load study tables through ajax

qiita_pet/handlers/study_handlers/__init__.py

@@ -7,7 +7,7 @@
 # -----------------------------------------------------------------------------
 
 from .listing_handlers import (ListStudiesHandler, StudyApprovalList,
-                               ShareStudyAJAX)
+                               ShareStudyAJAX, SearchStudiesAJAX)
 from .edit_handlers import StudyEditHandler, CreateStudyAJAX
 from .description_handlers import (StudyDescriptionHandler,
                                    PreprocessingSummaryHandler)
@@ -18,4 +18,4 @@
 __all__ = ['ListStudiesHandler', 'StudyApprovalList', 'ShareStudyAJAX',
            'StudyEditHandler', 'CreateStudyAJAX', 'StudyDescriptionHandler',
            'PreprocessingSummaryHandler', 'EBISubmitHandler',
-           'MetadataSummaryHandler', 'VAMPSHandler']
+           'MetadataSummaryHandler', 'VAMPSHandler', 'SearchStudiesAJAX']

qiita_pet/handlers/study_handlers/listing_handlers.py

@@ -15,6 +15,7 @@
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from qiita_db.user import User
 from qiita_db.study import Study, StudyPerson
+from qiita_db.search import QiitaStudySearch
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.handlers.util import study_person_linkifier, pubmed_linkifier
 
@@ -35,15 +36,24 @@ def _get_shared_links_for_study(study):
     return ", ".join(shared)
 
 
-def _build_study_info(studytype, user=None):
+def _build_study_info(studytype,  user, studies=None):
     """builds list of namedtuples for study listings"""
-    if studytype == "standard":
+    if studytype not in {"standard", "shared"}:
+        raise IncompetentQiitaDeveloperError("Must use private, shared, "
+                                             "or public!")
+    # get list of studies for table
+    if studies:
+        # filter info to given studies
+        if studytype == "standard":
+            studylist = (user.user_studies |
+                         Study.get_by_status('public')).intersection(studies)
+        elif studytype == "shared":
+            studylist = user.shared_studies.intersection(studies)
+    elif studytype == "standard":
         studylist = user.user_studies | Study.get_by_status('public')
     elif studytype == "shared":
         studylist = user.shared_studies
-    else:
-        raise IncompetentQiitaDeveloperError("Must use private, shared, "
-                                             "or public!")
+
     if not studylist:
         return []
 
@@ -85,22 +95,10 @@ class ListStudiesHandler(BaseHandler):
     def get(self):
         self.write(self.render_string('waiting.html'))
         self.flush()
-        user = self.current_user
-        user_studies = yield Task(self._get_standard, user)
-        shared_studies = yield Task(self._get_shared, user)
         all_emails_except_current = yield Task(self._get_all_emails)
         all_emails_except_current.remove(self.current_user.id)
         self.render('list_studies.html',
-                    user_studies=user_studies, shared_studies=shared_studies,
-                    all_emails_except_current=all_emails_except_current,
-                    query='')
-
-    def _get_standard(self, user, callback):
-        callback(_build_study_info("standard", user))
-
-    def _get_shared(self, user, callback):
-        """builds list of tuples for studies that are shared with user"""
-        callback(_build_study_info("shared", user))
+                    all_emails_except_current=all_emails_except_current)
 
     def _get_all_emails(self, callback):
         callback(list(User.iter()))
@@ -154,3 +152,102 @@ def get(self):
         users, links = yield Task(self._get_shared_for_study, study)
 
