some minor fixes

Author: antgonza

qiita_db/support_files/patches/python_patches/54.py

@@ -96,9 +96,11 @@ def create_non_rarefied_biom_artifact(analysis, biom_data, rarefied_table):
             biom_table = load_table(biom_fp)
             samples = set(samples).intersection(biom_table.ids())
             biom_table.filter(samples, axis='sample', inplace=True)
-            new_table = new_table.merge(biom_table)
-            ids_map.update({sid: "%d.%s" % (a_id, sid)
-                            for sid in biom_table.ids()})
+            # we need to check if the table has samples left before merging
+            if biom_table.shape[0] != 0 and biom_table.shape[1] != 0:
+                new_table = new_table.merge(biom_table)
+                ids_map.update({sid: "%d.%s" % (a_id, sid)
+                                for sid in biom_table.ids()})
 
         # Check if we need to rename the sample ids in the biom table
         new_table_ids = set(new_table.ids())

qiita_db/test/test_util.py

@@ -446,16 +446,6 @@ def test_move_filepaths_to_upload_folder(self):
 
             self.files_to_remove.append(new_fp)
 
-    def test_get_filepath_id(self):
-        _, base = qdb.util.get_mountpoint("raw_data")[0]
-        fp = join(base, '1_s_G1_L001_sequences.fastq.gz')
-        obs = qdb.util.get_filepath_id("raw_data", fp)
-        self.assertEqual(obs, 1)
-
-    def test_get_filepath_id_error(self):
-        with self.assertRaises(qdb.exceptions.QiitaDBError):
-            qdb.util.get_filepath_id("raw_data", "Not_a_path")
-
     def test_get_mountpoint(self):
         exp = [(5, join(qdb.util.get_db_files_base_dir(), 'raw_data'))]
         obs = qdb.util.get_mountpoint("raw_data")

qiita_db/util.py

@@ -48,7 +48,7 @@
 from binascii import crc32
 from bcrypt import hashpw, gensalt
 from functools import partial
-from os.path import join, basename, isdir, relpath, exists
+from os.path import join, basename, isdir, exists
 from os import walk, remove, listdir, makedirs, rename
 from shutil import move, rmtree, copy as shutil_copy
 from json import dumps
@@ -841,44 +841,6 @@ def move_filepaths_to_upload_folder(study_id, filepaths):
         qdb.sql_connection.TRN.execute()
 
 
-def get_filepath_id(table, fp):
-    """Return the filepath_id of fp
-
-    Parameters
-    ----------
-    table : str
-        The table type so we can search on this one
-    fp : str
-        The full filepath
-
-    Returns
-    -------
-    int
-        The filepath id forthe given filepath
-
-    Raises
-    ------
-    QiitaDBError
-        If fp is not stored in the DB.
-    """
-    with qdb.sql_connection.TRN:
-        _, mp = get_mountpoint(table)[0]
-        base_fp = join(get_db_files_base_dir(), mp)
-
-        sql = "SELECT filepath_id FROM qiita.filepath WHERE filepath=%s"
-        qdb.sql_connection.TRN.add(sql, [relpath(fp, base_fp)])
-        fp_id = qdb.sql_connection.TRN.execute_fetchindex()
-
-        # check if the query has actually returned something
-        if not fp_id:
-            raise qdb.exceptions.QiitaDBError(
-                "Filepath not stored in the database")
-
-        # If there was a result it was a single row and and single value,
-        # hence access to [0][0]
-        return fp_id[0][0]
-
-
 def filepath_id_to_rel_path(filepath_id):
     """Gets the relative to the base directory of filepath_id
 

qiita_pet/handlers/analysis_handlers/listing_handlers.py

@@ -19,7 +19,7 @@
 from qiita_pet.handlers.util import download_link_or_path
 from qiita_pet.handlers.analysis_handlers import check_analysis_access
 from qiita_pet.util import is_localhost
-from qiita_db.util import get_filepath_id
+from qiita_db.util import retrieve_filepaths
 from qiita_db.analysis import Analysis
 from qiita_db.logger import LogEntry
 from qiita_db.reference import Reference
@@ -37,27 +37,21 @@ def get(self):
         analyses = user.shared_analyses | user.private_analyses
 
         is_local_request = is_localhost(self.request.headers['host'])
-        gfi = partial(get_filepath_id, 'analysis')
         dlop = partial(download_link_or_path, is_local_request)
         mappings = {}
         bioms = {}
         tgzs = {}
         for analysis in analyses:
             _id = analysis.id
-            # getting mapping file
-            mapping = analysis.mapping_file
-            if mapping is not None:
-                mappings[_id] = dlop(mapping, gfi(mapping), 'mapping file')
-            else:
-                mappings[_id] = ''
-
-            bioms[_id] = ''
-            # getting tgz file
-            tgz = analysis.tgz
-            if tgz is not None:
-                tgzs[_id] = dlop(tgz, gfi(tgz), 'tgz file')
-            else:
-                tgzs[_id] = ''
+            mappings[_id], bioms[_id], tgzs[_id] = '', '', ''
+            for fid, fp, fpt in retrieve_filepaths('analysis_filepath',
+                                                   'analysis_id', _id):
+                if fpt == 'plain_text':
+                    mappings[_id] = dlop(fp, fid, 'mapping file')
+                if fpt == 'biom':
+                    bioms[_id] = dlop(fp, fid, 'biom file')
+                if fpt == 'tgz':
+                    tgzs[_id] = dlop(fp, fid, 'tgz file')
 
         self.render("list_analyses.html", analyses=analyses, message=message,
                     level=level, is_local_request=is_local_request,