1.5.1

docs/src/changelog.rst

@@ -2,6 +2,12 @@
 Change log
 ==========
 
+1.5.1
+-----
+
+* (`#327 <https://github.com/Ecogenomics/GTDBTk/issues/327>`_) Disallow spaces in genome names/file paths due to downstream application issues.
+* (`#326 <https://github.com/Ecogenomics/GTDBTk/issues/326>`_) Disallow genome names that are blank.
+
 1.5.0
 -----
 

gtdbtk/__init__.py

@@ -29,4 +29,4 @@
 __status__ = 'Production'
 __title__ = 'GTDB-Tk'
 __url__ = 'https://github.com/Ecogenomics/GTDBTk'
-__version__ = '1.5.0'
+__version__ = '1.5.1'

gtdbtk/main.py

@@ -76,7 +76,7 @@ def _check_package_compatibility(self):
                                        f'intended for this release: {Config.MIN_REF_DATA_VERSION}',
                                        ['bright'], fg='yellow'))
 
-    def _verify_genome_id(self, genome_id):
+    def _verify_genome_id(self, genome_id: str) -> bool:
         """Ensure genome ID will be valid in Newick tree.
 
         Parameters
@@ -91,16 +91,27 @@ def _verify_genome_id(self, genome_id):
 
         Raises
         ------
-        GenomeNameInvalid
+        GTDBTkExit
             If the genome identifier contains illegal characters.
         """
-
-        invalid_chars = set('()[],;=')
+        if genome_id is None or not isinstance(genome_id, str):
+            raise GTDBTkExit(f'The genome name is not a valid string: {genome_id}')
+        if len(genome_id) == 0:
+            raise GTDBTkExit('Genome name cannot be blank, check for input files '
+                             'without a name, or empty columns in the batchfile.')
+        invalid_chars = frozenset('()[],;= ')
         if any((c in invalid_chars) for c in genome_id):
             self.logger.error(f'Invalid genome ID: {genome_id}')
             self.logger.error(f'The following characters are invalid: '
                               f'{" ".join(invalid_chars)}')
-            raise GenomeNameInvalid(f'Invalid genome ID: {genome_id}')
+            raise GTDBTkExit(f'Invalid genome ID: {genome_id}')
+        return True
+
+    @staticmethod
+    def _verify_file_path(file_path: str) -> bool:
+        if ' ' in file_path:
+            raise GTDBTkExit(f'The genome path contains a space, this is '
+                             f'unsupported by downstream applications: {file_path}')
         return True
 
     def _genomes_to_process(self, genome_dir, batchfile, extension):
@@ -136,6 +147,10 @@ def _genomes_to_process(self, genome_dir, batchfile, extension):
         for genome_key in genomic_files:
             self._verify_genome_id(genome_key)
 
+        # Check that there are no illegal characters in the file path
+        for file_path in genomic_files.values():
+            self._verify_file_path(file_path)
+
         # Check that the prefix is valid and the path exists
         invalid_paths = list()
         for genome_key, genome_path in genomic_files.items():
@@ -620,6 +635,10 @@ def parse_options(self, options):
             check_dependencies(['prodigal', 'hmmalign'])
             check_dependencies(['FastTree' + ('MP' if options.cpus > 1 else '')])
 
+            if options.skip_gtdb_refs and options.custom_taxonomy_file is None:
+                raise GTDBTkExit("When running de_novo_wf, The '--skip_gtdb_refs' flag requires"
+                                 "'--custom_taxonomy_file' to be included to the command line.")
+
             options.write_single_copy_genes = False
             self.identify(options)