From cdfd69a42adf6ed017a443773eccfd8f021fea32 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Mon, 6 Jul 2015 22:31:35 -0400 Subject: [PATCH 1/1] 6264: Fix bin/cwl-runner to import correct module. --- sdk/cwl/arvados_cwl/{cwl_runner.py => __init__.py} | 4 ++-- sdk/cwl/bin/cwl-runner | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) rename sdk/cwl/arvados_cwl/{cwl_runner.py => __init__.py} (99%) diff --git a/sdk/cwl/arvados_cwl/cwl_runner.py b/sdk/cwl/arvados_cwl/__init__.py similarity index 99% rename from sdk/cwl/arvados_cwl/cwl_runner.py rename to sdk/cwl/arvados_cwl/__init__.py index 65f4940e1b..052ace930b 100644 --- a/sdk/cwl/arvados_cwl/cwl_runner.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -99,7 +99,7 @@ class ArvadosJob(object): vwd = arvados.collection.Collection() for t in self.generatefiles: if isinstance(self.generatefiles[t], dict): - src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"][7:-1]) + src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"][6:]) vwd.copy(rest, t, source_collection=src) else: with vwd.open(t, "w") as f: @@ -165,7 +165,7 @@ class ArvPathMapper(cwltool.pathmapper.PathMapper): for src in referenced_files: if isinstance(src, basestring) and pdh_path.match(src): - self._pathmap[src] = (src, "$(file %s)" % src) + self._pathmap[src] = (src, "/keep/%s" % src) else: ab = src if os.path.isabs(src) else os.path.join(basedir, src) st = arvados.commands.run.statfile("", ab) diff --git a/sdk/cwl/bin/cwl-runner b/sdk/cwl/bin/cwl-runner index 7008ae4990..f31aefdf2e 100755 --- a/sdk/cwl/bin/cwl-runner +++ b/sdk/cwl/bin/cwl-runner @@ -2,6 +2,6 @@ import sys -from arvados.commands.cwl_runner import main +from arvados_cwl import main sys.exit(main(sys.argv[1:], sys.stdout, sys.stderr)) -- 2.30.2