Merge pull request #3482 from jmchilton/placeholder_fixes

[17.01] Fix logs and unit tests for Conda placeholder bug resolution.
galaxyproject · Jan 25, 2017 · 71876f6 · 71876f6
2 parents 29c0c41 + 04eee64
commit 71876f6
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Showing 2 changed files with 9 additions and 21 deletions.
diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py
@@ -75,11 +75,6 @@ def get_option(name):
 
         self.conda_prefix_parent = os.path.dirname(conda_prefix)
 
-        # warning is related to conda problem discussed in https://github.com/galaxyproject/galaxy/issues/2537, remove when that is resolved
-        conda_prefix_warning_length = 50
-        if len(conda_prefix) >= conda_prefix_warning_length:
-            log.warning("Conda install prefix '%s' is %d characters long, this can cause problems with package installation, consider setting a shorter prefix (conda_prefix in galaxy.ini)" % (conda_prefix, len(conda_prefix)))
-
         condarc_override = get_option("condarc_override")
         if condarc_override is None:
             condarc_override = os.path.join(

diff --git a/test/unit/tools/test_conda_resolution.py b/test/unit/tools/test_conda_resolution.py
@@ -7,6 +7,7 @@
     conda_util,
     DependencyManager
 )
+from galaxy.tools.deps.requirements import ToolRequirement
 from galaxy.tools.deps.resolvers.conda import CondaDependencyResolver
 
 
@@ -29,25 +30,16 @@ def test_conda_resolution():
             auto_install=True,
             use_path_exec=False,  # For the test ensure this is always a clean install
         )
-        conda_context = resolver.conda_context
-        assert len(list(conda_util.installed_conda_targets(conda_context))) == 0
-        dependency = resolver.resolve(name="samtools", version=None, type="package", job_directory=job_dir)
+        req = ToolRequirement(name="samtools", version=None, type="package")
+        dependency = resolver.resolve(req, job_directory=job_dir)
         assert dependency.shell_commands(None) is not None
-        installed_targets = list(conda_util.installed_conda_targets(conda_context))
-        assert len(installed_targets) == 1
-        samtools_target = installed_targets[0]
-        assert samtools_target.package == "samtools"
-        assert samtools_target.version is None
     finally:
         shutil.rmtree(base_path)
 
 
 @skip_unless_environ("GALAXY_TEST_INCLUDE_SLOW")
-def test_conda_resolution_failure():
-    """This test is specifically designed to trigger https://github.com/rtfd/readthedocs.org/issues/1902
-    and thus it expects the install to fail. If this test fails it is a sign that the upstream
-    conda issue has been fixed.
-    """
+def test_against_conda_prefix_regression():
+    """Test that would fail if https://github.com/rtfd/readthedocs.org/issues/1902 regressed."""
 
     base_path = mkdtemp(prefix='x' * 80)  # a ridiculously long prefix
     try:
@@ -61,9 +53,10 @@ def test_conda_resolution_failure():
         )
         conda_context = resolver.conda_context
         assert len(list(conda_util.installed_conda_targets(conda_context))) == 0
-        dependency = resolver.resolve(name="samtools", version=None, type="package", job_directory=job_dir)
-        assert dependency.shell_commands(None) is None  # install should fail
+        req = ToolRequirement(name="samtools", version="0.1.16", type="package")
+        dependency = resolver.resolve(req, job_directory=job_dir)
+        assert dependency.shell_commands(None) is not None  # install should not fail anymore
         installed_targets = list(conda_util.installed_conda_targets(conda_context))
-        assert len(installed_targets) == 0
+        assert len(installed_targets) > 0
     finally:
         shutil.rmtree(base_path)