Test changes to submission code.

[htsworkflow.git] / htsworkflow / submission / test / submission_test_common.py

diff --git a/htsworkflow/submission/test/submission_test_common.py b/htsworkflow/submission/test/submission_test_common.py
new file mode 100644 (file)
index 0000000..1770b87
--- /dev/null
+++ b/htsworkflow/submission/test/submission_test_common.py
@@ -0,0 +1,70 @@
+"""Code shared between test cases.
+"""
+import RDF
+import os
+import tempfile
+import htsworkflow.util.rdfhelp
+
+S1_NAME = '1000-sample'
+S2_NAME = '2000-sample'
+
+S1_FILES = [
+    os.path.join(S1_NAME, 'file1_l8_r1.fastq'),
+    os.path.join(S1_NAME, 'file1_l8_r2.fastq'),
+]
+
+S2_FILES = [
+    os.path.join(S2_NAME, 'file1.bam'),
+    os.path.join(S2_NAME, 'file1_l5.fastq'),
+]
+
+TURTLE_PREFIX = htsworkflow.util.rdfhelp.get_turtle_header()
+
+S1_TURTLE = TURTLE_PREFIX + """
+<http://localhost/library/1000/>
+  htswlib:cell_line "Cell1000" ;
+  htswlib:library_id "1000" ;
+  htswlib:library_type "Single" ;
+  htswlib:replicate "1" ;
+  htswlib:has_lane <http://localhost/lane/1> ;
+  a htswlib:IlluminaLibrary .
+
+<http://localhost/lane/1>
+  htswlib:flowcell <http://localhost/flowcel/1234ABXXX> ;
+  htswlib:lane_number "1"@en;
+  a htswlib:IlluminaLane .
+"""
+
+S2_TURTLE = TURTLE_PREFIX + """
+<http://localhost/library/2000/>
+  htswlib:cell_line "Cell2000" ;
+  htswlib:library_id "2000" ;
+  htswlib:library_type "Paired" ;
+  htswlib:replicate "2" ;
+  htswlib:has_lane <http://localhost/lane/2> ;
+  a htswlib:Library .
+
+<http://localhost/lane/2>
+  htswlib:flowcell <http://localhost/flowcel/1234ABXXX> ;
+  htswlib:lane_number "2"@en ;
+  a htswlib:IlluminaLane .
+"""
+
+class MockAddDetails(object):
+    def __init__(self, model, turtle=None):
+        self.model = model
+        if turtle:
+            self.add_turtle(turtle)
+
+    def add_turtle(self, turtle):
+        parser = RDF.Parser('turtle')
+        parser.parse_string_into_model(self.model, turtle, "http://localhost")
+
+    def __call__(self, libNode):
+        q = RDF.Statement(libNode, None, None)
+        found = False
+        for s in self.model.find_statements(q):
+            found = True
+            break
+        assert found
+