style cleanup

Author: Will Trimble

tests/test_api.py

@@ -19,7 +19,7 @@ def test_500():
         assert False
     except SystemExit:
         pass
- 
+
 def test_private():
     URI = API_URL + '/matrix/organism?id=mgm4454266.3'  # mgm4454266.3 is private
     try:
@@ -37,14 +37,14 @@ def test_badkey():
         pass
 
 def test_heartbeat():
-    URI0 = API_URL + "heartbeat"   
+    URI0 = API_URL + "heartbeat"
     obj = obj_from_url(URI0)
-    SERVICES = [ obj["requests"][1]["parameters"]["required"]["service"][1][i][0] for i in range(len( obj["requests"][1]["parameters"]["required"]["service"][1]))] 
+    SERVICES = [obj["requests"][1]["parameters"]["required"]["service"][1][i][0] for i in range(len(obj["requests"][1]["parameters"]["required"]["service"][1]))]
     for service in SERVICES:
         URI = API_URL + "heartbeat/" + service
         obj_detail = obj_from_url(URI)
         assert obj_detail["status"] == 1, "Failed heartbeat on " + service
-    return 1 
+    return 1
 
 def test_async_matrix3():
     URI = API_URL + '1/matrix/organism?id=mgm4653781.3&id=mgm4653783.3&id=mgm4653789.3&id=mgm4662211.3&id=mgm4662212.3&id=mgm4662235.3&id=mgm4662210.3&group_level=phylum&source=RDP&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&asynchronous=1'  # takes too long??
@@ -59,34 +59,44 @@ def test_matrix_01():
     obj = obj_from_url(URI)
     o = open("1.txt", "w")
     o.write(str(obj))
+    os.remove("1.txt")
 def test_matrix_02():
     URI = API_URL + '/matrix/organism?id=mgm4440282.3&group_level=phylum&source=RDP&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0'
     obj = obj_from_url(URI)
     o = open("2.txt", "w")
     o.write(str(obj))
+    os.remove("2.txt")
+
 def test_matrix_03():
     URI = API_URL + '/matrix/organism?id=mgm4440283.3&group_level=phylum&source=RDP&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0'
     obj = obj_from_url(URI)
     o = open("3.txt", "w")
     o.write(str(obj))
+    os.remove("3.txt")
+
 def test_matrix_04():
     URI = API_URL + '/matrix/organism?id=mgm4440284.3&group_level=phylum&source=RDP&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0'
     obj = obj_from_url(URI)
     o = open("4.txt", "w")
     o.write(str(obj))
-    
+
 def test_large_01():
     URI = API_URL + '/matrix/organism?group_level=phylum&source=RDP&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4510219.3'
     obj = obj_from_url(URI)
     o = open("5.txt", "w")
     o.write(str(obj))
+    os.remove("5.txt")
+
 def test_large_02():
     URI = API_URL + '/matrix/organism?group_level=phylum&source=RefSeq&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4510219.3'
     obj = obj_from_url(URI)
     o = open("6.txt", "w")
     o.write(str(obj))
+    os.remove("6.txt")
+
 def test_large_03():
     URI = API_URL + '/matrix/organism?group_level=phylum&source=SEED&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4510219.3'
     obj = obj_from_url(URI)
     o = open("7.txt", "w")
     o.write(str(obj))
+    os.remove("7.txt")

tests/test_mgrtools.py

@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 from __future__ import print_function
 
-import pytest
-
+import sys
+import os
+from os.path import dirname, abspath
 from subprocess import Popen, PIPE
 import subprocess
-import sys, os 
-from os.path import dirname, abspath
+import pytest
 
 DATADIR = dirname(abspath(__file__)) + "/data/"
 
@@ -21,10 +21,10 @@ def runme(command, workingdir=".", fail_ok=False):
 #    oldout, olderr = sys.stdout, sys.stderr
 #    sys.stdout = StringIO()
 #    sys.stderr = StringIO()
-    os.chdir(workingdir)  
+    os.chdir(workingdir)
 
