Users can now select specific traits from collection when using collection tools (correlation matrix, wgcna, etc)

To do the above, changed the way form submission worked for those features; previously each feature had its own form, but that was dumb so instead I wrote a javascript function that just changed a single form's target url

Duplicate traits can no longer by added to collections

Fixed the digits for a few table columns in collection (additive effect, etc).

7 files changed, 149 insertions, 159 deletions

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 9566c192..f18481a8 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -116,7 +116,6 @@ class GeneralTrait(object):
         return stringy
 
 
-
     def display_name(self):
         stringy = ""
         if self.dataset and self.name:
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 15f60765..149ee553 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -4,6 +4,8 @@ from base.trait import GeneralTrait
 from base import data_set
 from base.species import TheSpecies
 
+from wqflask import user_manager
+
 
 def get_species_dataset_trait(self, start_vars):
     #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype"
@@ -23,13 +25,15 @@ def get_species_dataset_trait(self, start_vars):
 
 
 def get_trait_db_obs(self, trait_db_list):
-
+    if isinstance(trait_db_list, basestring):
+        trait_db_list = trait_db_list.split(",")
+        
     self.trait_list = []
-    for i, trait_db in enumerate(trait_db_list):
-        if i == (len(trait_db_list) - 1):
-            break
-        trait_name, dataset_name = trait_db.split(":")
-        #print("dataset_name:", dataset_name)
+    for trait in trait_db_list:
+        data, _separator, hmac = trait.rpartition(':')
+        data = data.strip()
+        assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?"
+        trait_name, dataset_name = data.split(":")
         dataset_ob = data_set.create_dataset(dataset_name)
         trait_ob = GeneralTrait(dataset=dataset_ob,
                                name=trait_name,
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 5484633b..7e7aba89 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -165,12 +165,19 @@ class UserCollection(object):
                 return create_new("Default")
         else:
             uc = model.UserCollection.query.get(params['existing_collection'])
-        members =  uc.members_as_set() #set(json.loads(uc.members))
+        members =  list(uc.members_as_set()) #set(json.loads(uc.members))
         len_before = len(members)
 
         traits = process_traits(params['traits'])
-
-        members_now = list(members | traits)
+        
+        members_now = members
+        for trait in traits:
+            if trait in members:
+                continue
+            else:
+                members_now.append(trait)
+              
+        #members_now = list(members | traits)
         len_now = len(members_now)
         uc.members = json.dumps(members_now)
 
@@ -184,28 +191,6 @@ class UserCollection(object):
         # Probably have to change that
         return redirect(url_for('view_collection', uc_id=uc.id))
 
-    def remove_traits(self, params):
-
-        #params = request.form
-        print("params are:", params)
-        uc_id = params['uc_id']
-        uc = model.UserCollection.query.get(uc_id)
-        traits_to_remove = params.getlist('traits[]')
-        print("traits_to_remove are:", traits_to_remove)
-        traits_to_remove = process_traits(traits_to_remove)
-        print("\n\n  after processing, traits_to_remove:", traits_to_remove)
-        all_traits = uc.members_as_set()
-        print("  all_traits:", all_traits)
-        members_now = all_traits - traits_to_remove
-        print("  members_now:", members_now)
-        print("Went from {} to {} members in set.".format(len(all_traits), len(members_now)))
-        uc.members = json.dumps(list(members_now))
-        uc.changed_timestamp = datetime.datetime.utcnow()
-        db_session.commit()
-
-        # We need to return something so we'll return this...maybe in the future
-        # we can use it to check the results
-        return str(len(members_now))
 
 def report_change(len_before, len_now):
     new_length = len_now - len_before
@@ -218,8 +203,6 @@ def report_change(len_before, len_now):
         print("No new traits were added.")
 
