fix docker container symlinks in dev environment, add missing test code

docker/install-dev-layer.sh

@@ -15,8 +15,8 @@
 # Must have $INSTALL_PATH and $VIRAL_NGS_PATH defined (from viral-core docker)
 set -e -o pipefail
 
-cd /opt/viral-ngs/viral-assemble
+VIRAL_ASSEMBLE_PATH=/opt/viral-ngs/viral-assemble
 
-$VIRAL_NGS_PATH/docker/install-conda-dependencies.sh requirements-conda.txt
+$VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_ASSEMBLE_PATH/requirements-conda.txt
 
-ln -s assemble test assembly.py $VIRAL_NGS_PATH
+ln -s $VIRAL_ASSEMBLE_PATH/assemble $VIRAL_ASSEMBLE_PATH/test $VIRAL_ASSEMBLE_PATH/assembly.py $VIRAL_NGS_PATH

test/__init__.py

@@ -0,0 +1,122 @@
+'''utilities for tests'''
+
+__author__ = "[email protected]"
+
+# built-ins
+import filecmp
+import os
+import re
+import unittest
+import hashlib
+import logging
+
+# third-party
+import Bio.SeqIO
+import pytest
+
+# intra-project
+import util.file
+from util.misc import available_cpu_count
+from tools.samtools import SamtoolsTool
+
+logging.getLogger('botocore').setLevel(logging.WARNING)
+logging.getLogger('boto3').setLevel(logging.WARNING)
+
+
+if 'PYTEST_XDIST_WORKER_COUNT' in os.environ:
+    _CPUS = 1
+else:
+    _CPUS = available_cpu_count()
+
+
+def assert_equal_contents(testCase, filename1, filename2):
+    'Assert contents of two files are equal for a unittest.TestCase'
+    testCase.assertTrue(filecmp.cmp(filename1, filename2, shallow=False))
+
+
+def assert_equal_bam_reads(testCase, bam_filename1, bam_filename2):
+    ''' Assert that two bam files are equivalent
+
+        This function converts each file to sam (plaintext) format,
+        without header, since the header can be variable.
+
+        Test data should be stored in bam format rather than sam
+        to save space, and to ensure the bam->sam conversion
+        is the same for both files.
+    '''
+
+    samtools = SamtoolsTool()
+
+    sam_one = util.file.mkstempfname(".sam")
+    sam_two = util.file.mkstempfname(".sam")
+
+    # write the bam files to sam format, without header (no -h)
+    samtools.view(args=[], inFile=bam_filename1, outFile=sam_one)
+    samtools.view(args=[], inFile=bam_filename2, outFile=sam_two)
+
+    try:
+        testCase.assertTrue(filecmp.cmp(sam_one, sam_two, shallow=False))
+    finally:
+        for fname in [sam_one, sam_two]:
+            if os.path.exists(fname):
+                os.unlink(fname)
+
+def assert_md5_equal_to_line_in_file(testCase, filename, checksum_file, msg=None):
+    ''' Compare the checksum of a test file with the expected checksum
+        stored in a second file
+          compare md5(test_output.bam) with expected_output.bam.md5:1
+    '''
+
+    hash_md5 = hashlib.md5()
+    with open(filename, "rb") as f:
+        for chunk in iter(lambda: f.read(4096), b""):
+            hash_md5.update(chunk)
+
+    expected_checksum = ""
+    with open(checksum_file, "rb") as f:
+        expected_checksum = str(f.readline().decode("utf-8"))
+
+    expected_checksum = expected_checksum.replace("\r","").replace("\n","")
+
+    assert len(expected_checksum) > 0
+
+    testCase.assertEqual(hash_md5.hexdigest(), expected_checksum, msg=msg)
+
+@pytest.mark.usefixtures('tmpdir_class')
+class TestCaseWithTmp(unittest.TestCase):
+    'Base class for tests that use tempDir'
+
+    def assertEqualContents(self, f1, f2):
+        assert_equal_contents(self, f1, f2)
+
+    def assertEqualFasta(self, f1, f2):
+        '''Check that two fasta files have the same sequence ids and bases'''
+        def seqIdPairs(f):
+            return [(rec.id, rec.seq) for rec in Bio.SeqIO.parse(f, 'fasta')]
+        self.assertEqual(seqIdPairs(f1), seqIdPairs(f2))
+
+    def assertEqualFastaSeqs(self, f1, f2):
+        '''Check that two fasta files have the same sequence bases (sequence ids may differ)'''
+        def seqs(f):
+            return [rec.seq for rec in Bio.SeqIO.parse(f, 'fasta')]
+        self.assertEqual(seqs(f1), seqs(f2))
+
+    def input(self, fname):
+        '''Return the full filename for a file in the test input directory for this test class'''
+        return os.path.join(util.file.get_test_input_path(self), fname)
+
+    def inputs(self, *fnames):
+        '''Return the full filenames for files in the test input directory for this test class'''
+        return [self.input(fname) for fname in fnames]
+
+"""
+When "nose" executes python scripts for automated testing, it excludes ones with
+the executable bit set (in case they aren't import safe). To prevent any of the
+tests in this folder from being silently excluded, assure this bit is not set.
+"""
+
+
+def assert_none_executable():
+    testDir = os.path.dirname(__file__)
+    assert all(not os.access(os.path.join(testDir, filename), os.X_OK) for filename in os.listdir(testDir)
+               if filename.endswith('.py'))

test/stubs.py

@@ -0,0 +1,79 @@
+import logging
+import os
+import pytest
+import tools
+
+
+class StubCondaPackage(tools.Tool):
+
+    # Skip gathering in all_tool_classes
+    _skiptest = True
+
+    def __init__(
+        self,
+        package,
+        channel="bioconda",
+        executable=None,
+        version="",
+        verifycmd=None,
+        verifycode=0,
+        require_executability=True,
+        env=None,
+        env_root_path=None,
+        conda_cache_path=None,
+        patches=None,
+        post_install_command=None,
+        post_install_ret=0,
+        post_verify_command=None,
+        post_verify_ret=0
+    ):
+        self.executable = executable or package
+        if type(version) == tools.CondaPackageVersion:
+            self.version = version
+        else:
+            self.version = tools.CondaPackageVersion(version)
+
+        self.env_path = None
+        if 'CONDA_PREFIX' in os.environ and len(os.environ['CONDA_PREFIX']):
+            last_path_component = os.path.basename(os.path.normpath(os.environ['CONDA_PREFIX']))
+            self.env_path = os.path.dirname(os.environ['CONDA_PREFIX']) if last_path_component == "bin" else os.environ['CONDA_PREFIX']
+
+        else:
+            raise Exception
+
+    def is_attempted(self):
+        return True
+
+    def is_installed(self):
+        return True
+
+    @property
+    def bin_path(self):
+        return os.path.join(self.env_path, 'bin')
+
+    def executable_path(self):
+        return os.path.join(self.bin_path, self.executable)
+
+    def apply_patches(self):
+        pass
+
+    def verify_install(self):
+        return
+
+    def package_available(self):
+        return True
+
+    def uninstall_package(self):
+        return True
+
+    def install_package(self):
+        return True
+
+    def get_installed_version(self):
+        return self.version
+
+    def post_install(self):
+        pass
+
+    def execute(self, cmd, loglevel=logging.DEBUG):
+        return {}