-    try: 
-        p=subprocess.Popen(command, stdout=PIPE, stderr=PIPE, shell=True)
+    try:
+        p = subprocess.Popen(command, stdout=PIPE, stderr=PIPE, shell=True)
     except SystemExit as err:
         p = err.code
     out, err = p.communicate()
@@ -37,7 +37,7 @@ def runme(command, workingdir=".", fail_ok=False):
 
 # Now undo all the renamed streams
 #    sys.stdout, sys.stderr = oldout, olderr
-    os.chdir(cwd)  
+    os.chdir(cwd)
     return status, out, err
 
 
@@ -52,7 +52,8 @@ def test_mginbox_help():
 #   stat, out, err = runme('mg-upload2shock.py -h')
 #   assert b'DESCRIPTION' in out
 
-binscripts = ['mg-abundant-functions.py',
+binscripts = [
+'mg-abundant-functions.py',
 'mg-abundant-taxa.py',
 'mg-biom-merge.py',
 'mg-biom-view.py',
@@ -87,33 +88,33 @@ def test_mginbox_help():
 @pytest.mark.known_failing
 def test_binscripts_help():
     for binscript in binscripts:
-          print("Invoking " + binscript+" -h") 
-          stat, out, err = runme(binscript + " -h") 
-          assert b'DESCRIPTION' in out
+        print("Invoking " + binscript+" -h")
+        stat, out, err = runme(binscript + " -h")
+        assert b'DESCRIPTION' in out
 
 def test_jsonviewer():
     s = '''echo '{"a": {"b": {"c": [1, 2, 3, 4, 5]}}, "x": ["y", "z"], "foo": "bar"}' | jsonviewer.py'''
-    stat, out, err = runme(s) 
+    stat, out, err = runme(s)
     s2 = '''echo '{"a": {"b": {"c": [1, 2, 3, 4, 5]}}, "x": ["y", "z"], "foo": "bar"}' | jsonviewer.py --value 'a.b.c' --json'''
-    stat, out, err = runme(s2) 
+    stat, out, err = runme(s2)
 
 def test_mg_abundant_functions():
     s = '''mg-abundant-functions.py --id mgm4662210.3 --level level3 --source Subsystems --top 20 --evalue 8'''
-    stat, out, err = runme(s) 
+    stat, out, err = runme(s)
 
 def test_mg_abundant_taxa():
     s = '''mg-abundant-taxa.py --id mgm4662210.3 --level genus --source RefSeq --top 20 --evalue 8'''
-    stat, out, err = runme(s) 
+    stat, out, err = runme(s)
 
 @pytest.mark.huge
 def test_mg_compare_taxa():
     s = '''mg-compare-taxa.py --ids mgm4441679.3,mgm4441680.3,mgm4441681.3,mgm4441682.3 --level class --source RefSeq --format text | mg-changing-annotation.py --input - --format text --groups '{"group1":["mgm4441679.3","mgm4441680.3"],"group2":["mgm4441681.3","mgm4441682.3"]}' --top 5 --stat_test Kruskal-Wallis'''
-    stat, out, err = runme(s) 
+    stat, out, err = runme(s)
 
 @pytest.mark.huge
 def test_mg_compare_alpha_diversity():
-    s= '''mg-compare-alpha-diversity.py --ids mgm4441679.3,mgm4441680.3,mgm4441681.3,mgm4441682.3 --level class --source RefSeq'''
-    stat, out, err = runme(s) 
+    s = '''mg-compare-alpha-diversity.py --ids mgm4441679.3,mgm4441680.3,mgm4441681.3,mgm4441682.3 --level class --source RefSeq'''
+    stat, out, err = runme(s)
 
 def test_annotation():
     stat, out, err = runme('annotation_table.py')
@@ -124,97 +125,96 @@ def test_abundance():
     assert b'Archaea' in out
 
