Merge pull request #1126 from josenavas/join-using-instead-on-db-issues

Join using instead on db issues

README.md

@@ -6,7 +6,7 @@ Qiita
 [![Build Status](https://travis-ci.org/biocore/qiita.png?branch=master)](https://travis-ci.org/biocore/qiita)
 [![Coverage Status](https://coveralls.io/repos/biocore/qiita/badge.png?branch=master)](https://coveralls.io/r/biocore/qiita)
 
-Qiita (canonically pronounced *cheetah*) is a meta-analysis environment for microbiome (and other "comparative -omics") datasets. You can find the public Qiita server at [qiita.microbio.me](http://qiita.microbio.me).
+Qiita (canonically pronounced *cheetah*) is an analysis environment for microbiome (and other "comparative -omics") datasets. You can find the public Qiita server at [qiita.microbio.me](http://qiita.microbio.me).
 
 Qiita is currently in pre-alpha status. We are very open to community contributions and feedback. If you're interested in contributing to Qiita, see [CONTRIBUTING.md](https://github.com/biocore/qiita/blob/master/CONTRIBUTING.md). If you'd like to report bugs or request features, you can do that in the [Qiita issue tracker](https://github.com/biocore/qiita/issues).
 

qiita_db/analysis.py

@@ -777,6 +777,9 @@ def _build_mapping_file(self, samples, conn_handler=None):
         merged_map.to_csv(mapping_fp, index_label='#SampleID',
                           na_rep='unknown', sep='\t')
 
+        self._add_file("%d_analysis_mapping.txt" % self._id,
+                       "plain_text", conn_handler=conn_handler)
+
     def _add_file(self, filename, filetype, data_type=None, conn_handler=None):
         """adds analysis item to database
 

qiita_db/data.py

@@ -1338,7 +1338,7 @@ def delete(cls, processed_data_id):
         QiitaDBStatusError
             If the processed data status is not sandbox
         QiitaDBError
-            If the processed data has (meta)analyses
+            If the processed data has analyses
         """
         if cls(processed_data_id).status != 'sandbox':
             raise QiitaDBStatusError(
@@ -1354,8 +1354,8 @@ def delete(cls, processed_data_id):
         if analyses:
             raise QiitaDBError(
                 "Processed data %d cannot be removed because it is linked to "
-                "the following (meta)analysis: %s" % (processed_data_id,
-                                                      ', '.join(analyses)))
+                "the following analysis: %s" % (processed_data_id,
+                                                ', '.join(analyses)))
 
         # delete
         queue = "delete_processed_data_%d" % processed_data_id

qiita_db/metadata_template/base_metadata_template.py

@@ -1014,13 +1014,8 @@ def to_dataframe(self):
         conn_handler = SQLConnectionHandler()
         cols = sorted(get_table_cols(self._table_name(self._id), conn_handler))
         # Get all metadata for the template
-        sql = """SELECT {0}
-                 FROM qiita.{1}
-                 JOIN qiita.{2} USING (sample_id)
-                 WHERE {3} = %s""".format(", ".join(cols),
-                                          self._table,
-                                          self._table_name(self.id),
-                                          self._id_column)
+        sql = "SELECT {0} FROM qiita.{1}".format(", ".join(cols),
+                                                 self._table_name(self.id))
         meta = conn_handler.execute_fetchall(sql, (self._id,))
 
         # Create the dataframe and clean it up a bit

qiita_db/search.py

@@ -343,8 +343,8 @@ def _parse_study_search_string(self, searchstr,
 
         sample_sql = ("SELECT ss.sample_id,%s "
                       "FROM qiita.study_sample ss "
-                      "JOIN qiita.sample_{0} sa USING (sample_id) "
-                      "JOIN qiita.study st USING (study_id) "
+                      "JOIN qiita.sample_{0} sa ON ss.sample_id = sa.sample_id"
+                      " JOIN qiita.study st ON st.study_id = ss.study_id "
                       "WHERE %s" %
                       (','.join(header_info), sql_where))
         return study_sql, sample_sql, meta_header_type_lookup.keys()

qiita_db/test/test_analysis.py

@@ -386,6 +386,7 @@ def test_get_samples(self):
         self.assertEqual(obs, exp)
 
     def test_build_mapping_file(self):
+        new_id = get_count('qiita.filepath') + 1
         samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
         self.analysis._build_mapping_file(samples,
                                           conn_handler=self.conn_handler)
@@ -401,13 +402,28 @@ def test_build_mapping_file(self):
 
         assert_frame_equal(obs, exp)
 
