[med-svn] [pbgenomicconsensus] 01/07: Adapt test suite for missing pbtestdata

[Afif Elghraoui]

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in repository pbgenomicconsensus.

commit 5d23226d65dba45bba1d800bf82a38ca4e94ae02
Author: Afif Elghraoui <afif at debian.org>
Date:   Sat Jan 21 15:36:15 2017 -0800

    Adapt test suite for missing pbtestdata
---
 debian/control                        |  2 +-
 debian/patches/missing-testdata.patch | 49 +++++++++++++++++++++++++++++++++++
 debian/patches/series                 |  1 +
 debian/tests/control                  |  2 --
 4 files changed, 51 insertions(+), 3 deletions(-)

diff --git a/debian/control b/debian/control
index 4b36a4d..7b5afde 100644
--- a/debian/control
+++ b/debian/control
@@ -17,7 +17,7 @@ Build-Depends:
 	python-h5py (>= 2.0.1),
 	python-numpy (>= 1.6.0),
 # Test-Depends:
-	pbtestdata,
+#	pbtestdata, (#832311)
 	python-nose,
 	python-cram,
 Standards-Version: 3.9.8
diff --git a/debian/patches/missing-testdata.patch b/debian/patches/missing-testdata.patch
new file mode 100644
index 0000000..f7dbf3e
--- /dev/null
+++ b/debian/patches/missing-testdata.patch
@@ -0,0 +1,49 @@
+Description: Disable test require missing package pbtestdata
+ pbtestdata is not yet available in Debian (due to now resolved issue
+ of missing explicit license terms), so we cannot run this test.
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2016-01-21
+--- pbgenomicconsensus.orig/tests/unit/test_tool_contract.py
++++ pbgenomicconsensus/tests/unit/test_tool_contract.py
+@@ -5,7 +5,11 @@
+ from pbcore.io import openDataSet, ContigSet
+ import pbcommand.testkit
+ 
+-import pbtestdata
++try:
++    import pbtestdata
++    have_pbtestdata = True
++except ImportError:
++    have_pbtestdata = False
+ 
+ DATA_DIR = os.path.join(os.path.dirname(os.path.dirname(__file__)), "data")
+ assert os.path.isdir(DATA_DIR)
+@@ -73,16 +77,17 @@
+     }
+ 
+ 
+-class TestSummarizeConsensus(pbcommand.testkit.PbTestApp):
+-    DRIVER_BASE = "summarizeConsensus"
+-    DRIVER_EMIT = DRIVER_BASE + " --emit-tool-contract "
+-    DRIVER_RESOLVE = DRIVER_BASE + " --resolved-tool-contract "
+-    REQUIRES_PBCORE = True
+-    INPUT_FILES = [
+-        pbtestdata.get_file("alignment-summary-gff"),
+-        pbtestdata.get_file("variants-gff")
+-    ]
+-    TASK_OPTIONS = {}
++#@unittest.skipIf(not have_pbtestdata, "pbtestdata is not installed")
++#class TestSummarizeConsensus(pbcommand.testkit.PbTestApp):
++#    DRIVER_BASE = "summarizeConsensus"
++#    DRIVER_EMIT = DRIVER_BASE + " --emit-tool-contract "
++#    DRIVER_RESOLVE = DRIVER_BASE + " --resolved-tool-contract "
++#    REQUIRES_PBCORE = True
++#    INPUT_FILES = [
++#        pbtestdata.get_file("alignment-summary-gff"),
++#        pbtestdata.get_file("variants-gff")
++#    ]
++#    TASK_OPTIONS = {}
+ 
+ 
+ if __name__ == "__main__":
diff --git a/debian/patches/series b/debian/patches/series
index 7db6f24..00448f4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 spelling.patch
 verbose-testing.patch
 no-poa-convenience-script.patch
+missing-testdata.patch
diff --git a/debian/tests/control b/debian/tests/control
index 3d92c7a..813cd3c 100644
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -4,7 +4,6 @@ Depends:
 	python-nose,
 	python-cram,
 	make,
-	pbtestdata,
 Restrictions: allow-stderr
 
 Test-Command: make extra-tests
@@ -12,4 +11,3 @@ Depends:
 	@,
 	python-cram,
 	make,
-	pbtestdata,

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