 def test_mg_compare_functions():
-    s='''mg-compare-functions.py --ids mgm4441679.3,mgm4441680.3,mgm4441681.3,mgm4441682.3 --level level2 --source KO --format text --evalue 8'''
-    s='''mg-compare-functions.py --ids mgm4662210.3,mgm4662211.3,mgm4662212.3,mgm4662235.3 --level level2 --source KO --format text --evalue 8'''
-    stat, out, err = runme(s) 
+    s = '''mg-compare-functions.py --ids mgm4662210.3,mgm4662211.3,mgm4662212.3,mgm4662235.3 --level level2 --source KO --format text --evalue 8'''
+    stat, out, err = runme(s)
 
 def test_mg_display_statistics():
-    s='''mg-display-statistics.py --id mgm4441680.3 --stat sequence'''
-    stat, out, err = runme(s) 
-  
+    s = '''mg-display-statistics.py --id mgm4441680.3 --stat sequence'''
+    stat, out, err = runme(s)
+
 def test_mg_download():
-    s='''mg-download.py --metagenome mgm4441680.3 --list''' 
-    stat, out, err = runme(s) 
+    s = '''mg-download.py --metagenome mgm4441680.3 --list'''
+    stat, out, err = runme(s)
 
 #def test_mg_extract_sequences():
-#    s='''mg-extract-sequences.py --function protease --biome marine'''
-#    stat, out, err = runme(s) 
+#    s = '''mg-extract-sequences.py --function protease --biome marine'''
+#    stat, out, err = runme(s)
 
 def test_mg_get_sequences_for_function():
-    s='''mg-get-sequences-for-function.py --id mgm4441680.3 --name "Central carbohydrate metabolism" --level level2 --source Subsystems --evalue 10'''
-    stat, out, err = runme(s) 
+    s = '''mg-get-sequences-for-function.py --id mgm4441680.3 --name "Central carbohydrate metabolism" --level level2 --source Subsystems --evalue 10'''
+    stat, out, err = runme(s)
     assert stat == 0
 
 def test_mg_get_sequences_for_taxon():
-    s='''mg-get-sequences-for-taxon.py --id mgm4441680.3 --name Lachnospiraceae --level family --source RefSeq --evalue 8'''
-    stat, out, err = runme(s) 
+    s = '''mg-get-sequences-for-taxon.py --id mgm4441680.3 --name Lachnospiraceae --level family --source RefSeq --evalue 8'''
+    stat, out, err = runme(s)
     assert stat == 0
 
 def test_mg_query_matrix():
-    s='''mg-query.py  'http://api.mg-rast.org/matrix/function?id=mgm4447943.3' '''
-    stat, out, err = runme(s) 
+    s = '''mg-query.py  'http://api.mg-rast.org/matrix/function?id=mgm4447943.3' '''
+    stat, out, err = runme(s)
     assert stat == 0
     assert b'acter' in out
 
 @pytest.mark.known_failing
 def test_mg_query_darkmatter():
-    s='''mg-query.py  'http://api.mg-rast.org/darkmatter/mgm4447943.3' '''
-    stat, out, err = runme(s) 
+    s = '''mg-query.py  'http://api.mg-rast.org/darkmatter/mgm4447943.3' '''
+    stat, out, err = runme(s)
     assert stat == 0
 
