Fix #2276 (#2294)

* Fix #2276

* Factoring out generate nginx directory file list

* Factoring out the nginx file list writing

* Factoring out generating the file list of an artifact

* Factoring out the header setting

* Addressing @antgonza's comment

* Addressing @wasade's comments

Author: josenavas

qiita_db/test/test_util.py

@@ -622,6 +622,16 @@ def test_get_timeseries_types(self):
                [10, 'mixed', 'combo intervention']]
         self.assertEqual(obs, exp)
 
+    def test_get_filepath_information(self):
+        obs = qdb.util.get_filepath_information(1)
+        # This path is machine specific. Just checking that is not empty
+        self.assertIsNotNone(obs.pop('fullpath'))
+        exp = {'filepath_id': 1L, 'filepath': '1_s_G1_L001_sequences.fastq.gz',
+               'filepath_type': 'raw_forward_seqs', 'checksum': '852952723',
+               'data_type': 'raw_data', 'mountpoint': 'raw_data',
+               'subdirectory': False, 'active': True}
+        self.assertEqual(obs, exp)
+
     def test_filepath_id_to_rel_path(self):
         obs = qdb.util.filepath_id_to_rel_path(1)
         exp = 'raw_data/1_s_G1_L001_sequences.fastq.gz'

qiita_db/util.py

@@ -649,6 +649,33 @@ def str_to_id(x):
             chain.from_iterable(qdb.sql_connection.TRN.execute()[idx:])))
 
 
+def _path_builder(db_dir, filepath, mountpoint, subdirectory, obj_id):
+    """Builds the path of a DB stored file
+
+    Parameters
+    ----------
+    db_dir : str
+        The DB base dir
+    filepath : str
+        The path stored in the DB
+    mountpoint : str
+        The mountpoint of the given file
+    subdirectory : bool
+        Whether the file is stored in a subdirectory in the mountpoint or not
+    obj_id : int
+        The id of the object to which the file is attached
+
+    Returns
+    -------
+    str
+        The full path of the given file
+    """
+    if subdirectory:
+        return join(db_dir, mountpoint, str(obj_id), filepath)
+    else:
+        return join(db_dir, mountpoint, filepath)
+
+
 def retrieve_filepaths(obj_fp_table, obj_id_column, obj_id, sort=None,
                        fp_type=None):
     """Retrieves the filepaths for the given object id
@@ -674,12 +701,6 @@ def retrieve_filepaths(obj_fp_table, obj_id_column, obj_id, sort=None,
         object id
     """
 
-    def path_builder(db_dir, filepath, mountpoint, subdirectory, obj_id):
-        if subdirectory:
-            return join(db_dir, mountpoint, str(obj_id), filepath)
-        else:
-            return join(db_dir, mountpoint, filepath)
-
     sql_sort = ""
     if sort == 'ascending':
         sql_sort = " ORDER BY filepath_id"
@@ -710,7 +731,7 @@ def path_builder(db_dir, filepath, mountpoint, subdirectory, obj_id):
         results = qdb.sql_connection.TRN.execute_fetchindex()
         db_dir = get_db_files_base_dir()
 
-        return [(fpid, path_builder(db_dir, fp, m, s, obj_id), fp_type_)
+        return [(fpid, _path_builder(db_dir, fp, m, s, obj_id), fp_type_)
                 for fpid, fp, fp_type_, m, s in results]
 
 
@@ -845,6 +866,38 @@ def move_filepaths_to_upload_folder(study_id, filepaths):
         qdb.sql_connection.TRN.execute()
 
 
+def get_filepath_information(filepath_id):
+    """Gets the filepath information of filepath_id
+
+    Parameters
+    ----------
+    filepath_id : int
+        The filepath id
+
+    Returns
+    -------
+    dict
+        The filepath information
+    """
+    with qdb.sql_connection.TRN:
+        sql = """SELECT filepath_id, filepath, filepath_type, checksum,
+                        data_type, mountpoint, subdirectory, active,
+                        artifact_id
+                 FROM qiita.filepath
+                    JOIN qiita.filepath_type USING (filepath_type_id)
+                    JOIN qiita.data_directory USING (data_directory_id)
+                    LEFT JOIN qiita.artifact_filepath USING (filepath_id)
+                 WHERE filepath_id = %s"""
+        qdb.sql_connection.TRN.add(sql, [filepath_id])
+        res = dict(qdb.sql_connection.TRN.execute_fetchindex()[0])
+
+        obj_id = res.pop('artifact_id')
+        res['fullpath'] = _path_builder(get_db_files_base_dir(),
+                                        res['filepath'], res['mountpoint'],
+                                        res['subdirectory'], obj_id)
+        return res
+
+
 def filepath_id_to_rel_path(filepath_id):
     """Gets the relative to the base directory of filepath_id