Merge pull request #1039 from squirrelo/list-proc-data-in-search

List proc data in search

Author: ElDeveloper

qiita_pet/handlers/study_handlers/listing_handlers.py

@@ -8,6 +8,7 @@
 from __future__ import division
 from json import dumps
 from future.utils import viewitems
+from collections import defaultdict
 
 from tornado.web import authenticated, HTTPError
 from tornado.gen import coroutine, Task
@@ -21,6 +22,7 @@
 from qiita_db.exceptions import QiitaDBIncompatibleDatatypeError
 from qiita_db.util import get_table_cols
 from qiita_db.data import ProcessedData
+from qiita_core.exceptions import IncompetentQiitaDeveloperError
 
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.handlers.util import study_person_linkifier, pubmed_linkifier
@@ -42,74 +44,149 @@ def _get_shared_links_for_study(study):
     return ", ".join(shared)
 
 
-def _build_study_info(user, results=None):
-    """builds list of dicts for studies table, with all html formatted"""
+def _build_single_study_info(study, info, study_proc, proc_samples):
+    """Clean up and add to the study info for HTML purposes
+
+    Parameters
+    ----------
+    study : Study object
+        The study to build information for
+    info : dict
+        Information from Study.get_info
+    study_proc : dict of dict of lists
+        Dictionary keyed on study_id that lists all processed data associated
+        with that study. This list of processed data ids is keyed by data type
+    proc_samples : dict of lists
+        Dictionary keyed on proc_data_id that lists all samples associated with
+        that processed data.
+
+    Returns
+    -------
+    dict
+        info-information + extra information for the study,
+        slightly HTML formatted
+    """
+    PI = StudyPerson(info['principal_investigator_id'])
+    status = study.status
+    if info['pmid'] is not None:
+        info['pmid'] = ", ".join([pubmed_linkifier([p])
+                                  for p in info['pmid']])
+    else:
+        info['pmid'] = ""
+    if info["number_samples_collected"] is None:
+        info["number_samples_collected"] = 0
+    info["shared"] = _get_shared_links_for_study(study)
+    info["num_raw_data"] = len(study.raw_data())
+    info["status"] = status
+    info["study_id"] = study.id
+    info["pi"] = study_person_linkifier((PI.email, PI.name))
+    del info["principal_investigator_id"]
+    del info["email"]
+    # Build the proc data info list for the child row in datatable
+    info["proc_data_info"] = []
+    for data_type, proc_datas in viewitems(study_proc[study.id]):
+        info["proc_data_info"].extend([
+            _build_single_proc_data_info(pd_id, data_type, proc_samples[pd_id])
+            for pd_id in proc_datas])
+    return info
+
+
+def _build_single_proc_data_info(proc_data_id, data_type, samples):
+    """Build the proc data info list for the child row in datatable
+
+    Parameters
+    ----------
+    proc_data_id : int
+        The processed data attached to he study, in the form
+        {study_id: [proc_data_id, proc_data_id, ...], ...}
+    data_type : str
+        Data type of the processed data
+    proc_samples : dict of lists
+        The samples available in the processed data, in the form
+        {proc_data_id: [samp1, samp2, ...], ...}
+
+    Returns
+    -------
+    dict
+        The information for the processed data, in the form {info: value, ...}
+    """
+    proc_data = ProcessedData(proc_data_id)
+    proc_info = proc_data.processing_info
+    proc_info['pid'] = proc_data_id
+    proc_info['data_type'] = data_type
+    proc_info['samples'] = sorted(samples)
+    proc_info['processed_date'] = str(proc_info['processed_date'])
+    return proc_info
+
+
+def _build_study_info(user, study_proc=None, proc_samples=None):
+    """Builds list of dicts for studies table, with all HTML formatted
+
+    Parameters
+    ----------
+    user : User object
+        logged in user
+    study_proc : dict of lists, optional
+        Dictionary keyed on study_id that lists all processed data associated
+        with that study. Required if proc_samples given.
+    proc_samples : dict of lists, optional
+        Dictionary keyed on proc_data_id that lists all samples associated with
+        that processed data. Required if study_proc given.
+
+    Returns
+    -------
+    infolist: list of dict of lists and dicts
+        study and processed data info for JSON serialiation for datatables
+        Each dict in the list is a single study, and contains the text
+
+    Notes
+    -----
+    Both study_proc and proc_samples must be passed, or neither passed.
+    """
+    build_samples = False
+    # Logic check to make sure both needed parts passed
+    if study_proc is not None and proc_samples is None:
+        raise IncompetentQiitaDeveloperError(
+            'Must pass proc_samples when study_proc given')
+    elif proc_samples is not None and study_proc is None:
+        raise IncompetentQiitaDeveloperError(
+            'Must pass study_proc when proc_samples given')
+    elif study_proc is None:
+        build_samples = True
+
     # get list of studies for table
-    study_list = user.user_studies.union(
+    study_set = user.user_studies.union(
         Study.get_by_status('public')).union(user.shared_studies)
-    if results is not None:
-        study_list = study_list.intersection(results)
-    if not study_list:
+    if study_proc is not None:
+        study_set = study_set.intersection(study_proc)
+    if not study_set:
         # No studies left so no need to continue
         return []
 
