enable proper handling of dcm2niix stdout and stderr when additional DICOM files come for a series

pymods/irods_utils/irods_utils.py

@@ -314,7 +314,8 @@ def streaming_transfer_file_to_object( args ):
         irods_obj_handle = target_obj.open('w', checksum=True)
     except Exception as ex:
         logging.error("Failed open irods object for transfer.  file: " + file_pathname + " to irods ipath: " + irods_ipath + " ex: " + str(ex) )
-        return -1, hasher256, hasher512, 0
+        raise
+        #return -1, hasher256, hasher512, 0
 
     try:
         with open( file_pathname, 'rb' ) as input_file:
@@ -337,7 +338,8 @@ def streaming_transfer_file_to_object( args ):
                      + " to irods_ipath: " + irods_ipath
                      + " ex: " + str(ex) )
         #return None
-        rc = -1
+        #rc = -1
+        raise
 
     irods_obj_handle.close()
 
@@ -365,9 +367,9 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
     # a network file system twice due to blowing cache.
     # So, we upload to temp, checkusmming along the way, and then check for a pre-existing irods object.
 
-    if irods_sesh == None:
-        logging.error( "irods_sesh == None" )
-        return None
+    #if irods_sesh == None:
+    #    logging.error( "irods_sesh == None" )
+    #    return None
 
     # Figure out if this path in the archive is occupied with pre-existing data.
     existing_obj = None
@@ -381,7 +383,7 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
         logging.debug( "OBJ_PATH_DOES_NOT_EXIST " + new_obj_ipath )
     except Exception as ex:
         logging.error("Failed using data_onject.get() (but not DataObjectDoesNotExist) ipath: " + new_obj_ipath + " ex: " + str(ex) + " type " + str(type(ex)) )
-        return None
+        raise
 
     try:
         upload_file_size = os.path.getsize( file_pathname )
@@ -390,9 +392,10 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
         raise
 
     if upload_file_size == 0 and existing_obj != None and replace_existing and skip_on_zero_len :
-        logging.warning( f"got zero len file with replace_existing -- removing current data object. ipath: {new_object_ipath}" )
+        logging.warning( f"got zero len file with replace_existing -- removing current data object. ipath: {new_obj_ipath}" )
         try:
             existing_obj.unlink(force=True)
+            return 0
         except Exception as ex:
             logging.warning( "Failed remove zero line file on replace_existing and skip_on_zero_len. ipath: {new_obj_ipath}  ex: {ex} " )
             raise
@@ -411,7 +414,7 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
                      + " file_pathname: " + file_pathname
                      + " tmp ipath: "     + new_obj_ipath_tmp
                      + " ex: " + str(axe) )
-        return None
+        raise
 
     run_args = [ file_pathname, irods_sesh, new_obj_ipath_tmp, block_size ]
 
@@ -425,11 +428,11 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
     hash_digest512 = run_results[ 2 ]
     transfer_size  = run_results[ 3 ]
 
-    if transfer_rc < 0:
+    if transfer_rc < 0:   # Maybe not needed ... take out the rc part of the return
         logging.error( "Falied transfer file to irods oobject."
                      + " file_pathname: " + file_pathname
                      + " tmp ipath: "     + new_obj_ipath_tmp )
-        return None
+        sys.exit( -1 )
 
     # Example here: https://github.com/irods/python-irodsclient/blob/main/irods/test/helpers.py#L251
     # ... in function: def compute_sha256_digest(file_path):
@@ -455,7 +458,7 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
     except Exception as ex:
         logging.error("Failed to create AVUS on iRODS object. ipath: " + new_obj_ipath + " ex: " + str(ex) )
         logging.error("metadata AVU dict >" + str( metadata_dict ) + "<" )
-        return None
+        raise
 
     mismatch = False
 
@@ -492,7 +495,7 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
                 logging.error( "Failed to move an existing object out of the way so can not upload current version."
                              + " path " + existing_obj.path
                              + " ex: " + str( ex ) )
-                return None
+                raise
             logging.warn( f"Moved mismatching existing object (reason: {mismatch_reason}) to ipath: {dup_ipath}" )
             # Fall through to move newly uploaded object into place.
         else:
@@ -503,10 +506,11 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
                 logging.error( "Failed to inlink newly created, but duplicate object."
                              + " new_obj_ipath_tmp: " + str( new_obj_ipath_tmp )
                              + " ex: " + str( ex ) )
+                raise
 
             logging.warn( "Existing object matched data and metadata at ipath (removed uploaded tmp object): "
                         + " ipath: " + new_obj_ipath )
-            return existing_obj
+            return transfer_size
 
     # Move the tmp object to the proper object ipath.
     try:
@@ -516,7 +520,7 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
                      + " new_obj_ipath_tmp: " + new_obj_ipath_tmp
                      + " new_obj_ipath: " + new_obj_ipath
                      + " ex: " + str( ex ) )
-        return None
+        raise
 
     logging.debug( "file " + file_pathname + " in place at ipath " + new_obj_ipath )
 
@@ -527,19 +531,22 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
             dup_obj.unlink(force=True)
         except Exception as ex:
             logging.warning( "Failed remove dup when remove_existing flag set. ipath: {dup_ipath}  ex: {ex} " )
+            raise
 
-    new_obj = None
-    try:
-        new_obj = irods_sesh.data_objects.get( new_obj_ipath )
-    except Exception as ex:
-        logging.error("Failed data_onject.open(). ipath: " + new_obj_ipath + " ex: " + str(ex) )
-        return None
-
-    logging.debug( "Returning new object handle for: "
-                 + " file_pathname: " + file_pathname
-                 + " new_obj.ipath: " + new_obj.path )
-
-    return new_obj
+    return transfer_size
+
+     #new_obj = None
+     #try:
+     #    new_obj = irods_sesh.data_objects.get( new_obj_ipath )
+     #except Exception as ex:
+     #    logging.error("Failed data_onject.open(). ipath: " + new_obj_ipath + " ex: " + str(ex) )
+     #
+     #
+     #logging.debug( "Returning new object handle for: "
+     #             + " file_pathname: " + file_pathname
+     #             + " new_obj.ipath: " + new_obj.path )
+     #
+     #return new_obj
 
 
 # Bring in the experiment validation code