Standardized and cleaned up test folder. All files no loaded from base...

Standardized and cleaned up test folder.  All files no loaded from base locations.  Each test class has a __name__ == __main__ to run just the individual test case.

chipathlon/test/database_tests.py

@@ -4,23 +4,24 @@ import yaml
 import os
 import sys
 
-# auth.yaml
-# ========
-# host: database url
-# username: database username
-# password: database password
-auth_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "auth.yaml")
-if not os.path.isfile(auth_file):
-    print "Please create a file at [%s] containing host, username, and password." % (auth_file,)
-    sys.exit(1)
-
-with open(auth_file, "r") as rh:
-    auth = yaml.load(rh)
 
 class DatabaseTestCase(unittest.TestCase):
 
     @classmethod
     def setUpClass(self):
+        # auth.yaml
+        # ========
+        # host: database url
+        # username: database username
+        # password: database password
+        auth_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "auth.yaml")
+        if not os.path.isfile(auth_file):
+            print "Please create a file at [%s] containing host, username, and password." % (auth_file,)
+            sys.exit(1)
+
+        with open(auth_file, "r") as rh:
+            auth = yaml.load(rh)
+
         print "Setting up database connection..."
         self.mdb = chipathlon.db.MongoDB(auth["host"], auth["username"], auth["password"])
         return

chipathlon/test/existance_tests.py

 import unittest
 from database_tests import DatabaseTestCase
 
+
+# NOTE: These tests can be fragile!  Everytime encode updates their
+# database they often switch around accession numbers.  If you perform
+# a database update you may need to adjust the accession numbers in this
+# file
 class SampleExistanceTests(DatabaseTestCase):
 
     def test_sample_exists(self):
-        print "Testing accession: ENCFF000RCB, file_type: fastq"
-        valid, msg, data = self.mdb.get_sample("ENCFF000RCB", "fastq")
-        self.assertTrue(valid)
+        print "Testing accession: ENCFF001HZS, file_type: fastq"
+        valid, msg, data = self.mdb.get_sample("ENCFF001HZS", "fastq")
+        self.assertTrue(valid, msg=msg)
 
     def test_sample_without_file_type(self):
-        print "Testing accession: ENCFF000RCB, file_type: bam"
-        valid, msg, data = self.mdb.get_sample("ENCFF000RCB", "bam")
-        self.assertFalse(valid)
+        print "Testing accession: ENCFF001HZS, file_type: bam"
+        valid, msg, data = self.mdb.get_sample("ENCFF001HZS", "bam")
+        self.assertFalse(valid, msg=msg)
 
     def test_sample_without_accession(self):
         print "Testing accession: ASDF, file_type: fastq"
         valid, msg, data = self.mdb.get_sample("ASDF", "fastq")
-        self.assertFalse(valid)
+        self.assertFalse(valid, msg=msg)
+
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run(
+        unittest.TestLoader().loadTestsFromTestCase(SampleExistanceTests)
+    )

chipathlon/test/genome_tests.py

 import unittest
+import os
 from chipathlon.genome import Genome
 
+
 class GenomeTests(unittest.TestCase):
 
+    def setUp(self):
+        self.base_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "genome")
+        return
+
     def test_valid_bwa_genome(self):
-        genome = Genome("grch38p6", "bwa", "test/genome/grch38p6.fna", "test/genome/grch38p6.chrom.sizes")
+        genome = Genome(
+            "grch38p6",
+            "bwa",
+            os.path.join(self.base_path, "grch38p6.fna"),
+            os.path.join(self.base_path, "grch38p6.chrom.sizes")
+        )
         self.assertTrue(genome.is_valid(), msg=genome.get_error_string())
 
     def test_valid_bowtie2_genome(self):
-        genome = Genome("grch38p6", "bowtie2", "test/genome/grch38p6.fna", "test/genome/grch38p6.chrom.sizes")
+        genome = Genome(
+            "grch38p6",
+            "bowtie2",
+            os.path.join(self.base_path, "grch38p6.fna"),
+            os.path.join(self.base_path, "grch38p6.chrom.sizes")
+        )
         self.assertTrue(genome.is_valid(), msg=genome.get_error_string())
 