     # get info for the studies
     cols = ['study_id', 'email', 'principal_investigator_id',
             'pmid', 'study_title', 'metadata_complete',
             'number_samples_collected', 'study_abstract']
-    study_info = Study.get_info(study_list, cols)
+    study_info = Study.get_info(study_set, cols)
 
     infolist = []
-    for row, info in enumerate(study_info):
+    for info in study_info:
+        # Convert DictCursor to proper dict
+        info = dict(info)
         study = Study(info['study_id'])
-        status = study.status
-        # Just passing the email address as the name here, since
-        # name is not a required field in qiita.qiita_user
-        PI = StudyPerson(info['principal_investigator_id'])
-        PI = study_person_linkifier((PI.email, PI.name))
-        if info['pmid'] is not None:
-            pmids = ", ".join([pubmed_linkifier([p])
-                               for p in info['pmid']])
-        else:
-            pmids = ""
-        if info["number_samples_collected"] is None:
-            info["number_samples_collected"] = "0"
-        shared = _get_shared_links_for_study(study)
-        meta_complete_glyph = "ok" if info["metadata_complete"] else "remove"
-        # build the HTML elements needed for table cell
-        title = ("<a href='#' data-toggle='modal' "
-                 "data-target='#study-abstract-modal' "
-                 "onclick='fillAbstract(\"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(study.id), info["study_title"])
-        meta_complete = "<span class='glyphicon glyphicon-%s'></span>" % \
-            meta_complete_glyph
-        if status == 'public':
-            shared = "Not Available"
-        else:
-            shared = ("<span id='shared_html_{0}'>{1}</span><br/>"
-                      "<a class='btn btn-primary btn-xs' data-toggle='modal' "
-                      "data-target='#share-study-modal-view' "
-                      "onclick='modify_sharing({0});'>Modify</a>".format(
-                          study.id, shared))
-
-        infolist.append({
-            "checkbox": "<input type='checkbox' value='%d' />" % study.id,
-            "id": study.id,
-            "title": title,
-            "meta_complete": meta_complete,
-            "num_samples": info["number_samples_collected"],
-            "shared": shared,
-            "num_raw_data": len(study.raw_data()),
-            "pi": PI,
-            "pmid": pmids,
-            "status": status,
-            "abstract": info["study_abstract"]
-
-        })
+        # Build the processed data info for the study if none passed
+        if build_samples:
+            proc_data_list = study.processed_data()
+            proc_samples = {}
+            study_proc = {study.id: defaultdict(list)}
+            for pid in proc_data_list:
+                proc_data = ProcessedData(pid)
+                study_proc[study.id][proc_data.data_type()].append(pid)
+                proc_samples[pid] = proc_data.samples
+
+        study_info = _build_single_study_info(study, info, study_proc,
+                                              proc_samples)
+        infolist.append(study_info)
     return infolist
 
 
@@ -195,12 +272,12 @@ def get(self, ignore):
 
         if user != self.current_user.id:
             raise HTTPError(403, 'Unauthorized search!')
-        res = None
         if query:
             # Search for samples matching the query
             search = QiitaStudySearch()
             try:
-                res, meta = search(query, self.current_user)
+                search(query, self.current_user)
+                study_proc, proc_samples, _ = search.filter_by_processed_data()
             except ParseException:
                 self.clear()
                 self.set_status(400)
@@ -223,9 +300,10 @@ def get(self, ignore):
                                 info={'User': self.current_user.id,
                                       'query': query})
                 return
-            if not res:
-                res = {}
-        info = _build_study_info(self.current_user, results=res)
+        else:
+            study_proc = proc_samples = None
+        info = _build_study_info(self.current_user, study_proc=study_proc,
+                                 proc_samples=proc_samples)
         # build the table json
         results = {
             "sEcho": echo,

qiita_pet/templates/list_studies.html

@@ -1,35 +1,75 @@
 {% extends sitebase.html %}
 {% block head %}
 <link rel="stylesheet" href="/static/vendor/css/jquery.dataTables.css" type="text/css">
-
+<style>
+td.details-control {
+  cursor: pointer;
+}
+</style>
 <script src="/static/vendor/js/jquery.dataTables.min.js"></script>
 <script src="/static/vendor/js/jquery.dataTables.plugin.natural.js"></script>
 
