Add testing and bump to 0.1.0.

Author: boydgreenfield

setup.py

@@ -17,7 +17,7 @@
 
 setup(
     name='taxonomy',
-    version='0.0.0',
+    version='0.1.0',
     url='http://github.com/refgenomics/taxonomy/',
     license='All rights reserved',
     author='Nick Boyd Greenfield',

tests/__init__.py

@@ -0,0 +1,8 @@
+from nose.tools import *
+import os
+from taxonomy.helpers import md5_for_file
+
+
+def test_md5_for_file():
+    init_md5 = md5_for_file(os.path.join(os.getcwd(), "tests/__init__.py"))
+    assert ("d41d8cd98f00b204e9800998ecf8427e" == init_md5)

tests/test_helpers.py

@@ -0,0 +1,82 @@
+from nose.tools import *
+import os
+import subprocess
+import urllib
+
+import taxonomy
+from taxonomy import Taxonomy
+
+
+# Download taxdmp.zip once to local directory
+# and uncompress if not already present
+def taxonomy_setup():
+    if not os.path.exists(os.path.join(os.getcwd(), 'sample_data/')):
+        os.mkdir(os.path.join(os.getcwd(), 'sample_data/'))
+    full_tax_path = os.path.join(os.getcwd(), "sample_data/taxonomy.json.gz")
+    taxdmp_path = os.path.join(os.getcwd(), "sample_data/taxdmp.zip")
+    taxdmp_dir = os.path.join(os.getcwd(), "sample_data/taxdmp")
+    names_head = os.path.join(os.getcwd(), "sample_data/taxdmp/names.1000.dmp")
+    nodes_head = os.path.join(os.getcwd(), "sample_data/taxdmp/nodes.1000.dmp")
+    ncbi_ftp = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip"
+    if not os.path.exists(taxdmp_path):
+        urllib.urlretrieve(ncbi_ftp,
+                           taxdmp_path)
+    if not os.path.exists(taxdmp_dir):
+        res0 = subprocess.call(["unzip", taxdmp_path,
+                               "-d", taxdmp_dir])
+        if res0 != 0:
+            raise Exception("Failed to unzip necessary taxdmp files.")
+
+    if not os.path.exists(names_head) or not os.path.exists(nodes_head):
+        res1 = subprocess.call(["head", "-n", "1000",
+                               os.path.join(taxdmp_dir, "names.dmp")],
+                               stdout=open(names_head, mode='w'))
+
+        res2 = subprocess.call(["head", "-n", "1000",
+                               os.path.join(taxdmp_dir, "nodes.dmp")],
+                               stdout=open(nodes_head, mode='w'))
+
+        if res1 != 0 or res2 != 0:
+            raise Exception("Failed to take the head of the names.dmp or "
+                            "nodes.dmp files.")
+
+    if not os.path.exists(full_tax_path):
+        tax = Taxonomy.build_from_ncbi(os.path.join(taxdmp_dir, "names.dmp"),
+                                       os.path.join(taxdmp_dir, "nodes.dmp"),
+                                       ncbi_ftp, ncbi_ftp,
+                                       "FTP Revision - See Date")
+        tax.save(full_tax_path)
+
+
+@with_setup(taxonomy_setup)
+def test_small_tax_create():
+    out_tax = os.path.join(os.getcwd(), "sample_data/small_tax.json")
+    names_head = os.path.join(os.getcwd(), "sample_data/taxdmp/names.1000.dmp")
+    nodes_head = os.path.join(os.getcwd(), "sample_data/taxdmp/nodes.1000.dmp")
+    tax = Taxonomy.build_from_ncbi(names_head, nodes_head,
+                                   "Test Names", "Test Nodes",
+                                   "Sample NCBI Revision")
+
+    assert tax.__class__ is taxonomy.taxonomy.Taxonomy
+    print out_tax
+    tax.save(out_tax)
+
+    # Assertion on root
+    print tax.G.node[1]
+    assert tax.G.node[1] == {'hidden': True, 'name': 'root',
+                             'rank': 'no rank'}
+
+    # Check that files are properly output
+    assert not os.path.exists(out_tax)
+    assert os.path.exists(out_tax + ".gz")  # auto-append works
+
+    # Reread file in
+    tax_b = Taxonomy.load(out_tax + ".gz")
+    assert len(tax_b.G.nodes()) == len(tax.G.nodes())
+    assert len(tax_b.G.edges()) == len(tax_b.G.edges())
+
+    # Assert on new file
+    assert tax_b.G.node[1] == {'hidden': True, 'name': 'root',
+                               'rank': 'no rank'}
+    # Final cleanup
+    os.remove(out_tax + ".gz")