Merge /home/zas1024/gene

14 files changed, 256 insertions, 40 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1668940c..03b24230 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -27,8 +27,12 @@ import string
 import collections
 
 import json
+import cPickle as pickle
 import itertools
 
+from redis import Redis
+Redis = Redis()
+
 from flask import Flask, g
 
 import reaper
@@ -46,17 +50,18 @@ from pprint import pformat as pf
 # Used by create_database to instantiate objects
 DS_NAME_MAP = {}
 
-def create_dataset(dataset_name):
+def create_dataset(dataset_name, dataset_type = None):
     #print("dataset_name:", dataset_name)
 
-    query = """
-        SELECT DBType.Name
-        FROM DBList, DBType
-        WHERE DBList.Name = '{}' and
-              DBType.Id = DBList.DBTypeId
-        """.format(escape(dataset_name))
-    #print("query is: ", pf(query))
-    dataset_type = g.db.execute(query).fetchone().Name
+    if not dataset_type:
+        query = """
+            SELECT DBType.Name
+            FROM DBList, DBType
+            WHERE DBList.Name = '{}' and
+                  DBType.Id = DBList.DBTypeId
+            """.format(escape(dataset_name))
+        #print("query is: ", pf(query))
+        dataset_type = g.db.execute(query).fetchone().Name
 
     #dataset_type = cursor.fetchone()[0]
     #print("[blubber] dataset_type:", pf(dataset_type))
@@ -69,6 +74,36 @@ def create_dataset(dataset_name):
     dataset_class = globals()[dataset_ob]
     return dataset_class(dataset_name)
 
+def create_datasets_list():
+    key = "all_datasets"
+    result = Redis.get(key)
+    
+    if result:
+        print("Cache hit!!!")
+        datasets = pickle.loads(result)
+        
+    else:
+        datasets = list()
+        with Bench("Creating DataSets object"):
+            type_dict = {'Publish': 'PublishFreeze',
+                         'ProbeSet': 'ProbeSetFreeze',
+                         'Geno': 'GenoFreeze'}
+        
+            for dataset_type in type_dict:
+                query = "SELECT Name FROM {}".format(type_dict[dataset_type])
+                for result in g.db.execute(query).fetchall():
+                    #The query at the beginning of this function isn't necessary here, but still would
+                    #rather just reuse it
+                    print("type: {}\tname: {}".format(dataset_type, result.Name))
+                    dataset = create_dataset(result.Name, dataset_type)
+                    datasets.append(dataset)
+            
+        Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
+        Redis.expire(key, 60*60)
+    
+    return datasets
+
+
 def create_in_clause(items):
     """Create an in clause for mysql"""
     in_clause = ', '.join("'{}'".format(x) for x in mescape(*items))
@@ -167,8 +202,8 @@ class DatasetGroup(object):
         
         self.incparentsf1 = False
         self.allsamples = None
-        
-        
+
+
     def get_markers(self):
         #print("self.species is:", self.species)
         if self.species == "human":
@@ -222,6 +257,27 @@ class DatasetGroup(object):
         self.samplelist = list(genotype.prgy)
 
 
+#class DataSets(object):
+#    """Builds a list of DataSets"""
+#    
+#    def __init__(self):
+#        self.datasets = list()
+#        
+
+        
+        #query = """SELECT Name FROM ProbeSetFreeze
+        #           UNION
+        #           SELECT Name From PublishFreeze
+        #           UNION
+        #           SELECT Name From GenoFreeze"""
+        #
+        #for result in g.db.execute(query).fetchall():
+        #    dataset = DataSet(result.Name)
+        #    self.datasets.append(dataset)
+
+#ds = DataSets()
+#print("[orange] ds:", ds.datasets)
+
 class DataSet(object):
     """
     DataSet class defines a dataset in webqtl, can be either Microarray,
@@ -234,6 +290,8 @@ class DataSet(object):
         assert name, "Need a name"
         self.name = name
         self.id = None
+        self.shortname = None
+        self.fullname = None
         self.type = None
 
         self.setup()
@@ -293,7 +351,7 @@ class DataSet(object):
             self.name,
             self.name,
             self.name))
-        #print("query_args are:", query_args)
+        print("query_args are:", query_args)
 
