11948: Fix unit tests for additional file checking and nameroot/nameext fields.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 5582d63cfc6362acd0477f7b5508346772d1d6d3..93e2819084601d784a973c33ca30bbbdb2d6db49 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -95,7 +95,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     def exists(self, fn):
         collection, rest = self.get_collection(fn)
-        if collection:
+        if collection is not None:
             if rest:
                 return collection.exists(rest)
             else:

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 19ce39375e62b99cd1bfee2e36e006604d2093c5..e76d6283f5cf925f965e0b98a33743569685982c 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -118,14 +118,9 @@ def upload_dependencies(arvrunner, name, document_loader,
             if "location" not in f and "path" in f:
                 f["location"] = f["path"]
                 del f["path"]
-            if not arvrunner.fs_access.exists(f["location"]):
+            if "location" in f and not arvrunner.fs_access.exists(f["location"]):
                 # Remove from sc
-                i = 0
-                while i < len(sc):
-                    if sc[i]["location"] == f["location"]:
-                        del sc[i]
-                    else:
-                        i += 1
+                sc[:] = [x for x in sc if x["location"] != f["location"]]
                 # Delete "default" from workflowobj
                 remove[0] = True
         visit_class(obj["default"], ("File", "Directory"), add_default)

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 15cdc1e7154ea093157c6e98517cf37fb6829478..3d6b91536a2f2732ad2e97d5c172bf41e2ee60e7 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -79,7 +79,12 @@ def stubs(func):
                 if uuid in (v["uuid"], v["portable_data_hash"]):
                     return CollectionExecute(v)
 
-        created_collections = {}
+        created_collections = {
+            "99999999999999999999999999999998+99": {
+                "uuid": "",
+                "portable_data_hash": "99999999999999999999999999999998+99",
+                "manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
+            }}
         stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
         stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
 
@@ -142,10 +147,22 @@ def stubs(func):
                     'runtime_constraints': {'docker_image': 'arvados/jobs:'+arvados_cwl.__version__, 'min_ram_mb_per_node': 1024},
                     'script_parameters': {
                         'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
-                        'x': {"value": {'basename': 'blorp.txt', 'class': 'File', 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'}},
+                        'x': {"value": {
+                            'basename': 'blorp.txt',
+                            'class': 'File',
+                            'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+                            "nameext": ".txt",
+                            "nameroot": "blorp"
+                        }},
                         'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
                               'listing': [
-                                  {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+                                  {
+                                      'basename': 'renamed.txt',
+                                      'class': 'File', 'location':
+                                      'keep:99999999999999999999999999999998+99/file1.txt',
+                                      "nameext": ".txt",
+                                      "nameroot": "renamed"
+                                  }
                               ]}},
                         'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
                         'arv:enable_reuse': True,
@@ -191,10 +208,24 @@ def stubs(func):
                 '/var/lib/cwl/cwl.input.json': {
                     'kind': 'json',
                     'content': {
-                        'y': {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'},
-                        'x': {'basename': u'blorp.txt', 'class': 'File', 'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt'},
+                        'y': {
+                            'basename': '99999999999999999999999999999998+99',
+                            'location': 'keep:99999999999999999999999999999998+99',
+                            'class': 'Directory'},
+                        'x': {
+                            'basename': u'blorp.txt',
+                            'class': 'File',
+                            'location': u'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
+                            "nameext": ".txt",
+                            "nameroot": "blorp"
+                        },
                         'z': {'basename': 'anonymous', 'class': 'Directory', 'listing': [
-                            {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
+                            {'basename': 'renamed.txt',
+                             'class': 'File',
+                             'location': 'keep:99999999999999999999999999999998+99/file1.txt',
+                             "nameext": ".txt",
+                             "nameroot": "renamed"
+                            }
                         ]}
                     },
                     'kind': 'json'

diff --git a/sdk/cwl/tests/wf/expect_packed.cwl b/sdk/cwl/tests/wf/expect_packed.cwl
index 561daf40ff186841dd28645373877aac89ba7d63..32a9255e90d442a475394036ea54dd55a797e6fa 100644 (file)
--- a/sdk/cwl/tests/wf/expect_packed.cwl
+++ b/sdk/cwl/tests/wf/expect_packed.cwl
@@ -24,7 +24,7 @@ $graph:
   - id: '#main/x'
     type: File
     default: {class: File, location: 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
-      basename: blorp.txt}
+      basename: blorp.txt, nameroot: blorp, nameext: .txt}
   - id: '#main/y'
     type: Directory
     default: {class: Directory, location: 'keep:99999999999999999999999999999998+99',
@@ -32,7 +32,8 @@ $graph:
   - id: '#main/z'
     type: Directory
     default: {class: Directory, basename: anonymous, listing: [{basename: renamed.txt,
-          class: File, location: 'keep:99999999999999999999999999999998+99/file1.txt'}]}
+          class: File, location: 'keep:99999999999999999999999999999998+99/file1.txt',
+          nameroot: renamed, nameext: .txt}]}
   outputs: []
   steps:
   - id: '#main/step1'