw.get('dataset', None)                  # database name
-        self.name = kw.get('name', None)                 # Trait ID, ProbeSet ID, Published ID, etc.
-        self.cellid = kw.get('cellid', None)
+        self.dataset = kw.get('dataset')           # database name
+        self.name = kw.get('name')                 # Trait ID, ProbeSet ID, Published ID, etc.
+        self.cellid = kw.get('cellid')
         self.identification = kw.get('identification', 'un-named trait')
-        #self.group = kw.get('group', None)
         self.haveinfo = kw.get('haveinfo', False)
-        self.sequence = kw.get('sequence', None)              # Blat sequence, available for ProbeSet
+        self.sequence = kw.get('sequence')         # Blat sequence, available for ProbeSet
         self.data = kw.get('data', {})
-        
+
         if kw.get('fullname'):
             name2 = value.split("::")
             if len(name2) == 2:
                 self.dataset, self.name = name2
+                # self.cellid is set to None above
             elif len(name2) == 3:
                 self.dataset, self.name, self.cellid = name2
-                
-        #if self.dataset and isinstance(self.dataset, basestring):
-        self.dataset = create_dataset(self.dataset)
 
-        print("self.dataset is:", self.dataset, type(self.dataset))
-        #if self.dataset:
-        
-        #self.dataset.get_group()
+        self.dataset = create_dataset(self.dataset)
         
-        #if self.dataset.type == "Temp":
-        #    self.cursor.execute('''
-        #            SELECT
-        #                    InbredSet.Name
-        #            FROM
-        #                    InbredSet, Temp
-        #            WHERE
-        #                    Temp.InbredSetId = InbredSet.Id AND
-        #                    Temp.Name = "%s"
-        #    ''', self.name)
-        #    self.group = self.cursor.fetchone()[0]
-        #else:
-        #    self.group = self.dataset.get_group()
-
-        #print("trinity, self.group is:", self.group)
-
-        #
-        # In ProbeSet, there are maybe several annotations match one sequence
-        # so we need use sequence(BlatSeq) as the identification, when we update
-        # one annotation, we update the others who match the sequence also.
-        #
-        # Hongqiang Li, 3/3/2008
-        #
-
-        #XZ, 05/08/2009: This block is not neccessary. We can add 'BlatSeq' into disfield.
-        # The variable self.sequence should be changed to self.BlatSeq
-        # It also should be changed in other places where it are used.
-
-        #if self.dataset:
-        #if self.dataset.type == 'ProbeSet':
-        #    print("Doing ProbeSet Query")
-        #    query = '''
-        #            SELECT
-        #                    ProbeSet.BlatSeq
-        #            FROM
-        #                    ProbeSet, ProbeSetFreeze, ProbeSetXRef
-        #            WHERE
-        #                    ProbeSet.Id=ProbeSetXRef.ProbeSetId and
-        #                    ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and
-        #                    ProbeSet.Name = %s and
-        #                    ProbeSetFreeze.Name = %s
-        #    ''', (self.name, self.dataset.name)
-        #    print("query is:", query)
-        #    self.sequence = g.db.execute(*query).fetchone()[0]
-        #    #self.sequence = self.cursor.fetchone()[0]
-        #    print("self.sequence is:", self.sequence)
+        # Todo: These two lines are necessary most of the time, but perhaps not all of the time
+        # So we could add a simple if statement to short-circuit this if necessary
+        self.retrieve_info()
+        self.retrieve_sample_data()
 
 
     def get_name(self):
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index fc45395c..a2eddfc6 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -63,7 +63,7 @@ class DoSearch(object):
 class MrnaAssaySearch(DoSearch):
     """A search within an mRNA expression dataset"""
 
-    DoSearch.search_types['ProbeSet'] = "ProbeSetSearch"
+    DoSearch.search_types['ProbeSet'] = "MrnaAssaySearch"
 
     base_query = """SELECT ProbeSet.Name as TNAME,
                 0 as thistable,
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index c605cb58..807761a2 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -34,45 +34,26 @@ from pprint import pformat as pf
 
 class ShowTrait(object):
 
-    def __init__(self, args):
-        print("in ShowTrait, args are:", args)
-        #self.group = args.group
-        self.trait_id = args['trait_id']
+    def __init__(self, kw):
+        print("in ShowTrait, kw are:", kw)
+        self.trait_id = kw['trait_id']
         
-        self.dataset = create_dataset(args['dataset'])
-        
-        #self.dataset = create_dataset(args['dataset'])
-        self.cell_id = None
+        self.dataset = create_dataset(kw['dataset'])
+
+        #self.cell_id = None
 
-        #assert self.openMysql(), "No database!"
 