         #print("""
         #        SELECT Id, Name, FullName, ShortName
@@ -301,17 +359,17 @@ class DataSet(object):
         #        WHERE public > %s AND
         #             (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
         #  """ % (query_args))
-
-        self.id, self.name, self.fullname, self.shortname = g.db.execute("""
-                SELECT Id, Name, FullName, ShortName
-                FROM %s
-                WHERE public > %s AND
-                     (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
-          """ % (query_args)).fetchone()
-
-        #self.cursor.execute(query)
-        #self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone()
         
+        try:
+            self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+                    SELECT Id, Name, FullName, ShortName
+                    FROM %s
+                    WHERE public > %s AND
+                         (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+              """ % (query_args)).fetchone()
+        except TypeError:
+            print("Dataset {} is not yet available in GeneNetwork.".format(self.name))
+            pass
 
 class PhenotypeDataSet(DataSet):
     DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
@@ -940,6 +998,5 @@ def geno_mrna_confidentiality(ob):
      authorized_users) = result.fetchall()[0]
 
     if confidential:
-        # Allow confidential data later
-        NoConfindetialDataForYouTodaySorry
+        return True
 
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 191f4535..ebc2bfed 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -56,6 +56,7 @@ class Chromosomes(object):
                         InbredSet.Name = %s
                 Order by OrderId
                 """, self.dataset.group.name).fetchall()
+        print("group: ", self.dataset.group.name)
         print("bike:", results)
 
         for item in results:
@@ -68,9 +69,14 @@ class Chromosomes(object):
     def set_mb_graph_interval(self):
         """Empirical megabase interval"""
         
+        if self.chromosomes:
+            self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
+        else:
+            self.mb_graph_interval = 1
+            
         #if self.chromosomes:
-        assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
-        self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
+        #assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
+        #self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
         #else:
             #self.mb_graph_interval = 1
 
diff --git a/wqflask/cfg/default_settings.py b/wqflask/cfg/default_settings.py
index 96f7f1a5..e638a9c0 100644
--- a/wqflask/cfg/default_settings.py
+++ b/wqflask/cfg/default_settings.py
@@ -13,3 +13,5 @@ SECURITY_REGISTERABLE = True
 SECURITY_RECOVERABLE = True
 
 SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
+
+SECURITY_POST_LOGIN_VIEW = "/thank_you"
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 03059d68..11eca936 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -203,6 +203,13 @@ class CorrelationResults(object):
                 #        mb = trait_object.mb
                 #    )
 
+            
+
+            #trait_list = self.getTissueCorrelationByList( primary_trait_symbol = self.this_trait.symbol,
+            #                                            corr_results = self.correlation_results,
+            #                                            TissueProbeSetFreezeId = 1,
+            #                                            method=1)
+
         #XZ, 09/18/2008: get all information about the user selected database.
         #target_db_name = fd.corr_dataset
         #self.target_db_name = start_vars['corr_dataset']
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index f76af374..504a67ce 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -162,8 +162,6 @@ class SearchResultPage(object):
         import redis
         Redis = redis.Redis()
         
-        
-        
     #def get_group_species_tree(self):
     #    self.species_groups = collections.default_dict(list)
     #    for key in self.results:
diff --git a/wqflask/wqflask/static/new/javascript/login.coffee b/wqflask/wqflask/static/new/javascript/login.coffee
index c49353d5..15dafd9a 100644
--- a/wqflask/wqflask/static/new/javascript/login.coffee
+++ b/wqflask/wqflask/static/new/javascript/login.coffee
@@ -13,8 +13,8 @@ $ ->
 
 
 
-
-    $(document).on("click", ".modalize", modalize)
+    $(document).one("click", ".modalize", modalize)
+    console.log("Modalized click!!!")
 
     form_success = (data) ->
         $.colorbox(
@@ -39,4 +39,4 @@ $ ->
         )
 
 
-    $("form").on("submit", submit_form)
+    $("#colorbox form").on("submit", submit_form)
diff --git a/wqflask/wqflask/static/new/javascript/login.js b/wqflask/wqflask/static/new/javascript/login.js
index 6c6120ec..ce301353 100644
--- a/wqflask/wqflask/static/new/javascript/login.js
+++ b/wqflask/wqflask/static/new/javascript/login.js
@@ -14,7 +14,8 @@
         }
       });
     };
-    $(document).on("click", ".modalize", modalize);
+    $(document).one("click", ".modalize", modalize);
+    console.log("Modalized click!!!");
     form_success = function(data) {
       return $.colorbox({
         open: true,
@@ -38,7 +39,7 @@
         success: form_success
       });
     };
-    return $("form").on("submit", submit_form);
+    return $("#colorbox form").on("submit", submit_form);
   });
 
