Merge pull request #94 from phac-nml/update_docs_0.6.0

Updated StarAMR README, Tutorial, and settings to include MLST

staramr/blast/JobHandler.py

@@ -48,6 +48,7 @@ def __init__(self, blast_database_objects_map: Dict[str, AbstractBlastDatabase],
             raise Exception("threads is None")
 
         self._threads = threads
+        self._mlst_version = None
 
         if output_directory is None:
             raise Exception("output_directory is None")
@@ -65,6 +66,7 @@ def __init__(self, blast_database_objects_map: Dict[str, AbstractBlastDatabase],
 
         self._thread_pool_executor = ThreadPoolExecutor(max_workers=self._threads)
         self._max_mlst_columns = 10
+
         self.reset()
 
     def reset(self):
@@ -185,14 +187,32 @@ def _get_blast_map(self, name: str) -> Dict:
 
     def _get_mlst_data(self) -> str:
 
-        return self._mlst_data;
+        return self._mlst_data
 
     def _get_future_blasts_from_map(self, name: str) -> Dict:
         if name not in self._future_blasts_map:
             self._future_blasts_map[name] = []
 
         return self._future_blasts_map[name]
 
+    def _get_mlst_version(self) -> str:
+      command = ['mlst', '--version']
+
+      try:
+          output = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
+
+          mlst_version = str(output.stdout, 'utf-8')
+
+          # Parses out the mlst when the string is given back ex `mlst 2.x.x` and removes new line
+          mlst_version = (mlst_version[5:]).rstrip()
+
+      except subprocess.CalledProcessError as e:
+          err_msg = str(e.stderr.strip())
+
+          raise Exception('Could not run mlst, error {}'.format(err_msg))
+
+      return mlst_version
+
     def is_pointfinder_configured(self) -> bool:
         """
         Whether or not PointFinder is being used.
@@ -232,6 +252,10 @@ def get_mlst_outputs(self) -> str:
 
         return self._get_mlst_data();
 
+    def get_mlst_version(self) -> str:
+
+      return self._get_mlst_version(self) # type: ignore
+
     def get_pointfinder_outputs(self) -> Dict:
         """
         Gets the PointFinder output files in the form of a dictionary which looks like:

staramr/subcommand/Database.py

@@ -8,6 +8,7 @@
 
 from staramr.SubCommand import SubCommand
 from staramr.Utils import get_string_with_spacing
+from staramr.blast.JobHandler import JobHandler
 from staramr.databases.AMRDatabasesManager import AMRDatabasesManager
 from staramr.databases.resistance.ARGDrugTable import ARGDrugTable
 from staramr.exceptions.CommandParseException import CommandParseException
@@ -294,8 +295,11 @@ def run(self, args):
 
             try:
                 database_info = database_repos.info()
+                database_info['mlst_version'] = JobHandler.get_mlst_version(JobHandler)
+
                 database_info.update(arg_drug_table.get_resistance_table_info())
                 sys.stdout.write(get_string_with_spacing(database_info))
+
             except DatabaseNotFoundException as e:
                 logger.error("No database found. Perhaps try restoring the default with 'staramr db restore-default'")
         else:

staramr/subcommand/Search.py

@@ -268,6 +268,8 @@ def _generate_results(self, database_repos, resfinder_database, pointfinder_data
             logger.info("Finished. Took %s minutes.", time_difference_minutes)
 
             settings = database_repos.info()
+
+            settings['mlst_version'] = JobHandler.get_mlst_version(JobHandler)
             settings['command_line'] = ' '.join(sys.argv)
             settings['version'] = self._version
             settings['start_time'] = start_time.strftime(self.TIME_FORMAT)