# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1390556311 -3600
# Node ID 53e1eee934300560fe567d186fd324cb085f678e
# Parent  777c1c2a17a269b59ebb7726ab622f0e4a87a75d
Last tested version

diff -r 777c1c2a17a2 -r 53e1eee93430 MsClust.jar
Binary file MsClust.jar has changed
diff -r 777c1c2a17a2 -r 53e1eee93430 rankfilter_GCMS/test/test_pdfread.py
--- a/rankfilter_GCMS/test/test_pdfread.py	Tue Jan 21 16:50:15 2014 +0100
+++ b/rankfilter_GCMS/test/test_pdfread.py	Fri Jan 24 10:38:31 2014 +0100
@@ -17,7 +17,7 @@
         '''
         Tests the reading and parsing of a NIST PDF file
         '''
-        [hitlist, hitlist_missed] = pdfread.getPDF(self.nist_pdf)
+        [hitlist, hitlist_missed] = pdfread.getPDF(self.nist_pdf, True)
         rows = [hitlist[row] for row in hitlist.keys()]
         data = [set(row) for row in zip(*rows)]
         expected_element = set(('12.3', ' Sucrose ', '14', 'undef', ' standards 2009', ' 660', 'not_def',
diff -r 777c1c2a17a2 -r 53e1eee93430 test/integration_tests.py
--- a/test/integration_tests.py	Tue Jan 21 16:50:15 2014 +0100
+++ b/test/integration_tests.py	Fri Jan 24 10:38:31 2014 +0100
@@ -119,7 +119,7 @@
 
         #Build up arguments and run
         input_txt = resource_filename(__name__, "data/integration/NIST_identification_results_tabular.txt")
-        library = resource_filename(__name__, "data/integration/Library_RI_DB_capillary_columns-noDuplicates.txt")
+        library = resource_filename(__name__, "../repositories/PRIMS-metabolomics/RI_DB_libraries/Library_RI_DB_capillary_columns-noDuplicates.txt")
         regress_model = resource_filename(__name__, "data/integration/regression_MODEL_for_columns.txt")
         sys.argv = ['test',
                     library,
diff -r 777c1c2a17a2 -r 53e1eee93430 test/test_library_lookup.py
--- a/test/test_library_lookup.py	Tue Jan 21 16:50:15 2014 +0100
+++ b/test/test_library_lookup.py	Fri Jan 24 10:38:31 2014 +0100
@@ -147,9 +147,9 @@
         '''
         Tests the match_library.py functionality
         '''
-        riqc_libs_dir = resource_filename(__name__, "../repositories")
+        riqc_libs_dir = resource_filename(__name__, "../repositories/PRIMS-metabolomics/RI_DB_libraries")
         get_library_files_output = match_library.get_directory_files(riqc_libs_dir)
-        self.assertEqual(4, len(get_library_files_output))
+        self.assertEqual(1, len(get_library_files_output))
         self.assertEqual("Library_RI_DB_capillary_columns-noDuplicates", get_library_files_output[0][0])
         #TODO change assert below to assert that the result is a file, so the test can run on other dirs as well:
         #self.assertEqual("E:\\workspace\\PRIMS-metabolomics\\python-tools\\tools\\GCMS\\test\\data\\riqc_libs\\RI DB library (capillary columns) Dec.2012.txt", get_library_files_output[0][1])