 }).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/thank_you.coffee b/wqflask/wqflask/static/new/javascript/thank_you.coffee
new file mode 100644
index 00000000..975f85c6
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/thank_you.coffee
@@ -0,0 +1,4 @@
+$ ->
+    console.log("Starting transform")
+    $('#login_out').text('Sign out').attr('href', '/logout').removeClass('modalize')
+    console.log("Transformed to sign out I hope")
diff --git a/wqflask/wqflask/static/new/javascript/thank_you.js b/wqflask/wqflask/static/new/javascript/thank_you.js
new file mode 100644
index 00000000..2871dd2d
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/thank_you.js
@@ -0,0 +1,10 @@
+// Generated by CoffeeScript 1.4.0
+(function() {
+
+  $(function() {
+    console.log("Starting transform");
+    $('#login_out').text('Sign out').attr('href', '/logout').removeClass('modalize');
+    return console.log("Transformed to sign out I hope");
+  });
+
+}).call(this);
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
new file mode 100644
index 00000000..df3eda33
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -0,0 +1,83 @@
+{% extends "base.html" %}
+{% block title %}Group Manager{% endblock %}
+{% block content %}
+<!-- Start of body -->
+    <header class="jumbotron subhead" id="overview">
+        <div class="container">
+            <h1>Group Manager</h1>
+        </div>
+    </header>
+
+    <div class="container">
+        <div class="page-header">
+
+        </div>
+        <form>
+            <div class="control-group">
+                <b>Group Name: </b>
+                <div class="input-append">
+                    <input type="text" name="group_name">
+                    <button type="submit" class="btn btn-primary">Save</button>
+                </div>
+            </div>
+
+            <table id="dataset_list" class="table table-hover">
+                <thead>
+                    <tr>
+                        <th>Read</th>
+                        <th>Type</th>
+                        <th>ID</th>
+                        <th>Name</th>
+                        <th>Full Name</th>
+                    </tr>
+                </thead>
+            {% for dataset in datasets %}
+                <tr>
+                    <td><input type="checkbox" name="read" value="{{ dataset.type }}:{{ dataset.name }}"></td>
+                    <td>{{ dataset.type }}</td>
+                    <td>{{ dataset.id }}</td>
+                    <td>{{ dataset.name }}</td>
+                    <td>{{ dataset.fullname }}</td>
+                </tr>
+            {% endfor %}
+            </table>
+        </form>
+    </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}  
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+    
+    <script type="text/javascript" charset="utf-8">
+        $(document).ready( function () {
+            console.time("Creating table");
+            $('#dataset_list').dataTable( {
+                "sDom": "Tftipr",
+                "oTableTools": {
+                    "aButtons": [
+                        "copy",
+                        "print",
+                        {
+                            "sExtends":    "collection",
+                            "sButtonText": 'Save <span class="caret" />',
+                            "aButtons":    [ "csv", "xls", "pdf" ]
+                        }
+                    ],
+                    "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
+                },
+                "iDisplayLength": 50,
+                "bLengthChange": true,
+                "bDeferRender": true,
+                "bSortClasses": false
+            } );
+            console.timeEnd("Creating table");
+        });
+    </script>
+{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 741c5425..cbed5859 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -70,9 +70,9 @@
                         </li>
                         <li class="">
                             {% if g.identity.name=="anon" %}
-                            <a id="login" class="modalize" href="/login">Sign in</a>
+                            <a id="login_out" class="modalize" href="/login">Sign in</a>
                             {% else %}
-                            <a href="/logout">Sign out</a>
+                            <a id="login_out" href="/logout">Sign out</a>
                             {% endif %}
                         </li>
                     </ul>
@@ -180,7 +180,7 @@
     <script src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.9.1/jquery-ui.min.js" type="text/javascript"></script>
 