+        sql = """SELECT * FROM qiita.filepath
+                 WHERE filepath=%s ORDER BY filepath_id"""
+        obs = self.conn_handler.execute_fetchall(
+            sql, ("%d_analysis_mapping.txt" % self.analysis.id,))
+
+        exp = [[15, '1_analysis_mapping.txt', 9, '852952723', 1, 1],
+               [new_id, '1_analysis_mapping.txt', 9, '2349935429', 1, 1]]
+        self.assertEqual(obs, exp)
+
+        sql = """SELECT * FROM qiita.analysis_filepath
+                 WHERE analysis_id=%s ORDER BY filepath_id"""
+        obs = self.conn_handler.execute_fetchall(sql, (self.analysis.id,))
+        exp = [[1L, 14L, 2L], [1L, 15L, None], [1L, new_id, None]]
+
     def test_build_mapping_file_duplicate_samples(self):
         samples = {1: ['1.SKB8.640193', '1.SKB8.640193', '1.SKD8.640184']}
         with self.assertRaises(QiitaDBError):
             self.analysis._build_mapping_file(samples,
                                               conn_handler=self.conn_handler)
 
     def test_build_biom_tables(self):
+        new_id = get_count('qiita.filepath') + 1
         samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
         self.analysis._build_biom_tables(samples, 100,
                                          conn_handler=self.conn_handler)
@@ -426,6 +442,17 @@ def test_build_biom_tables(self):
                'Processed_id': 1}
         self.assertEqual(obs, exp)
 
+        sql = """SELECT EXISTS(SELECT * FROM qiita.filepath
+                 WHERE filepath_id=%s)"""
+        obs = self.conn_handler.execute_fetchone(sql, (new_id,))[0]
+
+        self.assertTrue(obs)
+
+        sql = """SELECT * FROM qiita.analysis_filepath
+                 WHERE analysis_id=%s ORDER BY filepath_id"""
+        obs = self.conn_handler.execute_fetchall(sql, (self.analysis.id,))
+        exp = [[1L, 14L, 2L], [1L, 15L, None], [1L, new_id, None]]
+
     def test_build_files(self):
         self.analysis.build_files()
 