-        #print("red3 fd.group:", fd.group)
-        this_trait = self.get_this_trait()
+        this_trait = GeneralTrait(dataset=self.dataset.name,
+                                  name=self.trait_id,
+                                  cellid=None)
 
-        #print("red4 fd.group:", fd.group)
-        ##read genotype file
-        #fd.group = this_trait.group
 
-        #print("[red5] fd.group is:", fd.group)
         self.dataset.group.read_genotype_file()
-        #fd.readGenotype()
 
         if not self.dataset.group.genotype:
-            self.read_data(include_f1=True)  #incf1=1)
+            self.read_data(include_f1=True) 
 
-        ## determine data editing page format
-        #variance_data_page = 0
-        #if fd.formID == 'varianceChoice':
-        #    variance_data_page = 1
-        #
-        #if variance_data_page:
-        #    fmID='dataEditing'
-        #else:
-        #    if fd.enablevariance:
-        #        fmID='pre_dataEditing'
-        #    else:
-        #        fmID='dataEditing'
-        
+      
         # Todo: Add back in the ones we actually need from below, as we discover we need them
         hddn = OrderedDict()
 
@@ -111,55 +92,19 @@ class ShowTrait(object):
         #        export_data = None
         #        )
 
-        #if fd.enablevariance:
-        #    hddn['enablevariance']='ON'
-        #if fd.incparentsf1:
-        #    hddn['incparentsf1']='ON'
-
         #if this_trait:
-        #    hddn['fullname'] = str(this_trait)
-        #    try:
-        #        hddn['normalPlotTitle'] = this_trait.symbol
-        #        hddn['normalPlotTitle'] += ": "
-        #        hddn['normalPlotTitle'] += this_trait.name
-        #    except:
-        #        hddn['normalPlotTitle'] = str(this_trait.name)
-        #    hddn['fromDataEditingPage'] = 1
         #    if this_trait.dataset and this_trait.dataset.type and this_trait.dataset.type == 'ProbeSet':
-        #        hddn['trait_type'] = this_trait.dataset.type
-        #        if this_trait.cellid:
-        #            hddn['cellid'] = this_trait.cellid
-        #        else:
         #            self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" %
         #                                this_trait.mysqlid)
         #            heritability = self.cursor.fetchone()
-        #            hddn['heritability'] = heritability
-        #
-        #        hddn['attribute_names'] = ""
-        #
+
         #hddn['mappingMethodId'] = webqtlDatabaseFunction.getMappingMethod (cursor=self.cursor,
         #                                                                   groupName=fd.group)
-        #
-        #if fd.identification:
-        #    hddn['identification'] = fd.identification
-        #else:
-        #    hddn['identification'] = "Un-named trait"  #If no identification, set identification to un-named
-
-        self.dispTraitInformation(args, "", hddn, this_trait) #Display trait information + function buttons
 
-        if this_trait == None:
-            this_trait = webqtlTrait(data=args['allTraitData'], dataset=None)
+        self.dispTraitInformation(kw, "", hddn, this_trait) #Display trait information + function buttons
 
-        ## Variance submit page only
-        #if fd.enablevariance and not variance_data_page:
-        #    pass
-        #    #title2Body.append("Click the next button to go to the variance submission form.",
-        #    #        HT.Center(next,reset))
-        #else:
-        #    pass
-        #    # We'll get this part working later
-        #    print("Calling dispBasicStatistics")
-        #    self.dispBasicStatistics(fd, this_trait)
+        #if this_trait == None:
+        #    this_trait = webqtlTrait(data=kw['allTraitData'], dataset=None)
 
         self.build_correlation_tools(this_trait)
 