 def test_mg_get_similarity_for_taxon():
-    s='''mg-get-similarity-for-function.py --id mgm4441680.3 --name Central\ carbohydrate\ metabolism --level level2 --source Subsystems --evalue 10'''
-    stat, out, err = runme(s) 
+    s = '''mg-get-similarity-for-function.py --id mgm4441680.3 --name Central\ carbohydrate\ metabolism --level level2 --source Subsystems --evalue 10'''
+    stat, out, err = runme(s)
     assert stat == 0
 @pytest.mark.requires_auth
 def test_mg_inbox_view():
-    s='''mg-inbox.py view all'''
-    stat, out, err = runme(s) 
+    s = '''mg-inbox.py view all'''
+    stat, out, err = runme(s)
     assert stat == 0
 @pytest.mark.known_failing
 def test_mg_kegg2ss():
     s = '''mg-kegg2ss.py --input - --output text'''
-    stat, out, err = runme(s) 
+    stat, out, err = runme(s)
     assert stat == 0
 def test_mg_retrieve_uniprot():
-    s='''mg-retrieve-uniprot.py --md5 ffc62262a18b38671c3e337150ef535f --source SwissProt'''
-    stat, out, err = runme(s) 
+    s = '''mg-retrieve-uniprot.py --md5 ffc62262a18b38671c3e337150ef535f --source SwissProt'''
+    stat, out, err = runme(s)
     assert stat == 0
 
 def test_mg_project():
-    s='''mg-project.py get-info mgp128'''
-    stat, out, err = runme(s) 
+    s = '''mg-project.py get-info mgp128'''
+    stat, out, err = runme(s)
     assert stat == 0
 
-def test_mg_search_metagenomes__help(): 
-    s='''mg-search-metagenomes.py --help'''
-    stat, out, err = runme(s) 
+def test_mg_search_metagenomes__help():
+    s = '''mg-search-metagenomes.py --help'''
+    stat, out, err = runme(s)
     assert stat == 0
 
-def test_mg_display_metadata(): 
-    s='''mg-display-metadata.py --id "mgm4441680.3" --verbosity full'''
-    stat, out, err = runme(s) 
+def test_mg_display_metadata():
+    s = '''mg-display-metadata.py --id "mgm4441680.3" --verbosity full'''
+    stat, out, err = runme(s)
     assert stat == 0
     assert b"medium-quality grass-legume hay" in out
 
 @pytest.mark.requires_auth
 def test_mg_submit():
-    s='''mg-submit.py list'''
-    stat, out, err = runme(s) 
+    s = '''mg-submit.py list'''
+    stat, out, err = runme(s)
     assert stat == 0
 
 def test_mg_m5nrtoolspl():
-    s='''m5nr-tools.pl --api http://api.mg-rast.org/ --option annotation --source RefSeq --md5 0b95101ffea9396db4126e4656460ce5,068792e95e38032059ba7d9c26c1be78,0b96c9'''
-    stat, out, err = runme(s) 
+    s = '''m5nr-tools.pl --api http://api.mg-rast.org/ --option annotation --source RefSeq --md5 0b95101ffea9396db4126e4656460ce5,068792e95e38032059ba7d9c26c1be78,0b96c9'''
+    stat, out, err = runme(s)
     assert stat == 0
     assert b"alcohol dehydrogenase" in out
 
 def test_query_matrix():
-    s='''mg-query.py 'http://api.mg-rast.org/matrix/organism?group_level=phylum&source=SEED&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4510219.3' > matrix.biom'''
-    stat, out, err = runme(s) 
+    s = '''mg-query.py 'http://api.mg-rast.org/matrix/organism?group_level=phylum&source=SEED&hit_type=single&result_type=abundance&evalue=1&identity=60&length=15&taxid=0&id=mgm4510219.3' > matrix.biom'''
+    stat, out, err = runme(s)
     assert stat == 0
 def test_mg_biom_view():
-    s='''mg-biom-view.py < {}/mgm4514486.3.refseq.biom.json'''.format(DATADIR)
-    stat, out, err = runme(s) 
-    assert stat == 0   
+    s = '''mg-biom-view.py < {}/mgm4514486.3.refseq.biom.json'''.format(DATADIR)
+    stat, out, err = runme(s)
+    assert stat == 0
     assert b'Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Vibrio;Vibrio cholerae;Vibrio cholerae BX 330286	8' in out