Work with new files, fix paths

Author: Adam Robbins-Pianka

qiita_ware/test/test_ebi.py

@@ -18,6 +18,7 @@
 from unittest import TestCase, main
 from xml.dom import minidom
 from xml.etree import ElementTree as ET
+from functools import partial
 
 from qiita_ware.ebi import (SampleAlreadyExistsError, NoXMLError,
                             EBISubmission)
@@ -26,8 +27,15 @@
 
 class TestEBISubmission(TestCase):
     def setUp(self):
-        self.path = path.dirname(path.abspath(__file__)) + \
-            '/test_data/test_ebi'
+        self.path = join(path.dirname(path.abspath(__file__)), 'test_data',
+                         'test_ebi')
+
+        ebi_test_file = partial(join, self.path)
+
+        self.sample1_fp = ebi_test_file('sample1.fastq.gz')
+        self.sample2_fp = ebi_test_file('sample2.fastq.gz')
+        self.sample3_fp = ebi_test_file('sample3.fastq.gz')
+
         self.temp_dir = gettempdir()
 
     def test_init(self):
@@ -193,15 +201,18 @@ def test_add_sample_prep(self):
                                    new_investigation_type='metagenome')
         submission.add_sample('test1')
         submission.add_sample('test2')
+
         submission.add_sample_prep('test1', 'ILLUMINA', 'fastq',
-                                   self.path, 'experiment description',
+                                   self.sample1_fp, 'experiment description',
                                    'library protocol')
+
         prep_info = submission.samples['test1']['prep']
         self.assertEqual(prep_info['platform'], 'ILLUMINA')
-        self.assertEqual(prep_info['file_path'], self.path)
+        self.assertEqual(prep_info['file_path'], self.sample1_fp)
         with self.assertRaises(KeyError):
             submission.add_sample_prep('test3', 'ILLUMINA', 'fastq',
-                                       self.path, 'experiment description',
+                                       self.sample3_fp,
+                                       'experiment description',
                                        'library protocol')
 
     def test_add_sample_prep_exception(self):
@@ -212,11 +223,13 @@ def test_add_sample_prep_exception(self):
         submission.add_sample('test2')
         with self.assertRaises(ValueError):
             submission.add_sample_prep('test2', 'DOES-NOT-EXIST', 'fastq',
-                                       self.path, 'experiment description',
+                                       self.sample1_fp,
+                                       'experiment description',
                                        'library protocol')
         with self.assertRaises(KeyError):
             submission.add_sample_prep('test3', 'DOES-NOT-EXIST', 'fastq',
-                                       self.path, 'experiment description',
+                                       self.sample3_fp,
+                                       'experiment description',
                                        'library protocol')
 
     def test_generate_library_descriptor(self):
@@ -247,14 +260,17 @@ def test_generate_experiment_xml(self):
                                    new_investigation_type='metagenome')
         submission.add_sample('test1')
         submission.add_sample_prep('test1', 'ILLUMINA', 'fastq',
-                                   'fakepath',
+                                   self.sample1_fp,
                                    'experiment description',
                                    'library protocol')
         xmlelement = submission.generate_experiment_xml()
         xml = minidom.parseString(ET.tostring(xmlelement))
         xmlstring = xml.toprettyxml(indent='  ', encoding='UTF-8')
         obs_stripped = ''.join([l.strip() for l in xmlstring.splitlines()])
-        exp_stripped = ''.join([l.strip() for l in EXPERIMENTXML.splitlines()])
+        exp = EXPERIMENTXML % {
+            'path': self.sample1_fp,
+            'organization_prefix': qiita_config.ebi_organization_prefix}
+        exp_stripped = ''.join([l.strip() for l in exp.splitlines()])
         self.assertEqual(obs_stripped, exp_stripped)
 
