Merge branch 'master' of https://github.com/biocore/qiita into fix-1084

Author: josenavas

qiita_db/analysis.py

@@ -32,7 +32,7 @@
 from .base import QiitaStatusObject
 from .data import ProcessedData
 from .study import Study
-from .exceptions import QiitaDBStatusError, QiitaDBError
+from .exceptions import QiitaDBStatusError, QiitaDBError, QiitaDBUnknownIDError
 from .util import (convert_to_id, get_work_base_dir,
                    get_mountpoint, insert_filepaths)
 
@@ -66,9 +66,13 @@ class Analysis(QiitaStatusObject):
     unshare
     build_files
     summary_data
+    exists
+    create
+    delete
     """
 
     _table = "analysis"
+    _analysis_id_column = 'analysis_id'
 
     def _lock_check(self, conn_handler):
         """Raises QiitaDBStatusError if analysis is not in_progress"""
@@ -165,6 +169,73 @@ def create(cls, owner, name, description, parent=None, from_default=False):
         a_id = conn_handler.execute_queue(queue)[0]
         return cls(a_id)
 
+    @classmethod
+    def delete(cls, _id):
+        """Deletes an analysis
+
+        Parameters
+        ----------
+        _id : int
+            The analysis id
+
+        Raises
+        ------
+        QiitaDBUnknownIDError
+            If the analysis id doesn't exist
+        """
+        # check if the analysis exist
+        if not cls.exists(_id):
+            raise QiitaDBUnknownIDError(_id, "analysis")
+
+        queue = "delete_analysis_%d" % _id
+        conn_handler = SQLConnectionHandler()
+        conn_handler.create_queue(queue)
+
+        sql = ("DELETE FROM qiita.analysis_filepath WHERE "
+               "{0} = {1}".format(cls._analysis_id_column, _id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.analysis_workflow WHERE "
+               "{0} = {1}".format(cls._analysis_id_column, _id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.analysis_sample WHERE "
+               "{0} = {1}".format(cls._analysis_id_column, _id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.collection_analysis WHERE "
+               "{0} = {1}".format(cls._analysis_id_column, _id))
+        conn_handler.add_to_queue(queue, sql)
+
+        # TODO: issue #1176
+
+        sql = ("DELETE FROM qiita.{0} WHERE "
+               "{1} = {2}".format(cls._table, cls._analysis_id_column, _id))
+        conn_handler.add_to_queue(queue, sql)
+
+        conn_handler.execute_queue(queue)
+
+    @classmethod
+    def exists(cls, analysis_id):
+        r"""Checks if the given analysis _id exists
+
+        Parameters
+        ----------
+        analysis_id : int
+            The id of the analysis we are searching for
+
+        Returns
+        -------
+        bool
+            True if exists, false otherwise.
+        """
+        conn_handler = SQLConnectionHandler()
+
+        return conn_handler.execute_fetchone(
+            "SELECT EXISTS(SELECT * FROM qiita.{0} WHERE "
+            "{1}=%s)".format(cls._table, cls._analysis_id_column),
+            (analysis_id, ))[0]
+
     # ---- Properties ----
     @property
     def owner(self):

qiita_db/metadata_template/constants.py

@@ -15,7 +15,9 @@
 SAMPLE_TEMPLATE_COLUMNS = {
     # The following columns are required by EBI for submission
     'EBI': Restriction(columns={'collection_timestamp': 'timestamp',
-                                'physical_specimen_location': 'varchar'},
+                                'physical_specimen_location': 'varchar',
+                                'taxon_id': 'integer',
+                                'scientific_name': 'varchar'},
                        error_msg="EBI submission disabled"),
     # The following columns are required for the official main QIITA site
     'qiita_main': Restriction(columns={'sample_type': 'varchar',