@@ -168,9 +113,6 @@ class ShowTrait(object):
         if self.dataset.group.allsamples:
             hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ')
 
-        #if args['varianceDispName'] != 'Variance':
-        #    hddn['isSE'] = "yes"
-
         # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
         self.this_trait = this_trait
         self.hddn = hddn
@@ -188,34 +130,23 @@ class ShowTrait(object):
         self.js_data = js_data
 
 
-    def get_this_trait(self):
-        # When is traitInfos used?
-        #if traitInfos:
-        #    database, ProbeSetID, CellID = traitInfos
-        #else:
-        #dataset = self.fd['dataset']
-        #trait_id = self.fd['trait_id']
-        #cell_id = self.fd.get('CellID')
-
-        this_trait = GeneralTrait(dataset=self.dataset.name,
-                                 name=self.trait_id,
-                                 cellid=self.cell_id)
-
-        ##identification, etc.
-        self.identification = '%s : %s' % (self.dataset.shortname, self.trait_id)
-        this_trait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
-                &ProbeSetID=%s&group=%s&parentsf1=on' %(self.dataset, self.trait_id, self.dataset.group.name)
-
-        if self.cell_id:
-            self.identification = '%s/%s'%(self.identification, self.cell_id)
-            this_trait.returnURL = '%s&CellID=%s' % (this_trait.returnURL, self.cell_id)
-
-        print("yellow1:", self.dataset.group)
-        this_trait.retrieve_info()
-        print("yellow2:", self.dataset.group)
-        this_trait.retrieve_sample_data()
-        print("yellow3:", self.dataset.group)
-        return this_trait
+    #def get_this_trait(self):
+    #    this_trait = GeneralTrait(dataset=self.dataset.name,
+    #                             name=self.trait_id,
+    #                             cellid=self.cell_id)
+    #
+    #    ###identification, etc.
+    #    #self.identification = '%s : %s' % (self.dataset.shortname, self.trait_id)
+    #    #this_trait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
+    #    #        &ProbeSetID=%s&group=%s&parentsf1=on' %(self.dataset, self.trait_id, self.dataset.group.name)
+    #    #
+    #    #if self.cell_id:
+    #    #    self.identification = '%s/%s'%(self.identification, self.cell_id)
+    #    #    this_trait.returnURL = '%s&CellID=%s' % (this_trait.returnURL, self.cell_id)
+    #
+    #    this_trait.retrieve_info()
+    #    this_trait.retrieve_sample_data()
+    #    return this_trait
 
 
     def read_data(self, include_f1=False):
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index b1f5b186..d0fc869d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -1,11 +1,17 @@
 $ ->
-    run_marker_regression = ->
-        console.log("In marker regression")
-        url = "/marker_regression"
+    submit_special = ->
+        # Add submit_special class plus a data-url field to any button
+        # And it will submit to that url
+        # No js changes necessary
+        console.log("In submit_special")
+        console.log("this is:", this)
+        console.log("$(this) is:", $(this))
+        url = $(this).data("url")
+        console.log("url is:", url)
         $("#trait_data_form").attr("action", url);
         $("#trait_data_form").submit()
         
-    $("#do_marker_regression").click(run_marker_regression)
+    $(".submit_special").click(submit_special)
 
 
     composite_mapping_fields = ->
@@ -14,10 +20,10 @@ $ ->
     $("#use_composite_choice").change(composite_mapping_fields)
 
 
+    #### Todo: Redo below so its like submit_special and requires no js hardcoding
     toggle_enable_disable = (elem) ->
-        $(elem).prop("disabled", !$(elem.prop("disabled")))
+        $(elem).prop("disabled", !$(elem).prop("disabled"))
     
-
     $("#choose_closet_control").change(->
         toggle_enable_disable("#control_locus")
     )
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index c8328498..c6766288 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -2,21 +2,24 @@
 (function() {
 