 
-
-
 @app.route("/collections/add")
 def collections_add():
     traits=request.args['traits']
@@ -329,7 +312,6 @@ def list_collections():
 
 @app.route("/collections/remove", methods=('POST',))
 def remove_traits():
-
     params = request.form
     print("params are:", params)
 
@@ -337,14 +319,11 @@ def remove_traits():
         uc_id = params['uc_id']
         uc = model.UserCollection.query.get(uc_id)
         traits_to_remove = params.getlist('traits[]')
-        print("traits_to_remove are:", traits_to_remove)
         traits_to_remove = process_traits(traits_to_remove)
         print("\n\n  after processing, traits_to_remove:", traits_to_remove)
         all_traits = uc.members_as_set()
-        print("  all_traits:", all_traits)
         members_now = all_traits - traits_to_remove
         print("  members_now:", members_now)
-        print("Went from {} to {} members in set.".format(len(all_traits), len(members_now)))
         uc.members = json.dumps(list(members_now))
         uc.changed_timestamp = datetime.datetime.utcnow()
         db_session.commit()
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 17343186..5321e420 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -177,12 +177,10 @@ class UserCollection(Base):
         except:
             return 0
 
-
     #@property
     #def display_num_members(self):
     #    return display_collapsible(self.num_members)
 
-
     def members_as_set(self):
         return set(json.loads(self.members))
 
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index c5598e84..47b87d73 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -6,16 +6,6 @@
     </div>
     <div class="modal-body">
         <form action="/collections/new" data-validate="parsley" id="add_form">
-<!--
-            <fieldset>
-                <legend>Use your default collection</legend>
-                <span class="help-block">Choose this if you're in a hurry or don't plan on using the collection again.</span>
-                <span class="help-block"><em></em>If you are unsure this is probably the option you want.</em></span>
-                <button type="submit" name="Default" class="btn">Continue</button>
-            </fieldset>
-            <hr />
--->
-
             <input type="hidden" name="traits" value="{{ traits }}" />
             <fieldset>
                 <legend>Create a new named collection</legend>
@@ -28,7 +18,6 @@
                 {% endif %}
                 <button type="submit" name="create_new" class="btn">Create and add traits</button>
             </fieldset>
-
             <hr />
             <fieldset>
                 <legend>Or add to an existing collection</legend>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 68d2886f..6a11600c 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -21,64 +21,41 @@
 
     <div class="container">
         <div>
-            <form action="/collections/delete" method="post">
-                {% if uc %}
-                <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
-                {% else %}
-                <input type="hidden" name="collection_name" id="collection_name" value="{{ collection_name }}" />
-                {% endif %}
-                <div class="col-xs-3 controls">
-                    <input type="submit" class="btn btn-danger" value="Delete this collection" />
-                </div>
-            </form>
-            <form action="/corr_matrix" method="post">
-                {% if uc %}
-                <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
-                {% endif %}
-                <input type="hidden" name="trait_list" id="trait_list" value= "
-                {% for this_trait in trait_obs %}
-                    {{ this_trait.name }}:{{ this_trait.dataset.name }},
-                {% endfor %}" >
-                <div class="col-xs-2 controls">
-                    <input type="submit" class="btn btn-primary" value="Correlation Matrix" />
-                </div>
-            </form>
-            <form action="/wgcna_setup" method="post">
-                {% if uc %}
-                <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
-                {% endif %}
-                <input type="hidden" name="trait_list" id="trait_list" value= "
-                {% for this_trait in trait_obs %}
-                    {{ this_trait.name }}:{{ this_trait.dataset.name }},
-                {% endfor %}" >
-                <div class="col-xs-2 controls">
-                    <input type="submit" class="btn btn-primary" value="WGCNA Analysis" />
-                </div>
-            </form>
-            <form action="/ctl_setup" method="post">
-                {% if uc %}
-                <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
-                {% endif %}
-                <input type="hidden" name="trait_list" id="trait_list" value= "
-                {% for this_trait in trait_obs %}
-                    {{ this_trait.name }}:{{ this_trait.dataset.name }},
-                {% endfor %}" >
-                <div class="col-xs-2 controls">
-                    <input type="submit" class="btn btn-primary" value="CTL Analysis" />
-                </div>
-            </form>
-            <form action="/heatmap" method="post">
-                {% if uc %}
-                <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
-                {% endif %}
-                <input type="hidden" name="trait_list" id="trait_list" value= "
-                {% for this_trait in trait_obs %}
-                    {{ this_trait.name }}:{{ this_trait.dataset.name }},
-                {% endfor %}" >
-                <div class="col-xs-2 controls">
-                    <input type="submit" class="btn btn-primary" value="Heatmap" />
-                </div>
-            </form>
+          <form id="collection_form" action="/delete" method="post">
+            {% if uc %}
+            <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
+            {% endif %}
+            <input type="hidden" name="collection_name" id="collection_name" value="{{ collection_name }}" />
+            <input type="hidden" name="trait_list" id="trait_list" value= "
+            {% for this_trait in trait_obs %}
+                {{ this_trait.name }}:{{ this_trait.dataset.name }},
+            {% endfor %}" >
+            <div class="col-xs-3 controls">
+                <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" >
+                Delete this collection
+                </button>
+            </div>
+            <div class="col-xs-2 controls">
+                <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
+                    Correlation Matrix
+                </button>
+            </div>
+            <div class="col-xs-2 controls">
+                <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
+                    WGCNA Analysis
+                </button>
+            </div>
+            <div class="col-xs-2 controls">
+                <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
+                    CTL Analysis
+                </button>
+            </div>
+            <div class="col-xs-2 controls">
+                <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
+                    Heatmap
+                </button>
+            </div>
+          </form>
         </div>
 
