[ARVADOS] created: ef49a174d282122b8131960a0cc9c3898c42b2e3

[Git user]

        at  ef49a174d282122b8131960a0cc9c3898c42b2e3 (commit)


commit ef49a174d282122b8131960a0cc9c3898c42b2e3
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Apr 6 11:58:38 2017 -0400

    11423: Fix bug checking existence of Directories which refer to root of keep
    collections.

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 70aa69f..3a3d160 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -80,7 +80,10 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
     def exists(self, fn):
         collection, rest = self.get_collection(fn)
         if collection:
-            return collection.exists(rest)
+            if rest:
+                return collection.exists(rest)
+            else:
+                return True
         else:
             return super(CollectionFsAccess, self).exists(fn)
 
diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 1f6aa57..7884614 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -17,7 +17,7 @@ class ArvPathMapper(PathMapper):
     """Convert container-local paths to and from Keep collection ids."""
 
     pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+$')
-    pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.+)?$')
+    pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.*)?$')
 
     def __init__(self, arvrunner, referenced_files, input_basedir,
                  collection_pattern, file_pattern, name=None, **kwargs):
@@ -33,7 +33,7 @@ class ArvPathMapper(PathMapper):
         if srcobj["class"] == "File":
             if "#" in src:
                 src = src[:src.index("#")]
-            if isinstance(src, basestring) and ArvPathMapper.pdh_path.match(src):
+            if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
                 self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "File")
             if src not in self._pathmap:
                 # Local FS ref, may need to be uploaded or may be on keep
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 1187962..4472713 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -8,3 +8,52 @@
     }
   tool: keep-dir-test-input.cwl
   doc: Test directory in keep
+
+- job: dir-job2.yml
+  output:
+    "outlist": {
+        "size": 20,
+        "location": "output.txt",
+        "class": "File",
+        "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
+    }
+  tool: keep-dir-test-input.cwl
+  doc: Test directory in keep
+
+- job: null
+  output:
+    "outlist": {
+        "size": 20,
+        "location": "output.txt",
+        "class": "File",
+        "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
+    }
+  tool: keep-dir-test-input2.cwl
+  doc: Test default directory in keep
+
+- job: null
+  output:
+    "outlist": {
+        "size": 20,
+        "location": "output.txt",
+        "class": "File",
+        "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
+    }
+  tool: keep-dir-test-input3.cwl
+  doc: Test default directory in keep
+
+- job: null
+  output:
+    "outlist": {
+        "size": 20,
+        "location": "output.txt",
+        "class": "File",
+        "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
+    }
+  tool: cat.cwl
+  doc: Test default directory in keep
+
+- job: octo.yml
+  output: {}
+  tool: cat.cwl
+  doc: Test hashes in filenames
diff --git a/sdk/cwl/tests/cat.cwl b/sdk/cwl/tests/cat.cwl
new file mode 100644
index 0000000..93af517
--- /dev/null
+++ b/sdk/cwl/tests/cat.cwl
@@ -0,0 +1,8 @@
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  - id: inp
+    type: File
+    inputBinding: {}
+outputs: []
+baseCommand: cat
diff --git a/sdk/cwl/tests/keep-dir-test-input2.cwl b/sdk/cwl/tests/keep-dir-test-input2.cwl
new file mode 100644
index 0000000..7a355ab
--- /dev/null
+++ b/sdk/cwl/tests/keep-dir-test-input2.cwl
@@ -0,0 +1,24 @@
+class: CommandLineTool
+cwlVersion: v1.0
+requirements:
+  - class: ShellCommandRequirement
+inputs:
+  indir:
+    type: Directory
+    inputBinding:
+      prefix: cd
+      position: -1
+    default:
+      class: Directory
+      location: keep:d7514270f356df848477718d58308cc4+94
+outputs:
+  outlist:
+    type: File
+    outputBinding:
+      glob: output.txt
+arguments: [
+  {shellQuote: false, valueFrom: "&&"},
+  "find", ".",
+  {shellQuote: false, valueFrom: "|"},
+  "sort"]
+stdout: output.txt
\ No newline at end of file
diff --git a/sdk/cwl/tests/keep-dir-test-input3.cwl b/sdk/cwl/tests/keep-dir-test-input3.cwl
new file mode 100644
index 0000000..f7321c8
--- /dev/null
+++ b/sdk/cwl/tests/keep-dir-test-input3.cwl
@@ -0,0 +1,24 @@
+class: CommandLineTool
+cwlVersion: v1.0
+requirements:
+  - class: ShellCommandRequirement
+inputs:
+  indir:
+    type: Directory
+    inputBinding:
+      prefix: cd
+      position: -1
+    default:
+      class: Directory
+      location: keep:d7514270f356df848477718d58308cc4+94/
+outputs:
+  outlist:
+    type: File
+    outputBinding:
+      glob: output.txt
+arguments: [
+  {shellQuote: false, valueFrom: "&&"},
+  "find", ".",
+  {shellQuote: false, valueFrom: "|"},
+  "sort"]
+stdout: output.txt
\ No newline at end of file
diff --git a/sdk/cwl/tests/octo.yml b/sdk/cwl/tests/octo.yml
new file mode 100644
index 0000000..f6530df
--- /dev/null
+++ b/sdk/cwl/tests/octo.yml
@@ -0,0 +1,3 @@
+inp:
+  class: File
+  location: "octothorpe/item %231.txt"
\ No newline at end of file
diff --git a/sdk/cwl/tests/octothorpe/item #1.txt b/sdk/cwl/tests/octothorpe/item #1.txt
new file mode 100644
index 0000000..e69de29

-----------------------------------------------------------------------


hooks/post-receive
--