qiita_db/test/test_search.py

@@ -29,8 +29,9 @@ def test_parse_study_search_string(self):
                       "in ('integer', 'float8')")
         exp_samp_sql = ("SELECT ss.sample_id,sa.altitude "
                         "FROM qiita.study_sample ss "
-                        "JOIN qiita.sample_{0} sa USING (sample_id) "
-                        "JOIN qiita.study st USING (study_id) "
+                        "JOIN qiita.sample_{0} sa "
+                        "ON ss.sample_id = sa.sample_id "
+                        "JOIN qiita.study st ON st.study_id = ss.study_id "
                         "WHERE sa.altitude > 0")
         self.assertEqual(st_sql, exp_st_sql)
         self.assertEqual(samp_sql, exp_samp_sql)
@@ -44,8 +45,9 @@ def test_parse_study_search_string(self):
                       "in ('integer', 'float8')")
         exp_samp_sql = ("SELECT ss.sample_id,sa.altitude "
                         "FROM qiita.study_sample ss "
-                        "JOIN qiita.sample_{0} sa USING (sample_id) "
-                        "JOIN qiita.study st USING (study_id) "
+                        "JOIN qiita.sample_{0} sa "
+                        "ON ss.sample_id = sa.sample_id "
+                        "JOIN qiita.study st ON st.study_id = ss.study_id "
                         "WHERE NOT sa.altitude > 0")
         self.assertEqual(st_sql, exp_st_sql)
         self.assertEqual(samp_sql, exp_samp_sql)
@@ -59,8 +61,9 @@ def test_parse_study_search_string(self):
                       "('integer', 'float8')")
         exp_samp_sql = ("SELECT ss.sample_id,sa.ph "
                         "FROM qiita.study_sample ss "
-                        "JOIN qiita.sample_{0} sa USING (sample_id) "
-                        "JOIN qiita.study st USING (study_id) "
+                        "JOIN qiita.sample_{0} sa "
+                        "ON ss.sample_id = sa.sample_id "
+                        "JOIN qiita.study st ON st.study_id = ss.study_id "
                         "WHERE (sa.ph > 7 AND sa.ph < 9)")
         self.assertEqual(st_sql, exp_st_sql)
         self.assertEqual(samp_sql, exp_samp_sql)
@@ -74,8 +77,9 @@ def test_parse_study_search_string(self):
                       "('integer', 'float8')")
         exp_samp_sql = ("SELECT ss.sample_id,sa.ph "
                         "FROM qiita.study_sample ss "
-                        "JOIN qiita.sample_{0} sa USING (sample_id) "
-                        "JOIN qiita.study st USING (study_id) "
+                        "JOIN qiita.sample_{0} sa "
+                        "ON ss.sample_id = sa.sample_id "
+                        "JOIN qiita.study st ON st.study_id = ss.study_id "
                         "WHERE (sa.ph > 7 OR sa.ph < 9)")
         self.assertEqual(st_sql, exp_st_sql)
         self.assertEqual(samp_sql, exp_samp_sql)
@@ -90,8 +94,9 @@ def test_parse_study_search_string(self):
                       "and column_type in ('varchar')")
         exp_samp_sql = ("SELECT ss.sample_id,sa.host_subject_id "
                         "FROM qiita.study_sample ss "
-                        "JOIN qiita.sample_{0} sa USING (sample_id) "
-                        "JOIN qiita.study st USING (study_id) "
+                        "JOIN qiita.sample_{0} sa "
+                        "ON ss.sample_id = sa.sample_id "
+                        "JOIN qiita.study st ON st.study_id = ss.study_id "
                         "WHERE LOWER(sa.host_subject_id) "
                         "LIKE '%chicken little%'")
         self.assertEqual(st_sql, exp_st_sql)
@@ -110,8 +115,9 @@ def test_parse_study_search_string(self):
         exp_samp_sql = (
             "SELECT ss.sample_id,sa.name "
             "FROM qiita.study_sample ss "
-            "JOIN qiita.sample_{0} sa USING (sample_id) "
-            "JOIN qiita.study st USING (study_id) "
+            "JOIN qiita.sample_{0} sa "
+            "ON ss.sample_id = sa.sample_id "
+            "JOIN qiita.study st ON st.study_id = ss.study_id "
             "WHERE (sa.name = 'Billy Bob' OR sa.name = 'Timmy' OR "
             "(sa.name = 'Jimbo' AND sa.name > 25) OR sa.name < 5)")
         self.assertEqual(st_sql, exp_st_sql)
@@ -131,8 +137,9 @@ def test_parse_study_search_string(self):
                       "lower('ph') and column_type in ('integer', 'float8')"]
         exp_samp_sql = ("SELECT ss.sample_id,sa.pH,sa.ph "
                         "FROM qiita.study_sample ss "
-                        "JOIN qiita.sample_{0} sa USING (sample_id) "
-                        "JOIN qiita.study st USING (study_id) "
+                        "JOIN qiita.sample_{0} sa "
+                        "ON ss.sample_id = sa.sample_id "
+                        "JOIN qiita.study st ON st.study_id = ss.study_id "
                         "WHERE (sa.ph > 7 OR sa.ph < 9)")
         # use the split list to make sure the SQL is properly formed
         self.assertEqual(len(st_sql), 2)