   $(function() {
-    var composite_mapping_fields, run_marker_regression, toggle_enable_disable;
-    run_marker_regression = function() {
+    var composite_mapping_fields, submit_special, toggle_enable_disable;
+    submit_special = function() {
       var url;
-      console.log("In marker regression");
-      url = "/marker_regression";
+      console.log("In submit_special");
+      console.log("this is:", this);
+      console.log("$(this) is:", $(this));
+      url = $(this).data("url");
+      console.log("url is:", url);
       $("#trait_data_form").attr("action", url);
       return $("#trait_data_form").submit();
     };
-    $("#do_marker_regression").click(run_marker_regression);
+    $(".submit_special").click(submit_special);
     composite_mapping_fields = function() {
       return $(".composite_fields").toggle();
     };
     $("#use_composite_choice").change(composite_mapping_fields);
     toggle_enable_disable = function(elem) {
-      return $(elem).prop("disabled", !$(elem.prop("disabled")));
+      return $(elem).prop("disabled", !$(elem).prop("disabled"));
     };
     $("#choose_closet_control").change(function() {
       return toggle_enable_disable("#control_locus");
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
new file mode 100644
index 00000000..db2de604
--- /dev/null
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -0,0 +1,51 @@
+{% extends "base.html" %}
+{% block title %}Marker Regression{% endblock %}
+{% block content %} <!-- Start of body -->
+
+    <header class="jumbotron subhead" id="overview">
+        <div class="container">
+            <h1>Marker Regression</h1>
+            <p class="lead">
+                {{ this_trait.name }}: {{ this_trait.description_fmt }}
+            </p>
+        </div>
+    </header>
+
+    <dl class="dl-horizontal">
+        <dt>Aliases</dt>
+        <dd>{{ this_trait.alias_fmt }}</dd>
+    
+        <dt>Location</dt>
+        <dd>{{ this_trait.location_fmt }}</dd>
+    
+        <dt>Database</dt>
+        <dd>
+            <a href="{{ url_for('static', filename='/dbdoc/' + dataset.fullname + '.html') }}" target="_blank">
+                {{ dataset.name }}
+            </a>
+        </dd>
+    
+        {% if this_trait.probe_set_specificity %}
+        <dt>
+            <a href="/blatInfo.html" target="_blank"
+               title="Values higher than 2 for the specificity are good">
+                BLAT Specifity
+            </a>
+        </dt>
+        <dd>{{ "%.1f" % (this_trait.probe_set_specificity) }}</dd>
+        {% endif %}
+        {% if this_trait.probe_set_blat_score %}
+        <dt>BLAT Score</dt>
+        <dd>{{ "%i" % (this_trait.probe_set_blat_score) }}</dd>
+        {% endif %}
+    </dl>
+
+    <!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+    <script>
+        js_data = {{ js_data | safe }}
+    </script>
+{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 8436703d..72b152fa 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -101,7 +101,8 @@
 
                     <div class="control-group">
                         <div class="controls">
-                            <button id="do_interval_mapping" class="btn btn-inverse"
+                            <button class="btn btn-inverse submit_special"
+                                    data-url="/interval_mapping"
                                     title="Compute Interval Mapping">
                                 <i class="icon-ok-circle icon-white"></i> Compute
                             </button>
@@ -135,8 +136,9 @@
                     
                     <div class="control-group">
                         <div class="controls">
-                            <button id="do_marker_regression"
-                                    class="btn btn-inverse" title="Compute Marker Regression">
+                            <button class="btn btn-inverse submit_special"
+                                    data-url="/marker_regression"
+                                    title="Compute Marker Regression">
                                 <i class="icon-ok-circle icon-white"></i> Compute
                             </button>
                         </div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 503b0972..f6c0dfb0 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -18,6 +18,7 @@ from flask import render_template, request, make_response, Response, Flask, g, c
 from wqflask import search_results
 from wqflask.show_trait import show_trait
 from wqflask.show_trait import export_trait_data
+from wqflask.marker_regression import marker_regression
 from wqflask.correlation import CorrelationPage
 
 from wqflask.dataSharing import SharingInfo, SharingInfoPage
@@ -89,27 +90,6 @@ def whats_new_page():
         print("\nnews_item is: %s\n" % (news_item))
     return render_template("whats_new.html", news_items=news_items)
 