         self.write(dumps({'users': users, 'links': links}))
+
+
+class SearchStudiesAJAX(BaseHandler):
+    def _get_standard(self, user, callback):
+        callback(_build_study_info("standard", user))
+
+    def _get_shared(self, user, callback):
+        """builds list of tuples for studies that are shared with user"""
+        callback(_build_study_info("shared", user))
+
+    @authenticated
+    def get(self, ignore):
+        search_type = self.get_argument('type')
+        user = self.get_argument('user')
+        query = self.get_argument('query')
+        echo = int(self.get_argument('sEcho'))
+
+        res = None
+        if query != "":
+            # Search for samples matching the query
+            search = QiitaStudySearch()
+            res, meta = search(query)
+            info = _build_study_info(search_type, self.current_user,
+                                     studies=search.keys())
+        else:
+            # show everything
+            info = _build_study_info(search_type, self.current_user)
+
+        # build the table json
+        results = {
+            "sEcho": echo,
+            "iTotalRecords": len(info),
+            "iTotalDisplayRecords": len(info),
+            "aaData": []
+        }
+        if search_type == "standard":
+            for row, s in enumerate(info):
+                # build the HTML elements needed for table cell
+                meta_complete = "ok" if s.meta_complete else "remove"
+                share = "Not Available" if s.status == 'public' else \
+                    ("<span id='shared_html_{0}'>{1}</span><br/>"
+                     "<a class='btn btn-primary' data-toggle='modal' "
+                     "data-target='#share-study-modal-view' "
+                     "onclick='modify_sharing({0});'>Modify</a>".format(
+                        s.id, s.shared))
+                # add study to table
+                results['aaData'].append([
+                    "<input type='checkbox' value='%s'>" % s.id,
+
+                    "<a href='#'' data-toggle='modal' "
+                    "data-target='#study-abstract-modal' "
+                    "onclick='fillAbstract(\"user-studies-table\", {0})'>"
+                    "<span class=\'glyphicon glyphicon-file\' "
+                    "aria-hidden=\'true\'></span></a> | "
+                    "<a href=\'/study/description/{1}\' "
+                    "id=\'study{0}-title\'>{2}</a>".format(
+                        str(row), str(s.id), s.title),
+
+                    s.abstract,
+                    s.id,
+                    "<span class='glyphicon glyphicon-%s'></span>" %
+                    meta_complete,
+                    s.num_samples_collected,
+                    s.num_raw_data,
+                    share,
+                    s.pi,
+                    s.pmids,
+                    s.status
+                ])
+        elif search_type == "shared": 
+            for row, s in enumerate(info):
+                # build the HTML elements needed for table cell
+                meta_complete = "ok" if s.meta_complete else "remove"
+                # add study to table
+                results['aaData'].append([
+                    "<input type='checkbox' value='%s'>" % s.id,
+
+                    "<a href='#'' data-toggle='modal' "
+                    "data-target='#study-abstract-modal' "
+                    "onclick='fillAbstract(\"shared-studies-table\", {0})'>"
+                    "<span class=\'glyphicon glyphicon-file\' "
+                    "aria-hidden=\'true\'></span></a> | "
+                    "<a href=\'/study/description/{1}\' "
+                    "id=\'study{0}-title\'>{2}</a>".format(
+                        str(row), str(s.id), s.title),
+
+                    s.abstract,
+                    s.id,
+                    s.owner,
+                    "<span class='glyphicon glyphicon-%s'></span>" %
+                    meta_complete,
+                    s.num_samples_collected,
+                    s.num_raw_data,
+                    s.pi,
+                    s.pmids
+                ])
+
+        # return the json
+        self.write(dumps(results))

qiita_pet/static/js/qiita.js

@@ -23,6 +23,6 @@ function bootstrapAlert(message, severity){
 }
 
 function fillAbstract(table, row) {
-    $('#title-text-area').text($('#study' + row + "-title").text());
+    $('#title-text-area').text($('#' + table).find('#study' + row + "-title").text());
     $('#abstract-text-area').text($('#'+table).dataTable().fnGetData(row, 2));
 }