     def test_generate_run_xml(self):
@@ -263,7 +279,7 @@ def test_generate_run_xml(self):
                                    new_investigation_type='metagenome')
         submission.add_sample('test1')
         submission.add_sample_prep('test1', 'ILLUMINA', 'fastq',
-                                   join(self.path, '__init__.py'),
+                                   self.sample1_fp,
                                    'experiment description',
                                    'library protocol')
         xmlelement = submission.generate_run_xml()
@@ -338,13 +354,16 @@ def test_write_experiment_xml(self):
                                    new_investigation_type='metagenome')
         submission.add_sample('test1')
         submission.add_sample_prep('test1', 'ILLUMINA', 'fastq',
-                                   'fakepath', 'experiment description',
+                                   self.sample1_fp, 'experiment description',
                                    'library protocol')
         fh, output = mkstemp()
         close(fh)
         submission.write_experiment_xml(output)
         obs_stripped = ''.join([l.strip() for l in open(output)])
-        exp_stripped = ''.join([l.strip() for l in EXPERIMENTXML.splitlines()])
+        exp = EXPERIMENTXML % {
+            'path': self.sample1_fp,
+            'organization_prefix': qiita_config.ebi_organization_prefix}
+        exp_stripped = ''.join([l.strip() for l in exp.splitlines()])
         self.assertEqual(obs_stripped, exp_stripped)
         remove(output)
 
@@ -363,7 +382,7 @@ def test_add_samples_from_templates(self):
                          'ILLUMINA')
         self.assertEqual(
             submission.samples['sample2']['prep']['file_path'],
-            self.path + '/sample2.fastq.gz')
+            self.sample2_fp)
         with self.assertRaises(KeyError):
             submission.samples['nothere']
 
@@ -388,7 +407,7 @@ def test_from_templates_and_per_sample_fastqs(self):
                          'ILLUMINA')
         self.assertEqual(
             submission.samples['sample2']['prep']['file_path'],
-            self.path + '/sample2.fastq.gz')
+            self.sample2_fp)
         with self.assertRaises(KeyError):
             submission.samples['nothere']
 
@@ -553,7 +572,7 @@ def test_generate_curl_command(self):
       </EXPERIMENT_ATTRIBUTE>
       <EXPERIMENT_ATTRIBUTE>
         <TAG>file_path</TAG>
-        <VALUE>fakepath</VALUE>
+        <VALUE>%(path)s</VALUE>
       </EXPERIMENT_ATTRIBUTE>
       <EXPERIMENT_ATTRIBUTE>
         <TAG>file_type</TAG>
@@ -563,25 +582,29 @@ def test_generate_curl_command(self):
         <TAG>library_construction_protocol</TAG>
         <VALUE>library protocol</VALUE>
       </EXPERIMENT_ATTRIBUTE>
+      <EXPERIMENT_ATTRIBUTE>
+        <TAG>md5</TAG>
+        <VALUE>506d31c82999a2cbcda138a369955e7d</VALUE>
+      </EXPERIMENT_ATTRIBUTE>
       <EXPERIMENT_ATTRIBUTE>
         <TAG>platform</TAG>
         <VALUE>ILLUMINA</VALUE>
       </EXPERIMENT_ATTRIBUTE>
     </EXPERIMENT_ATTRIBUTES>
   </EXPERIMENT>
 </EXPERIMENT_SET>
-""" % {'organization_prefix': qiita_config.ebi_organization_prefix}
+"""
 
 RUNXML = """
 <?xml version="1.0" encoding="UTF-8"?>
 <RUN_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:no\
 NamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_3/SRA.run.xsd">
-  <RUN alias="%(study_alias)s___init__.py_run" center_name="CCME-COLORADO">
+  <RUN alias="%(study_alias)s_sample1.fastq.gz_run" center_name="CCME-COLORADO">
     <EXPERIMENT_REF refname="%(organization_prefix)s_ppdid_001:test1"/>
     <DATA_BLOCK>
       <FILES>
-        <FILE checksum="612cbff13a4f0e236e5e62ac2e00329a" checksum_method=\
-"MD5" filename="%(ebi_dir)s/__init__.py" filetype="fastq" \
+        <FILE checksum="506d31c82999a2cbcda138a369955e7d" checksum_method=\
+"MD5" filename="%(ebi_dir)s/sample1.fastq.gz" filetype="fastq" \
 quality_scoring_system="phred"/>
       </FILES>
     </DATA_BLOCK>