         <div>
@@ -92,53 +69,54 @@
             <button class="btn" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Remove Record</button>
             <br />
             <br />
-        <div style="background-color: #eeeeee; border: 1px solid black;">
-        <table class="table table-hover table-striped" id='trait_table'>
-            <thead>
-                <tr>
-                    <th style="background-color: #eeeeee;"></th>
-                    <th style="background-color: #eeeeee;">Index</th>
-                    <th style="background-color: #eeeeee;">Record</th>
-                    <th style="background-color: #eeeeee;">Description</th>
-                    <th style="background-color: #eeeeee;">Location</th>
-                    <th style="background-color: #eeeeee;">Mean</th>
-                    <th style="background-color: #eeeeee;">Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00">  ?</sup></a></th>
-                    <th style="background-color: #eeeeee;">Max LRS Location</th>
-                    <th style="background-color: #eeeeee;">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00">  ?</sup></a></th>
-                </tr>
-            </thead>
-
-            <tbody>
-                {% for this_trait in trait_obs %}
-                <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
-                    <TD>
-                        <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox"
-                               VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}">
-                    </TD>
-                    <TD>{{ loop.index }}</TD>
-                    <TD>
-                        <a href="{{ url_for('show_trait_page',
-                                trait_id = this_trait.name,
-                                dataset = this_trait.dataset.name
-                                )}}">
-                            {{ this_trait.name }}
-                        </a>
-                    </TD>
-
-                    <TD>{{ this_trait.description_display }}</TD>
-                    <TD>{{ this_trait.location_repr }}</TD>
-                    <TD>{{ this_trait.mean }}</TD>
-                    <TD>{{ this_trait.LRS_score_repr }}</TD>
-                    <TD>{{ this_trait.LRS_location_repr }}</TD>
-                    <TD>{{ this_trait.additive }}</TD>
-
-                </TR>
-                {% endfor %}
-            </tbody>
-
-        </table>
-        </div>
-        <br />
+            <div style="background-color: #eeeeee; border: 1px solid black;">
+                <table id="trait_table" class="table table-hover table-striped">
+                    <thead>
+                        <tr>
+                            <th style="background-color: #eeeeee;"></th>
+                            <th style="background-color: #eeeeee;">Index</th>
+                            <th style="background-color: #eeeeee;">Dataset</th>
+                            <th style="background-color: #eeeeee;">Record</th>
+                            <th style="background-color: #eeeeee;">Description</th>
+                            <th style="background-color: #eeeeee;">Location</th>
+                            <th style="background-color: #eeeeee;">Mean</th>
+                            <th style="background-color: #eeeeee;">Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00">  ?</sup></a></th>
+                            <th style="background-color: #eeeeee;">Max LRS Location</th>
+                            <th style="background-color: #eeeeee;">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00">  ?</sup></a></th>
+                        </tr>
+                    </thead>
+
+                    <tbody>
+                    {% for this_trait in trait_obs %}
+                        <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
+                            <TD>
+                                <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox"
+                                       VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}">
+                            </TD>
+                            <TD>{{ loop.index }}</TD>
+                            <TD>{{ this_trait.dataset.name }}</TD>
+                            <TD>
+                                <a href="{{ url_for('show_trait_page',
+                                        trait_id = this_trait.name,
+                                        dataset = this_trait.dataset.name
+                                        )}}">
+                                    {{ this_trait.name }}
+                                </a>
+                            </TD>
+                            <TD>{{ this_trait.description_display }}</TD>
+                            <TD>{{ this_trait.location_repr }}</TD>
+                            <TD>{{ '%0.3f' % this_trait.mean|float }}</TD>
+                            <TD>{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD>
+                            <TD>{{ this_trait.LRS_location_repr }}</TD>
+                            <TD>{{ '%0.3f' % this_trait.additive|float }}</TD>
+
+                        </TR>
+                    {% endfor %}
+                    </tbody>
+
+                </table>
+            </div>
+            <br />
         </div>
     </div>
 