qiita_pet/templates/list_studies.html

@@ -7,20 +7,29 @@
 
 <script type="text/javascript">
 var current_study;
-
+var query = "";
 $(document).ready(function() {
+        var randomnumber=Math.floor(Math.random()*11);
         $('#user-studies-table').dataTable({
             order: [[10, "asc"], [ 1, "asc" ]],
             columnDefs: [{type:'natural', targets:[3,4,5,9]}, {"targets": [ 2 ],"visible": false}],
             "oLanguage": {
-                "sSearch": "Refine search results:"
-            }
+                "sSearch": "Refine search results:",
+                "sLoadingRecords": "Loading table data"
+            }, 
+            "ajax": {
+                "url": "/study/search/?type=standard&user={{current_user.id}}&query=" + query + "&sEcho=" + randomnumber
+            }  
         });
         $('#shared-studies-table').dataTable({
             order: [[ 1, "asc" ]],
             columnDefs: [{type:'natural', targets:[4,5,6]}, {"targets": [ 2 ],"visible": false}],
             "oLanguage": {
-                "sSearch": "Refine search results:"
+                "sSearch": "Refine search results:",
+                "sLoadingRecords": "Loading table data"
+            },
+            "ajax": {
+                "url": "/study/search/?type=shared&user={{current_user.id}}&query=" + query + "&sEcho=" + randomnumber
             }
         });
     $('#waiting').hide();
@@ -61,17 +70,16 @@
     <h1>Search</h1>
     <p><a href="#" data-toggle="modal" data-target="#searchexample">Search help</a></p>
     <form id="search-form" name="search-form" class="form-inline" method="POST" action="/study/search/">
-        <input type="textbox" id="searchbox" name="searchbox" class="form-control" style="width:80%;white-space:nowrap;" value='{{query}}' />
+        <input type="textbox" id="searchbox" name="searchbox" class="form-control" style="width:80%;white-space:nowrap;" />
       <button type="submit" class="btn btn-default">Submit</button>
     </form>
   </div>
   <div class="col-sm-12" id="searchmsg" name="searchmsg"></div>
 </div>
 <!--User Studies-->
 <div class="row">
-  <div class="col-sm-12">
+  <div class="col-sm-12" id="user-studies-div">
     <h1>Your Studies</h1>
-{% if len(user_studies) %}
     <table id="user-studies-table" class="display table-bordered table-hover">
         <thead>
             <tr>
@@ -89,65 +97,13 @@ <h1>Your Studies</h1>
             </tr>
         </thead>
         <tbody>
-            {% set row = 0 %}
-            {% for s in user_studies %}
-            <tr>
-                <td><input type="checkbox" value="{{s.id}}"></td>
-                {# Title #}
-                <td><a href="#" data-toggle="modal" data-target="#study-abstract-modal" onclick="fillAbstract('user-studies-table', {{row}})"><span class="glyphicon glyphicon-file" aria-hidden="true"></span></a> | <a href="/study/description/{{ s.id }}" id="study{{row}}-title">{{ s.title }}</a></td>
-                {# Abstract (hidden on page) #}
-                <td>{% raw s.abstract %}</td>
-                {# Study ID #}
-                <td>{% raw s.id %}</td>
-                {# Metadata Comlete #}
-                {% if s.meta_complete %}
-                <td><span class="glyphicon glyphicon-ok"></span></td>
-                {% else %}
-                <td><span class="glyphicon glyphicon-remove"></span></td>
-                {% end %}
-                {# Samples #}
-                <td>{{ s.num_samples_collected }}</td>
-                {# Sequence Files #}
-                {% if s.num_raw_data %}
-                <td>{{ s.num_raw_data }}</td>
-                {% else %}
-                <td><span class="glyphicon glyphicon-remove"></span></td>
-                {% end %}
-                {# Shared #}
-                {% if s.status == 'public' %}
-                <td>Not available</td>
-                {% else %}
-                <td><span id="shared_html_{{ s.id }}">{% raw s.shared %}</span>
-                <br/>
