Add option to copy source files for a submission.

[htsworkflow.git] / htsworkflow / submission / results.py

diff --git a/htsworkflow/submission/results.py b/htsworkflow/submission/results.py
index daeb7d1fed1d65b867b57b5b9a1e3dbaf60c3013..50077523aca3970a517973adbd69f119f4f17e3d 100644 (file)
--- a/htsworkflow/submission/results.py
+++ b/htsworkflow/submission/results.py
@@ -1,5 +1,6 @@
 """Help collect and process results for submission
 """
+from collections import MutableMapping
 import os
 import logging
 
@@ -7,25 +8,34 @@ from collections import namedtuple
 
 LOGGER = logging.getLogger(__name__)
 
-class ResultMap(object):
+class ResultMap(MutableMapping):
     """Store list of results
     """
     def __init__(self):
         self.results_order = []
         self.results = {}
 
-    def keys(self):
-        return self.results_order
+    def __iter__(self):
+        for item in self.results_order:
+            yield item
 
-    def values(self):
-        return ( self.results[r] for r in self.results_order )
+    def __len__(self):
+        l = len(self.results)
+        assert l == len(self.results_order)
+        return l
 
-    def items(self):
-        return ( (r, self.results[r]) for r in self.results_order )
+    def __setitem__(self, key, value):
+        self.results_order.append(key)
+        self.results[key] = value
 
     def __getitem__(self, key):
         return self.results[key]
 
+    def __delitem__(self, key):
+        del self.results[key]
+        i = self.results_order.index(key)
+        del self.results_order[i]
+
     def add_results_from_file(self, filename):
         pathname = os.path.abspath(filename)
         basepath, name = os.path.split(pathname)
@@ -33,21 +43,23 @@ class ResultMap(object):
         for lib_id, lib_path in results:
             if not os.path.isabs(lib_path):
                 lib_path = os.path.join(basepath, lib_path)
-            self.add_result(lib_id, lib_path)
-
-    def add_result(self, lib_id, lib_path):
-        self.results_order.append(lib_id)
-        self.results[lib_id] = lib_path
+            self[lib_id] = lib_path
 
-    def make_tree_from(self, source_path, destpath = None):
+    def make_tree_from(self, source_path, destpath = None, link=True):
         """Create a tree using data files from source path.
         """
-        print source_path, destpath
         if destpath is None:
             destpath = os.getcwd()
 
+        LOGGER.debug("Source_path: %s", source_path)
+        LOGGER.debug("Dest_path: %s", destpath)
         for lib_id in self.results_order:
             lib_path = self.results[lib_id]
+            LOGGER.debug("lib_path: %s", lib_path)
+            if os.path.isabs(lib_path):
+                lib_path = os.path.relpath(lib_path, destpath)
+
+            LOGGER.debug('lib_path: %s', lib_path)
             lib_destination = os.path.join(destpath, lib_path)
             if not os.path.exists(lib_destination):
                 LOGGER.info("Making dir {0}".format(lib_destination))
@@ -55,17 +67,19 @@ class ResultMap(object):
 
             source_rel_dir = os.path.join(source_path, lib_path)
             source_lib_dir = os.path.abspath(source_rel_dir)
+            LOGGER.debug("source_lib_dir: %s", source_lib_dir)
 
-            print "source_lib_dir", source_lib_dir
             for filename in os.listdir(source_lib_dir):
                 source_pathname = os.path.join(source_lib_dir, filename)
                 target_pathname = os.path.join(lib_destination, filename)
                 if not os.path.exists(source_pathname):
                     raise IOError(
                         "{0} does not exist".format(source_pathname))
-                print target_pathname
                 if not os.path.exists(target_pathname):
-                    os.symlink(source_pathname, target_pathname)
+                    if link:
+                        os.symlink(source_pathname, target_pathname)
+                    else:
+                        os.copy(source_pathname, target_pathname)
                     LOGGER.info(
                         'LINK {0} to {1}'.format(source_pathname,
                                                  target_pathname))