     <script language="javascript" type="text/javascript" src="/static/packages/colorbox/jquery.colorbox.js"></script>
-<!--    <script type="text/javascript" src="/static/new/javascript/login.js"></script>-->
+    <script type="text/javascript" src="/static/new/javascript/login.js"></script>
     {% block js %}
     {% endblock %}
 
diff --git a/wqflask/wqflask/templates/security/thank_you.html b/wqflask/wqflask/templates/security/thank_you.html
new file mode 100644
index 00000000..dd6c7297
--- /dev/null
+++ b/wqflask/wqflask/templates/security/thank_you.html
@@ -0,0 +1,8 @@
+{% from "security/_macros.html" import render_only_errors %}
+{% include "security/_messages.html" %}
+
+<div class="security_box">
+    <h4>Thank you for signing in!</h4>
+</div>
+
+<script src="/static/new/javascript/thank_you.js"></script>
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index b8ebc71f..9e666bbd 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -13,6 +13,8 @@ from flask import Flask, g
 
 from pprint import pformat as pf
 
+from base.data_set import create_datasets_list
+
 #from app import db
 print("globals are:", globals())
 
@@ -32,6 +34,20 @@ class UserManager(object):
         #print("user is:", user)
         self.user = model.User.query.get(self.user_id)
         print("user is:", self.user)
+        datasets = create_datasets_list()
+        for dataset in datasets:
+            if not dataset.check_confidentiality():
+                continue
+            print("\n  Name:", dataset.name)
+            print("  Type:", dataset.type)
+            print("  ID:", dataset.id)
+            print("  Confidential:", dataset.check_confidentiality())
+        #print("   ---> self.datasets:", self.datasets)
+
+
+class GroupsManager(object):
+    def __init__(self, kw):
+        self.datasets = create_datasets_list()
 
 
 class RolesManager(object):
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b9aa3acf..813075b8 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -27,6 +27,7 @@ from flask import render_template, request, make_response, Response, Flask, g, c
 
 from wqflask import search_results
 from base.data_set import DataSet    # Used by YAML in marker_regression
+from base.data_set import create_datasets_list
 from wqflask.show_trait import show_trait
 from wqflask.show_trait import export_trait_data
 from wqflask.marker_regression import marker_regression
@@ -53,6 +54,18 @@ def connect_db():
 @app.route("/")
 def index_page():
     print("Sending index_page")
+    #create_datasets_list()
+    #key = "all_datasets"
+    #result = Redis.get(key)
+    #if result:
+    #    print("Cache hit!!!")
+    #    result = pickle.loads(result)
+    #else:
+    #    with Bench("Creating DataSets object"):
+    #        ds = DataSets()
+    #    Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
+    #    Redis.expire(key, 2*60)
+    #print("[orange] ds:", ds.datasets)
     return render_template("index_page.html")
 
 @app.route("/data_sharing")
@@ -87,7 +100,7 @@ def search_page():
         print("key is:", pf(key))
         with Bench("Loading cache"):
             result = Redis.get(key)
-            
+
         if result:
             print("Cache hit!!!")
             with Bench("Loading results"):
@@ -97,9 +110,9 @@ def search_page():
             print("request.args is", request.args)
             the_search = search_results.SearchResultPage(request.args)
             result = the_search.__dict__
-            
+
             print("result: ", pf(result))
-            Redis.set(key, pickle.dumps(result))
+            Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
             Redis.expire(key, 60*60)
 
         if result['quick']:
@@ -219,7 +232,7 @@ def marker_regression_page():
         #    print("  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
 
         #causeerror
-        Redis.set(key, pickle.dumps(result))
+        Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
         Redis.expire(key, 60*60)
 
     with Bench("Rendering template"):
@@ -249,11 +262,17 @@ def sharing_info_page():
     return template_vars
 
 
+# Take this out or secure it before going into production
 @app.route("/get_temp_data")
 def get_temp_data():
     temp_uuid = request.args['key']
     return flask.jsonify(temp_data.TempData(temp_uuid).get_all())
 
+
+@app.route("/thank_you")
+def thank_you():
+    return render_template("security/thank_you.html")
+
 @app.route("/manage/users")
 def manage_users():
     template_vars = user_manager.UsersManager()
@@ -264,6 +283,11 @@ def manage_user():
     template_vars = user_manager.UserManager(request.args)
     return render_template("admin/ind_user_manager.html", **template_vars.__dict__)
 
+@app.route("/manage/groups")
+def manage_groups():
+    template_vars = user_manager.GroupsManager(request.args)
+    return render_template("admin/group_manager.html", **template_vars.__dict__)
+
 
 def json_default_handler(obj):
     '''Based on http://stackoverflow.com/a/2680060/1175849'''