-                <a class="btn btn-primary" data-toggle="modal" data-target="#share-study-modal-view" onclick="modify_sharing({{ s.id }});">Modify</a>
-                </td>
-                {% end %}
-                {# Principal Investigator #}
-                <td>{% raw s.pi %}</td>
-                {# Pubmed ID(s) #}
-                <td>{% raw s.pmids %}</td>
-                <td>{{ s.status }}</td>
-            </tr>
-            {% set row = row + 1 %}
-            {% end %}
         </tbody>
     </table>
-{% else %}
-    <div id="jumbotron" class="jumbotron">
-        <h1><span class="glyphicon glyphicon-thumbs-down"></span> There are no studies available.</h1>
-        <p>
-        This means that you have not yet created a study. <a href="/study/create/">Create a study</a>.
-        </p>
-    </div>
-  </div>
-</div>
-{% end %}
 <!--Shared Studies-->
 <form id="study-sel-form" name="study-sel-form">
 <div class="row">
-  <div class="col-sm-12">
+  <div class="col-sm-12" id="user-studies-div">
     <h1>Shared Studies</h1>
-{% if len(shared_studies) %}
     <table id="shared-studies-table" class="display table-bordered table-hover">
         <thead>
             <tr>
@@ -164,42 +120,8 @@ <h1>Shared Studies</h1>
             </tr>
         </thead>
         <tbody>
-            {% set row = 0 %}
-            {% for s in shared_studies %}
-            <tr>
-                <td><input type="checkbox" value="{{s.id}}"></td>
-                <td><a href="#" data-toggle="modal" data-target="#study-abstract-modal" onclick="fillAbstract('shared-studies-table', {{row}})"><span class="glyphicon glyphicon-file" aria-hidden="true"></span></a> | <a href="/study/description/{{ s.id }}" id="study{{row}}-title">{{ s.title }}</a></td>
-                <td>{% raw s.abstract %}</a></td>
-                <td>{% raw s.id %}</td>
-                <td>{% raw s.owner %}</td>
-                {% if s.meta_complete %}
-                <td><span class="glyphicon glyphicon-ok"></span></td>
-                {% else %}
-                <td><span class="glyphicon glyphicon-remove"></span></td>
-                {% end %}
-                <td>{{ s.num_samples_collected }}</td>
-                {% if s.num_raw_data %}
-                <td>{{ s.num_raw_data }}</td>
-                {% else %}
-                <td><span class="glyphicon glyphicon-remove"></span></td>
-                {% end %}
-                <td>{% raw s.pi %}</td>
-                <td>{% raw s.pmids %}</td>
-            </tr>
-            {% set row = row + 1 %}
-            {% end %}
         </tbody>
     </table>
-{% else %}
-    <div id="jumbotron" class="jumbotron">
-        <h1><span class="glyphicon glyphicon-thumbs-down"></span> There are no studies available.</h1>
-        <p>
-        This means that no one has shared any studies with you yet.
-        </p>
-    </div>
-  </div>
-</div>
-{% end %}
 <!--Abstract Modal-->
 <div class="modal fade" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel" aria-hidden="true" id="study-abstract-modal">
   <div class="modal-dialog modal-med">

qiita_pet/webserver.py

@@ -18,7 +18,7 @@
     SelectCommandsHandler, AnalysisWaitHandler, AnalysisResultsHandler,
     ShowAnalysesHandler, SearchStudiesHandler, ResultsHandler)
 from qiita_pet.handlers.study_handlers import (
-    StudyEditHandler, ListStudiesHandler,
+    StudyEditHandler, ListStudiesHandler, SearchStudiesAJAX,
     StudyDescriptionHandler, MetadataSummaryHandler, EBISubmitHandler,
     CreateStudyAJAX, ShareStudyAJAX, StudyApprovalList,
     PreprocessingSummaryHandler, VAMPSHandler)
@@ -74,6 +74,7 @@ def __init__(self):
             (r"/study/create/", StudyEditHandler),
             (r"/study/edit/(.*)", StudyEditHandler),
             (r"/study/list/", ListStudiesHandler),
+            (r"/study/search/(.*)", SearchStudiesAJAX),
             (r"/study/add_files_to_raw_data", AddFilesToRawData),
             (r"/study/unlink_all_files", UnlinkAllFiles),
             (r"/study/preprocess", PreprocessHandler),