Add diamond database creation\nFix bug\nImprove logging

dbman/helper.py

@@ -45,7 +45,7 @@ def create_metadata(name,
 
 def save_metadata(metadata, path="./metadata.json"):
   with open(path, "w") as metadata_file:
-    logging.info("Writing metadata " + json.dumps(metadata))
+    logging.debug("Writing metadata to '%s'", os.path.abspath(path))
     json.dump(metadata, metadata_file)
 
 def load_metadata(path="./metadata.json"):

dbman/main.py

@@ -8,6 +8,7 @@ import pathlib
 import prettytable
 import shutil
 import pkg_resources
+import shutil
 import dbman.helper as h
 
 def main():
@@ -91,7 +92,7 @@ def prepare(args):
   if not transform_recipe:
     logging.warn("Recipe '%s - %s' does not exits", args.tool, args.tool)
     return
-  db_info = _getdb(_local_databases(args), args.database, args.tool)
+  db_info = _getdb(_local_databases(args), args.database, 'download')
   if not db_info or args.force_download:
     logging.info("Database '%s' not found. Downloading it.", args.database)
     db_info = run_in_tempdir(func = lambda: h.run_external_tool(download_recipe['script'], download_recipe['params'] if 'params' in download_recipe else None), 
@@ -136,10 +137,10 @@ def _rename_directory_after_metadata(path):
     oldpath = pathlib.Path(path)
     newpath = oldpath.parent.parent.joinpath(newname)
     if newpath.exists():
-      import shutil
       shutil.rmtree(str(newpath))
     logging.debug("Renaming '%s' to '%s'", oldpath, newpath)
     oldpath.rename(newpath)
+    metadata['location'] = str(newpath.absolute())
   return metadata
 
 def run_in_tempdir(func=None, success=None, fail=None):
@@ -163,10 +164,12 @@ def run_in_tempdir(func=None, success=None, fail=None):
 def _recipes(args):
    recipes = {
      'card': {'download': {'script': _pkgres('recipes/download_card.py')},
-              'blast': {'script': _pkgres('recipes/create_blast_dbs.py')}
+              'blast': {'script': _pkgres('recipes/create_blast_dbs.py')},
+              'diamond': {'script': _pkgres('recipes/create_diamond_dbs.py')},
               },
      'swissprot': {'download': {'script': _pkgres('recipes/download_uniprotkb.py'), 'params': ['--database', 'swissprot', '--type', 'fasta']},
                    'blast': {'script': _pkgres('recipes/create_blast_dbs.py')},
+                   'diamond': {'script': _pkgres('recipes/create_diamond_dbs.py')},
                   }
    }
    return recipes

dbman/recipes/create_diamond_dbs.py

+#!/usr/bin/env python
+import dbman.helper as h
+import subprocess
+import sys
+import os
+import json
+from pathlib import Path
+
+metadata = h.load_metadata('./.source_metadata.json')
+
+fasta_parts = [p for p in metadata['parts'] if 'fasta' in p['tags'] and 'protein' in p['tags']]
+new_parts = []
+for part in fasta_parts:
+  type = None
+
+  for file in part['files']:
+    name = Path(file).stem
+    command = 'diamond makedb --db {} --in {}'.format(name, file)
+    cp = subprocess.run(command, shell=True)
+    if (cp.returncode != 0):
+      sys.exit(cp)
+    files = [f.name for f in os.scandir('.') if f.name.startswith(name + '.') and not f.name.endswith('.fasta')]
+
+    tags = ['diamond_db']
+    tags.extend(part['tags'])
+    tags.remove('fasta')
+
+    new_parts.append({'files': files, 'tags': tags})
+    
+h.create_metadata(metadata['name'], 'diamond', metadata['description'], metadata['version'], other={'parts': new_parts})