 <script type="text/javascript">
 var current_study;
 var ajaxURL = "/study/search/?&user={{current_user.id}}&sEcho=" + Math.floor(Math.random()*1001);
 $(document).ready(function() {
+
+        function format ( d ) {
+            // `d` is the original data object for the row
+            var proc_data_table = '<h4>Processed Data</h4><table class="table" cellpadding="5" cellspacing="0" border="0" style="padding-left:50px;"><tr><th></th><th>ID</th><th>Data type</th><th>Processed Date</th><th>Algorithm</th><th>Reference</th><th>Samples</th></tr>';
+            for(i=0;i<d.proc_data_info.length;i++) {
+              var proc_data = d.proc_data_info[i];
+              proc_data_table += '<tr><td><input type="checkbox"></td><td>' + proc_data.pid + '</td><td>' + proc_data.data_type + '</td><td>' + proc_data.processed_date + '</td><td>' + proc_data.algorithm + '</td><td>' + proc_data.reference_name + ' ' + proc_data.reference_version + '</td><td>' + proc_data.samples.length + '</td></tr>';
+            }
+            proc_data_table += '</table>';
+            return proc_data_table;
+        }
+
         $('#studies-table').dataTable({
             "columns": [
-              { "data": "checkbox" },
-              { "data": "title" },
-              { "data": "abstract" },
-              { "data": "id" },
-              { "data": "meta_complete" },
-              { "data": "num_samples" },
+              { "className": 'details-control', "orderable": false},
+              { "data": "study_title" },
+              { "data": "study_abstract" },
+              { "data": "study_id" },
+              { "data": "metadata_complete" },
+              { "data": "number_samples_collected" },
               { "data": "num_raw_data" },
               { "data": "shared" },
               { "data": "pi" },
               { "data": "pmid" },
-              { "data": "status" }
+              { "data": "status" },
+              {"className": 'details-control', "orderable": false, "data": null, "defaultContent": '<span class="glyphicon glyphicon-chevron-down"></span>'}
             ],
             order: [[10, "desc"], [ 1, "asc" ]],
-            columnDefs: [{type:'natural', targets:[3,4,5,9]}, {"targets": [ 2 ],"visible": false}],
+            columnDefs: [
+              {type:'natural', targets:[3,4,5,9]},
+              {"targets": [ 2 ],"visible": false},
+              // render the study checkbox cell
+              {"render": function ( data, type, row, meta ) {
+                    return "<input type='checkbox' value='"+ row.study_id +"'>";
+              }, targets: [0]},
+              // render the title cell
+              {"render": function ( data, type, row, meta ) {
+                    return "<a href='#' data-toggle='modal' data-target='#study-abstract-modal' onclick=\"fillAbstract('studies-table', "+ meta.row +")\"><span class='glyphicon glyphicon-file' aria-hidden='true'></span></a> | <a href='/study/description/"+ row.study_id +"' id='study"+ meta.row +"-title'>"+ data +"</a>";
+              }, targets: [1]},
+              // render the metadata complete cell
+              {"render": function ( data, type, row, meta ) {
+                    var glyph = 'remove';
+                    if(data === true) { glyph = 'ok' } 
+                    return "<span class='glyphicon glyphicon-"+ glyph +"'></span>";
+              }, targets: [4]},
+              // render the shared with cell
+              {"render": function ( data, type, row, meta ) {
+                    var glyph = 'remove';
+                    if(data === true) { glyph = 'ok' } 
+                    return "<span id='shared_html_"+ row.study_id +"'>"+ data +"</span><br/><a class='btn btn-primary btn-xs' data-toggle='modal' data-target='#share-study-modal-view' onclick='modify_sharing("+ row.study_id +");'>Modify</a>";
+              }, targets: [7]},
+              ],
             "oLanguage": {
                 "sSearch": "Narrow search results by column data (Title, abstract, PI, etc):",
                 "sLoadingRecords": "Loading table data",
                 "sZeroRecords": "No studies found"
-            }, 
+            },
             "ajax": {
                 "url": ajaxURL + "&query=",
                 "error": function(jqXHR, textStatus, ex) {
@@ -39,6 +79,23 @@
                 }
             } 
         });
+    // Add event listener for opening and closing details
+    $('#studies-table tbody').on('click', 'td.details-control', function () {
+        var table = $('#studies-table').DataTable();
+        var tr = $(this).closest('tr');
+        var row = table.row( tr );
+ 
+        if ( row.child.isShown() ) {
+            // This row is already open - close it
+            row.child.hide();
+            tr.removeClass('shown');
+        }
+        else {
+            // Open this row
+            row.child( format(row.data()) ).show();
+            tr.addClass('shown');
+        }
+    } );
 
     $('#users_list').chosen({width: "100%"});
     $('#users_list').on('change', function(evt, params) {
@@ -105,7 +162,7 @@ <h1>Metadata Search</h1>
 <div class="row">
   <div class="col-sm-12" id="user-studies-div">
     <h1>Available Studies</h1>
-    <table id="studies-table" class="display table-bordered table-hover">
+    <table id="studies-table" class="table table-bordered">
         <thead>
             <tr>
                 <th></th>
@@ -119,10 +176,9 @@ <h1>Available Studies</h1>
                 <th>Principal Investigator</th>
                 <th>Pubmed ID(s)</th>
                 <th>Status</th>
+                <th>Expand</th>
             </tr>
         </thead>
-        <tbody>
-        </tbody>
     </table>
 <!--Abstract Modal-->
 <div class="modal fade" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel" aria-hidden="true" id="study-abstract-modal">