     def test_invalid_bwa_genome(self):
-        genome = Genome("mm9", "bwa", "test/genome/mm9.fna", "test/genome/mm9.chrom.sizes")
+        genome = Genome(
+            "mm9",
+            "bwa",
+            os.path.join(self.base_path, "mm9.fna"),
+            os.path.join(self.base_path, "mm9.chrom.sizes")
+        )
         self.assertFalse(genome.is_valid(), msg=genome.get_error_string())
 
     def test_invalid_bowtie2_genome(self):
-        genome = Genome("mm9", "bowtie2", "test/genome/mm9.fna", "test/genome/mm9.chrom.sizes")
+        genome = Genome(
+            "mm9",
+            "bowtie2",
+            os.path.join(self.base_path, "mm9.fna"),
+            os.path.join(self.base_path, "mm9.chrom.sizes")
+        )
         self.assertFalse(genome.is_valid(), msg=genome.get_error_string())
 
     def test_missing_chrom_sizes(self):
-        genome = Genome("mm9", "bowtie2", "test/genome/mm9.fna", "not/a/file")
+        genome = Genome(
+            "mm9",
+            "bowtie2",
+            os.path.join(self.base_path, "mm9.fna"),
+            "not/a/file"
+        )
         self.assertFalse(genome.is_valid(), msg=genome.get_error_string())
 
     def test_missing_base_file(self):
-        genome = Genome("mm9", "bwa", "not/a/file", "test/genome/mm9.chrom.sizes")
+        genome = Genome(
+            "mm9",
+            "bwa",
+            "not/a/file",
+            os.path.join(self.base_path, "mm9.chrom.sizes")
+        )
         self.assertFalse(genome.is_valid(), msg=genome.get_error_string())
+
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run(
+        unittest.TestLoader().loadTestsFromTestCase(GenomeTests)
+    )

chipathlon/test/insert_tests.py

-import unittest
-from database_tests import DatabaseTestCase
-
-class InsertResultsTests(DatabaseTestCase):
-
-    def setUp(self):
-        print "setting up insert..."
-        super(self.__class__, self).setUp()
-        self.result_id = ""
-        return
-
-    def tearDown(self):
-        print "tearing down insert..."
-        if self.result_id:
-            self.mdb.delete_result(self.result_id)
-        super(self.__class__, self).tearDown()
-        return
-
-    def test_insert_bed(self):
-        print "Inserting sample bed file..."
-        valid, msg, result_id = self.mdb.save_bed(
-                                    "test/insert_tests/sample.bed",
-                                    [],
-                                    ["ENCFF000RCB"],
-                                    {"align_tool": "bowtie2", "read_end": "single"}
-                                )
-        if valid:
-            self.result_id = result_id
-        print msg
-        self.assertTrue(valid)
-        return
-
-    def test_insert_peak(self):
-        print "Inserting sample peak file..."
-        valid, msg, result_id = self.mdb.save_peak(
-                                    "test/insert_tests/sample.narrowPeak",
-                                    ["ENCFF000RCB"],
-                                    ["ENCFF000RCB"],
-                                    {"align_tool": "bwa", "read_end": "single", "peak_tool": "macs2"}
-                                )
-        if valid:
-            self.result_id = result_id
-        print msg
-        self.assertTrue(valid)
-        return

chipathlon/test/insert_tests/bed_test.yaml

-control_ids:
-- !!python/unicode 'ENCSR000BKT'
-experiment_ids: []
-other:
-- information
-result_type: bed

chipathlon/test/paired_end/config.yaml

-notify:
-  pegasus_home: "/usr/share/pegasus/"
-  email: "avi@kurtknecht.com"
-profile:
-  pegasus:
-    style: "glite"
-  condor:
-    grid_resource: "pbs"
-    universe: "vanilla"
-  env:
-    PATH: "/work/walia/common/pymodules/anaconda/bin"
-    PYTHONPATH: "/work/walia/common/pymodules/anaconda/lib/python2.7/site-packages/"