@@ -175,13 +153,14 @@
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
+                    { "type": "natural" },
                     { "type": "natural",
                       "width": "35%"  },
                     { "type": "natural",
                       "width": "15%"  },
                     { "type": "cust-txt" },
                     { "type": "natural",
-                      "width": "12%"  },
+                      "width": "9%"  },
                     { "type": "natural",
                       "width": "15%"  },
                     { "type": "natural" }
@@ -193,7 +172,7 @@
                        title: 'collection',
                        fieldBoundary: '"',
                        exportOptions: {
-                           columns: [1, 2, 3, 4, 5, 6, 7, 8]
+                           columns: [1, 2, 3, 4, 5, 6, 7, 8, 9]
                        }
                     }
                 ],
@@ -208,6 +187,48 @@
             } );
             console.timeEnd("Creating table");
 
+            submit_special = function(url) {
+                $("#collection_form").attr("action", url);
+                return $("#collection_form").submit();
+            };
+
+            $("#delete").on("click", function() {
+                url = $(this).data("url")
+                return submit_special(url)
+            });
+
+            $("#corr_matrix").on("click", function() {
+                traits = $("#trait_table input:checked").map(function() {
+                    return $(this).val();
+                }).get();
+                $("#trait_list").val(traits)
+                url = $(this).data("url")
+                return submit_special(url)
+            });
+            $("#wgcna_setup").on("click", function() {
+                traits = $("#trait_table input:checked").map(function() {
+                    return $(this).val();
+                }).get();
+                $("#trait_list").val(traits)
+                url = $(this).data("url")
+                return submit_special(url)
+            });
+            $("#ctl_setup").on("click", function() {
+                traits = $("#trait_table input:checked").map(function() {
+                    return $(this).val();
+                }).get();
+                $("#trait_list").val(traits)
+                url = $(this).data("url")
+                return submit_special(url)
+            });
+            $("#heatmap").on("click", function() {
+                traits = $("#trait_table input:checked").map(function() {
+                    return $(this).val();
+                }).get();
+                $("#trait_list").val(traits)
+                url = $(this).data("url")
+                return submit_special(url)
+            });
         });
         
     </script>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 02c97862..bf1475ff 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -122,7 +122,7 @@
                                     {{ this_trait.pubmed_text }}
                                 </a>
                             </TD>
-                            <TD>{{ this_trait.LRS_score_repr }}</TD>
+                            <TD>{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD>
                             <TD>{{ this_trait.LRS_location_repr }}</TD>
                             <TD>{{ '%0.3f' % this_trait.additive|float }}</TD>
                         {% elif dataset.type == 'Geno' %}