test clean up

physcraper/opentree_helpers.py

@@ -157,18 +157,22 @@ def generate_ATT_from_phylesystem(aln,
             "your alignment `%s` ist not of type DnaCharacterMatrix" % aln
     for tax in aln.taxon_namespace:
         tax.label = tax.label.replace(" ", "_")  # Forcing all spaces to underscore
-    nexson = get_nexson(study_id, phylesystem_loc)
-    newick = extract_tree(nexson,
-                          tree_id,
-                          PhyloSchema('newick',
+    try:
+        nexson = get_nexson(study_id, phylesystem_loc)
+        newick = extract_tree(nexson,
+                              tree_id,
+                              PhyloSchema('newick',
                                       output_nexml2json='1.2.1',
                                       content="tree",
                                       tip_label="ot:originalLabel"))
-    newick = newick.replace(" ", "_")  # UGH Very heavy handed, need to make sure happens on alignment side as well.
-    tre = Tree.get(data=newick,
+        newick = newick.replace(" ", "_")  # UGH Very heavy handed, need to make sure happens on alignment side as well.
+        tre = Tree.get(data=newick,
                    schema="newick",
                    preserve_underscores=True,
                    taxon_namespace=aln.taxon_namespace)
+    except:
+        sys.stderr.write("failure getting tree {} from study {} from phylesystem".format(tree_id, study_id))
+        sys.exit()
     # this gets the taxa that are in the subtree with all of their info - ott_id, original name,
     otus = get_subtree_otus(nexson, tree_id=tree_id)
     otu_dict = {}

pytest.ini

@@ -1,11 +1,5 @@
 [pytest]
 
-# defines the root dir?
-env = 
-	HOME=~/home/blubb/Documents/gitdata
-
-# will stop running after two test failures
-addopts = --maxfail=2 -rf --durations=0 --num auto -v
 
 # custom flags to group tests?
 markers =

tests/test_from_phylesystem.py

@@ -1,12 +1,10 @@
 import physcraper
 import sys
+import pytest
 from pytest import mark
 from dendropy import DnaCharacterMatrix
 
-web = mark.web
 
-
-@web
 def test_generate_ATT_from_phylesystem():
     seqaln = "tests/data/input.fas"
     study_id = "pg_873"
@@ -29,4 +27,25 @@ def test_generate_ATT_from_phylesystem():
                                                     tree_id=tree_id)
 
     data_obj == True
-
+
+@pytest.mark.xfail
+def test_generate_ATT_from_phylesystem_fail():
+    seqaln = "tests/data/input.fas"
+    study_id = "pg_873"
+    tree_id = "tree1679"
+    seqaln = "tests/data/minitest.fas"
+    mattype = "fasta"
+    workdir = "tests/output/opentree"
+    configfi = "tests/data/remotencbi.config"
+
+
+    sys.stdout.write("\nTesting 'generate_ATT_from_files (fromfile.py)'\n")
+
+    conf = physcraper.ConfigObj(configfi, interactive=False)
+    aln = DnaCharacterMatrix.get(path=seqaln, schema=mattype)
+    data_obj = physcraper.generate_ATT_from_phylesystem(aln=aln,
+                                                    workdir=workdir,
+                                                    config_obj=conf,
+                                                    study_id=study_id,
+                                                    tree_id=tree_id)
+