chipathlon/test/paired_end/param.yaml

-bwa_sai_to_sam:
-  arguments: null
-  walltime: 2000
-  memory: 2000
-bwa_align_single:
-  arguments:
-    "-q": 5
-    "-l": 32
-    "-k": 2
-    "-t": 1
-  walltime: 2000
-  memory: 2000
-bwa_align_paired:
-  arguments:
-    "-t": 1
-  walltime: 2000
-  memory: 2000
-bowtie2_align_single:
-  arguments: null
-  walltime: 2000
-  memory: 2000
-bowtie2_align_paired:
-  arguments: null
-  walltime: 2000
-  memory: 2000
-samtools_sam_to_bam:
-  arguments: null
-  walltime: 2000
-  memory: 2000
-bedtools_bam_to_bed:
-  arguments: null
-  walltime: 2000
-  memory: 2000
-macs2_callpeak:
-  arguments: null
-  walltime: 2000
-  memory: 8000
-picard_mark_duplicates:
-  arguments: null
-  walltime: 2000
-  memory: 2000
-picard_sort_sam:
-  arguments: null
-  walltime: 2000
-  memory: 2000
-r_spp_nodups:
-  arguments: null
-  walltime: 2000
-  memory: 2000
-samtools_remove_duplicates:
-  arguments: null
-  walltime: 2000
-  memory: 2000
-samtools_filter_bam:
-  arguments: null
-  walltime: 2000
-  memory: 2000

chipathlon/test/paired_end/run.yaml

-runs:
-  - experiment: "ENCSR922MYB"
-    align: bwa
-    peak: spp
-  - experiment: "ENCSR992MYB"
-    align: bowtie2
-    peak: spp
-genomes:
-  bwa:
-    hg19: "/path/to/genome/base"
-    mm9: "/path/to/genome/base"
-  bowtie2:
-    hg19: "/path/to/genome/base"
-    mm9: "/path/to/genome/base"

chipathlon/test/parser_tests.py

 import unittest
+import os
 from database_tests import DatabaseTestCase
 from chipathlon.run_parser import RunParser
 
+
 class RunParserTests(DatabaseTestCase):
 
+    def setUp(self):
+        self.base_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "run_parser")
+        return
+
     def test_valid_parse(self):
-        parser = RunParser("test/run_parser/run_valid.yaml", self.mdb)
+        parser = RunParser(os.path.join(self.base_path, "run_valid.yaml"), self.mdb)
         self.assertTrue(parser.is_valid(), parser.get_error_string())
 
     def test_missing_keys(self):
-        parser = RunParser("test/run_parser/run_missing_keys.yaml", self.mdb)
+        parser = RunParser(os.path.join(self.base_path, "run_missing_keys.yaml"), self.mdb)
         self.assertFalse(parser.is_valid(), msg=parser.get_error_string())
 
     def test_no_genome(self):
-        parser = RunParser("test/run_parser/run_no_genome.yaml", self.mdb)
+        parser = RunParser(os.path.join(self.base_path, "run_no_genome.yaml"), self.mdb)
         self.assertFalse(parser.is_valid(), msg=parser.get_error_string())
 
     def test_idr_invalid_signal(self):
-        parser = RunParser("test/run_parser/run_idr_invalid_signal.yaml", self.mdb)
+        parser = RunParser(os.path.join(self.base_path, "run_idr_invalid_signal.yaml"), self.mdb)
         self.assertFalse(parser.is_valid(), msg=parser.get_error_string())
 
     def test_idr_not_enough_signals(self):
-        parser = RunParser("test/run_parser/run_idr_not_enough_signals.yaml", self.mdb)
+        parser = RunParser(os.path.join(self.base_path, "run_idr_not_enough_signals.yaml"), self.mdb)
         self.assertFalse(parser.is_valid(), msg=parser.get_error_string())
 
     def test_peak_type_invalid(self):
-        parser = RunParser("test/run_parser/run_peak_type_invalid.yaml", self.mdb)
+        parser = RunParser(os.path.join(self.base_path, "run_peak_type_invalid.yaml"), self.mdb)
         self.assertFalse(parser.is_valid(), msg=parser.get_error_string())
+
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run(
+        unittest.TestLoader().loadTestsFromTestCase(RunParserTests)
+    )

chipathlon/test/workflow_job_tests.py

@@ -3,15 +3,16 @@ from chipathlon.workflow_job import WorkflowJob
 import yaml
 import os
 
