Merge pull request #3632 from jmchilton/conda_43_fix

[17.01] Fix Conda --offline logic for bug in 4.0,4.1,4.3.

lib/galaxy/tools/deps/conda_util.py

@@ -82,6 +82,41 @@ class CondaContext(installable.InstallableContext):
             ensure_channels = None
         self.ensure_channels = ensure_channels
         self.ensured_channels = False
+        self._conda_version = None
+        self._miniconda_version = None
+
+    @property
+    def conda_version(self):
+        if self._conda_version is None:
+            self._guess_conda_version()
+        return self._conda_version
+
+    def _guess_conda_version(self):
+        conda_meta_path = self._conda_meta_path
+        # Perhaps we should call "conda info --json" and parse it but for now we are going
+        # to assume the default.
+        conda_version = LooseVersion(CONDA_VERSION)
+        miniconda_version = "3"
+
+        if os.path.exists(conda_meta_path):
+            for package in os.listdir(conda_meta_path):
+                package_parts = package.split("-")
+                if len(package_parts) < 3:
+                    continue
+                package = '-'.join(package_parts[:-2])
+                version = package_parts[-2]
+                # build = package_parts[-1]
+                if package == "conda":
+                    conda_version = LooseVersion(version)
+                if package == "python" and version.startswith("2"):
+                    miniconda_version = "2"
+
+        self._conda_version = conda_version
+        self._miniconda_version = miniconda_version
+
+    @property
+    def _conda_meta_path(self):
+        return os.path.join(self.conda_prefix, "conda-meta")
 
     def ensure_channels_configured(self):
         if not self.ensured_channels:
@@ -495,7 +530,16 @@ def build_isolated_environment(
                 export_path
             )
             export_paths.append(export_path)
-        create_args = ["--unknown", "--offline"]
+        create_args = ["--unknown"]
+        # Works in 3.19, 4.0 - 4.2 - not in 4.3.
+        # Adjust fix if they fix Conda - xref
+        # - https://github.com/galaxyproject/galaxy/issues/3635
+        # - https://github.com/conda/conda/issues/2035
+        offline_works = conda_context.conda_version < LooseVersion("4.3")
+        if offline_works:
+            create_args.extend(["--offline"])
+        else:
+            create_args.extend(["--use-index-cache"])
         if path is None:
             create_args.extend(["--name", tempdir_name])
         else:

test/functional/tools/mulled_example_multi_incomplete.xml

@@ -0,0 +1,22 @@
+<tool id="mulled_example_multi_incomplete" name="mulled_example_multi_incomplete" version="0.1.0">
+    <command><![CDATA[
+        bedtools --version > $out_file1 ;
+        echo "Moo" >> $out_file1 ;
+        samtools >> $out_file1 2>&1 ;
+        echo "Cow" >> $out_file1 ;
+    ]]></command>
+    <requirements>
+        <requirement type="package" version="1.3.1">samtools</requirement>
+        <requirement type="package" version="2.26.0">bedtools</requirement>
+        <!-- Because the Conda resolver will fail to install all three of these together
+             it will need to build a per-job environment out of just the first two.
+        -->
+        <requirement type="package" version="4.5">notarealpackage</requirement>
+    </requirements>
+    <inputs>
+        <param name="input1" type="data" optional="true" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -128,6 +128,7 @@
   <!-- Tools for dependency and container testing. -->
   <tool file="legacy_r.xml" />
   <tool file="mulled_example_multi_1.xml" />
+  <tool file="mulled_example_multi_incomplete.xml" />
   <tool file="mulled_example_conflict.xml" />
 
   <tool file="simple_constructs.yml" />