-
-@app.route("/show_trait")
-def show_trait_page():
-    # Here it's currently too complicated not to use an fd that is a webqtlFormData
-    #fd = webqtlFormData.webqtlFormData(request.args)
-    #print("stp y1:", pf(vars(fd)))
-    template_vars = show_trait.ShowTrait(request.args)
-
-    print("js_data before dump:", template_vars.js_data)
-
-    template_vars.js_data = json.dumps(template_vars.js_data,
-                                       default=json_default_handler,
-                                       indent="   ")
-    # Sorting the keys messes up the ordered dictionary, so don't do that
-                                       #sort_keys=True)
-
-    print("js_data after dump:", template_vars.js_data)
-
-    print("show_trait template_vars:", pf(template_vars.__dict__))
-    return render_template("show_trait.html", **template_vars.__dict__)
-
 @app.route('/export_trait_csv', methods=('POST',))
 def export_trait_excel():
     """Excel file consisting of the sample data from the trait data and analysis page"""
@@ -150,33 +130,52 @@ def export_trait_csv():
                     mimetype='text/csv',
                     headers={"Content-Disposition":"attachment;filename=test.csv"})
 
+@app.route("/show_trait")
+def show_trait_page():
+    # Here it's currently too complicated not to use an fd that is a webqtlFormData
+    #fd = webqtlFormData.webqtlFormData(request.args)
+    #print("stp y1:", pf(vars(fd)))
+    template_vars = show_trait.ShowTrait(request.args)
+    print("js_data before dump:", template_vars.js_data)
+    template_vars.js_data = json.dumps(template_vars.js_data,
+                                       default=json_default_handler,
+                                       indent="   ")
+    # Sorting the keys messes up the ordered dictionary, so don't do that
+                                       #sort_keys=True)
+
+    print("js_data after dump:", template_vars.js_data)
+    print("show_trait template_vars:", pf(template_vars.__dict__))
+    return render_template("show_trait.html", **template_vars.__dict__)
+
+@app.route("/marker_regression", methods=('POST',))
+def marker_regression_page():
+    template_vars = marker_regression.MarkerRegression(request.form)
+    #print("js_data before dump:", template_vars.js_data)
+    #template_vars.js_data = json.dumps(template_vars.js_data,
+    #                                   default=json_default_handler,
+    #                                   indent="   ")
+    #print("js_data after dump:", template_vars.js_data)
+    print("marker_regression template_vars:", pf(template_vars.__dict__))
+    return render_template("marker_regression.html", **template_vars.__dict__)
 
 @app.route("/corr_compute", methods=('POST',))
 def corr_compute_page():
-    #print("In corr_compute, request.args is:", pf(request.form))
+    print("In corr_compute, request.args is:", pf(request.form))
     fd = webqtlFormData.webqtlFormData(request.form)
-    print("Have fd")
     template_vars = CorrelationPage.CorrelationPage(fd)
-    print("Made it to  rendering")
     return render_template("correlation_page.html", **template_vars.__dict__)
 
 @app.route("/int_mapping", methods=('POST',))
 def interval_mapping_page():
-    fd = webqtlFormData.webqtlFormData(request.form)
-    print("Have fd")
-    template_vars = CorrelationPage.CorrelationPage(fd)
-    print("Made it to  rendering")
-    return render_template("correlation_page.html", **template_vars.__dict__)
-
+    template_vars = interval_mapping.IntervalMapping(request.args)
+    return render_template("interval_mapping.html", **template_vars.__dict__)
 
 # Todo: Can we simplify this? -Sam
 def sharing_info_page():
     """Info page displayed when the user clicks the "Info" button next to the dataset selection"""
     print("In sharing_info_page")
     fd = webqtlFormData.webqtlFormData(request.args)
-    print("2Have fd")
     template_vars = SharingInfoPage.SharingInfoPage(fd)
-    print("2 Made it to rendering")
     return template_vars