added --no-graph, added graphviz to pip req

croo/croo.py

@@ -31,7 +31,8 @@ class Croo(object):
     def __init__(self, metadata_json, out_def_json, out_dir,
                  soft_link=True,
                  ucsc_genome_db=None,
-                 ucsc_genome_pos=None):
+                 ucsc_genome_pos=None,
+                 no_graph=False):
         """Initialize croo with output definition JSON
         """
         if isinstance(metadata_json, dict):
@@ -52,6 +53,7 @@ def __init__(self, metadata_json, out_def_json, out_dir,
         self._cm = CromwellMetadata(self._metadata)
         self._ucsc_genome_db = ucsc_genome_db
         self._ucsc_genome_pos = ucsc_genome_pos
+        self._no_graph = no_graph
 
         if isinstance(out_def_json, dict):
             self._out_def_json = out_def_json
@@ -103,7 +105,7 @@ def organize_output(self):
                     full_path = node.output_path
                     shard_idx = node.shard_idx
 
-                    if node_format is not None:
+                    if node_format is not None and not self._no_graph:
                         interpreted_node_format = Croo.__interpret_inline_exp(
                             node_format, full_path, shard_idx)
                         if subgraph is not None:
@@ -170,7 +172,7 @@ def organize_output(self):
                                 ucsc_track, full_path, shard_idx)
                             report.add_to_ucsc_track(target_url,
                                                      interpreted_ucsc_track)
-                        if node_format is not None:
+                        if node_format is not None and not self._no_graph:
                             interpreted_node_format = Croo.__interpret_inline_exp(
                                 node_format, full_path, shard_idx)
                             if subgraph is not None:
@@ -296,7 +298,8 @@ def main():
         out_dir=args['out_dir'],
         ucsc_genome_db=args['ucsc_genome_db'],
         ucsc_genome_pos=args['ucsc_genome_pos'],
-        soft_link=args['method'] == 'link')
+        soft_link=args['method'] == 'link',
+        no_graph=args['no_graph'])
 
     co.organize_output()
 

croo/croo_args.py

@@ -13,7 +13,7 @@
     MAX_DURATION_SEC_PRESIGNED_URL_GCS)
 
 
-__version__ = '0.3.1'
+__version__ = '0.3.2'
 
 def parse_croo_arguments():
     """Argument parser for Cromwell Output Organizer (COO)
@@ -36,6 +36,9 @@ def parse_croo_arguments():
         'Original output files will be kept in Cromwell\'s output '
         'directory. '
         '"copy" makes copies of Cromwell\'s original outputs')
+    p.add_argument(
+        '--no-graph', action='store_true',
+        help='No task graph.')
     p.add_argument(
         '--ucsc-genome-db',
         help='UCSC genome browser\'s "db=" parameter. '

croo/croo_html_report_task_graph.py

@@ -8,7 +8,6 @@
 import os
 from copy import deepcopy
 from base64 import b64encode
-from graphviz import (Source, render)
 from caper.caper_uri import CaperURI, URI_LOCAL, URI_URL
 
 
@@ -60,6 +59,10 @@ def __make_svg(self):
         Returns:
             An SVG string, but also saves to CrooHtmlReportTaskGraph.TASK_GRAPH_SVG
         """
+        if not self._items:
+            return None
+        from graphviz import Source
+
         # define call back functions for node format, href, subgraph
         def fnc_node_format(n):
             if (n.type, n.output_name, n.task_name, n.shard_idx) in self._items:
@@ -78,7 +81,6 @@ def fnc_subgraph(n):
                 return self._items[(n.type, n.output_name, n.task_name, n.shard_idx)][2]
             else:
                 return None
-
         # convert to dot string
         dot_str = self._dag.to_dot(
             fnc_node_format=fnc_node_format,

setup.py

@@ -21,5 +21,5 @@
         'License :: OSI Approved :: MIT License',
         'Operating System :: POSIX :: Linux',
     ],
-    install_requires=['caper>=0.6.1']
+    install_requires=['caper>=0.6.1', 'graphviz']
 )