[ARVADOS] created: 1.1.4-751-g9a752eae7

[Git user]

        at  9a752eae723dfe23d5b98db8ba7ca600ab9f9573 (commit)


commit 9a752eae723dfe23d5b98db8ba7ca600ab9f9573
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Mon Aug 6 14:14:04 2018 -0400

    13931: Support for getting file sizes of files in Keep
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 15689a901..9a893df78 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -139,6 +139,17 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
         else:
             return super(CollectionFsAccess, self).exists(fn)
 
+    def size(self, fn):  # type: (unicode) -> bool
+        collection, rest = self.get_collection(fn)
+        if collection is not None:
+            if rest:
+                arvfile = collection.find(rest)
+                if isinstance(arvfile, arvados.arvfile.ArvadosFile):
+                    return arvfile.size()
+            raise IOError(errno.EINVAL, "Not a path to a file %s" % (fn))
+        else:
+            return super(CollectionFsAccess, self).size(fn)
+
     def isfile(self, fn):  # type: (unicode) -> bool
         collection, rest = self.get_collection(fn)
         if collection is not None:

commit d49a9ee4cd176e35f1929c1bb60caa751b53903d
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Mon Aug 6 14:13:16 2018 -0400

    13931: Add test that file sizes are available.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/tests/13931-size-job.yml b/sdk/cwl/tests/13931-size-job.yml
new file mode 100644
index 000000000..97b46dd36
--- /dev/null
+++ b/sdk/cwl/tests/13931-size-job.yml
@@ -0,0 +1,3 @@
+fastq1:
+  class: File
+  location: keep:20850f01122e860fb878758ac1320877+71/sample1_S01_R1_001.fastq.gz
\ No newline at end of file
diff --git a/sdk/cwl/tests/13931-size.cwl b/sdk/cwl/tests/13931-size.cwl
new file mode 100644
index 000000000..aed1bd635
--- /dev/null
+++ b/sdk/cwl/tests/13931-size.cwl
@@ -0,0 +1,10 @@
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  fastq1: File
+outputs:
+  out: stdout
+baseCommand: echo
+arguments:
+  - $(inputs.fastq1.size)
+stdout: size.txt
\ No newline at end of file
diff --git a/sdk/cwl/tests/arvados-tests.sh b/sdk/cwl/tests/arvados-tests.sh
index 4869e3e52..8635aae65 100755
--- a/sdk/cwl/tests/arvados-tests.sh
+++ b/sdk/cwl/tests/arvados-tests.sh
@@ -12,4 +12,8 @@ fi
 if ! arv-get 4d8a70b1e63b2aad6984e40e338e2373+69 > /dev/null ; then
     arv-put --portable-data-hash secondaryFiles/hello.txt*
 fi
+if ! arv-get 20850f01122e860fb878758ac1320877+71 > /dev/null ; then
+    arv-put --portable-data-hash samples/sample1_S01_R1_001.fastq.gz
+fi
+
 exec cwltest --test arvados-tests.yml --tool arvados-cwl-runner $@ -- --disable-reuse --compute-checksum

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