+
 class WorkflowJobTests(unittest.TestCase):
 
     def setUp(self):
-        self.base_path = os.path.dirname(os.path.abspath(__file__))
+        self.base_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "workflow_job")
         return
 
     def test_invalid_base(self):
         job = WorkflowJob(
-            "%s/workflow_job/invalid_base.yaml" % (self.base_path,),
+            os.path.join(self.base_path, "invalid_base.yaml"),
             {},
             debug=True
         )
@@ -20,7 +21,7 @@ class WorkflowJobTests(unittest.TestCase):
 
     def test_no_file_type(self):
         job = WorkflowJob(
-            "%s/workflow_job/no_file_type.yaml" % (self.base_path,),
+            os.path.join(self.base_path, "no_file_type.yaml"),
             {},
             debug=True
         )
@@ -29,7 +30,7 @@ class WorkflowJobTests(unittest.TestCase):
 
     def test_missing_resources(self):
         job = WorkflowJob(
-            "%s/workflow_job/missing_resources.yaml" % (self.base_path,),
+            os.path.join(self.base_path, "missing_resources.yaml"),
             {},
             debug=True
         )
@@ -38,7 +39,7 @@ class WorkflowJobTests(unittest.TestCase):
 
     def test_bad_resources(self):
         job = WorkflowJob(
-            "%s/workflow_job/bad_resources.yaml" % (self.base_path,),
+            os.path.join(self.base_path, "bad_resources.yaml"),
             {},
             debug=True
         )
@@ -47,7 +48,7 @@ class WorkflowJobTests(unittest.TestCase):
 
     def test_bad_arguments(self):
         job = WorkflowJob(
-            "%s/workflow_job/bad_arguments.yaml" % (self.base_path,),
+            os.path.join(self.base_path, "bad_arguments.yaml"),
             {},
             debug=True
         )
@@ -56,7 +57,7 @@ class WorkflowJobTests(unittest.TestCase):
 
     def test_bad_references(self):
         job = WorkflowJob(
-            "%s/workflow_job/bad_references.yaml" % (self.base_path,),
+            os.path.join(self.base_path, "bad_references.yaml"),
             {},
             debug=True
         )
@@ -65,7 +66,7 @@ class WorkflowJobTests(unittest.TestCase):
 
     def test_valid_job(self):
         job = WorkflowJob(
-            "%s/workflow_job/download_from_encode.yaml" % (self.base_path,),
+            os.path.join(self.base_path, "download_from_encode.yaml"),
             {},
             debug=True
         )

chipathlon/test/yaml_job/params1.yaml

-bwa_sai_to_sam:
-  arguments: None
-  walltime: 2000
-  memory: 2000
-bwa_align_single:
-  arguments:
-    "-q": 5
-    "-l": 32
-    "-k": 2
-    "-t": 1
-  walltime: 2000
-  memory: 2000
-bwa_align_paired:
-  arguments:
-    "-t": 1
-  walltime: 2000
-  memory: 2000
-samtools_sam_to_bam:
-  arguments: None
-  walltime: 2000
-  memory: 2000

chipathlon/test/yaml_job/params2.yaml

-bwa_sai_to_sam:
-  arguments: None
-  walltime: 2000
-  memory: 2000
-bwa_align_single:
-  arguments:
-    "-q": 5
-    "-l": 32
-    "-k": 2
-    "-t": 1
-  walltime: 2000
-  memory: 2000
-bwa_align_paired:
-  arguments:
-    "-M": ""
-  walltime: 2000
-  memory: 2000
-samtools_sam_to_bam:
-  arguments: None
-  walltime: 2000
-  memory: 2000

chipathlon/test/yaml_job/params3.yaml

-INVALID YAML FILE

chipathlon/test/yaml_job/params4.yaml

-bwa_sai_to_sam:
-  arguments: None
-  walltime: 2000
-  memory: 2000
-bwa_align_single:
-  arguments:
-    "-q": 5
-    "-l": 32
-    "-k": 2
-    "-t": 1
-  walltime: 2000
-  memory: 2000
-bwa_align_paired:
-  arguments: None
-  walltime: 2000
-  memory: 2000
-  batman: nana
-samtools_sam_to_bam:
-  arguments: None
-  walltime: 2000
-  memory: 2000