qiita_pet/static/vendor/js/moi.js

@@ -66,15 +66,15 @@ var moi = new function () {
      * websocket. On construction, this method will send a message over the
      * socket to get all known job information associated with this client.
      *
-     * @param {host} The URL for the websocket, minus the ws:// header, or null
-     * to use the default moi-ws.
      * @param {group_id} A group ID to get initial data from, or null to fetch
      * all records associated with the user.
+     * @param {host} The URL for the websocket, minus the ws:// header, or null
+     * to use the default moi-ws.
      * @param {on_open} Optional function for action when websocket is opened.
      * @param {on_close} Optional function for action when websocket is closed.
      * @param {on_error} Optional function for action when websocket errors.
      */
-    this.init = function(host, group_id, on_open, on_close, on_error) {
+    this.init = function(group_id, host, on_open, on_close, on_error) {
         host = host || window.location.host + '/moi-ws/';
         if (!("WebSocket" in window)) {
             alert("Your browser does not appear to support websockets!");

qiita_pet/templates/analysis_selected.html

@@ -58,7 +58,7 @@
     check_color();
 }
 $(document).ready(function() {
-      moi.init(window.location.host + '/analysis/selected/socket/', null, function(){}, error, error);
+      moi.init(null, window.location.host + '/analysis/selected/socket/', function(){}, error, error);
       moi.add_callback('remove_pd', remove_pd_from_html);
       moi.add_callback('remove_sample', remove_sample_from_html);
       moi.add_callback('clear', clear_from_html);
@@ -149,7 +149,7 @@ <h4 class="modal-title" id="myModalLabel">Processed Data {{pid}}</h4>
         <div class="modal-content">
           <div class="modal-header">
             <button type="button" class="close" data-dismiss="modal" aria-hidden="true">&times;</button>
-            <h4 class="modal-title" id="myModalLabel">Create new meta-analysis</h4>
+            <h4 class="modal-title" id="myModalLabel">Create new analysis</h4>
           </div>
           <form role="form" action="/analysis/3" method="post">
           <input type="hidden" name="action" value="create">

qiita_pet/templates/list_studies.html

@@ -55,7 +55,7 @@
 }
 
 $(document).ready(function() {
-        moi.init(window.location.host + '/study/list/socket/', null, function(){}, error, error);
+        moi.init(null, window.location.host + '/study/list/socket/', function(){}, error, error);
         moi.add_callback('sel', show_alert);
         function format ( d, row ) {
             // `d` is the original data object for the row

qiita_pet/templates/sitebase.html

@@ -117,12 +117,12 @@
                 <img style="max-width:100px; margin-top: -7px;" src="/static/img/logo-clear.png">
               </a>
             </li>
-            <!-- meta-analysis menu -->
+            <!-- analysis menu -->
             {% if user %}
             <li class="dropdown">
-              <a href="#" data-toggle="dropdown" class="dropdown-toggle">Meta Analysis<b class="caret"></b></a>
+              <a href="#" data-toggle="dropdown" class="dropdown-toggle">Analysis<b class="caret"></b></a>
               <ul class="dropdown-menu">
-                <li><a href="/analysis/selected/">View Selected Samples</a></li>
+                <li><a href="/analysis/selected/">Create From Selected Samples</a></li>
                 <li><a href="/analysis/show/">See Previous Analyses</a></li>
               </ul>
             </li>

qiita_ware/dispatchable.py

@@ -66,7 +66,7 @@ def submit_to_VAMPS(preprocessed_data_id):
 
 def run_analysis(analysis_id, commands, comm_opts=None,
                  rarefaction_depth=None, **kwargs):
-    """Run a meta-analysis"""
+    """Run an analysis"""
     analysis = Analysis(analysis_id)
     ar = RunAnalysis(**kwargs)
     return ar(analysis, commands, comm_opts, rarefaction_depth)