Update to brew_exts to latest platform-brew.

lib/galaxy/tools/deps/brew_exts.py

@@ -28,6 +28,7 @@ import glob
 import os
 import re
 import sys
+import string
 import subprocess
 
 WHITESPACE_PATTERN = re.compile("[\s]+")
@@ -43,6 +44,7 @@ NO_BREW_ERROR_MESSAGE = "Could not find brew on PATH, please place on path or pa
 CANNOT_DETERMINE_TAP_ERROR_MESSAGE = "Cannot determine tap of specified recipe - please use fully qualified recipe (e.g. homebrew/science/samtools)."
 VERBOSE = False
 RELAXED = False
+BREW_ARGS = []
 
 
 class BrewContext(object):
@@ -104,6 +106,7 @@ class RecipeContext(object):
 def main():
     global VERBOSE
     global RELAXED
+    global BREW_ARGS
     parser = argparse.ArgumentParser(description=DESCRIPTION)
     parser.add_argument("--brew", help="Path to linuxbrew 'brew' executable to target")
     actions = ["vinstall", "vuninstall", "vdeps", "vinfo", "env"]
@@ -114,11 +117,13 @@ def main():
     parser.add_argument('version', metavar='version', help="Version for action (e.g. 0.1.19).")
     parser.add_argument('--relaxed', action='store_true', help="Relaxed processing - for instance allow use of env on non-vinstall-ed recipes.")
     parser.add_argument('--verbose', action='store_true', help="Verbose output")
+    parser.add_argument('restargs', nargs=argparse.REMAINDER)
     args = parser.parse_args()
     if args.verbose:
         VERBOSE = True
     if args.relaxed:
         RELAXED = True
+    BREW_ARGS = args.restargs
     if not action:
         action = args.action
     brew_context = BrewContext(args)
@@ -159,7 +164,7 @@ class CommandLineException(Exception):
         return self.message
 
 
-def versioned_install(recipe_context, package=None, version=None):
+def versioned_install(recipe_context, package=None, version=None, installed_deps=[]):
     if package is None:
         package = recipe_context.recipe
         version = recipe_context.version
@@ -176,10 +181,15 @@ def versioned_install(recipe_context, package=None, version=None):
             versioned = version_info[2]
             if versioned:
                 dep_to_version[dep] = dep_version
+                if dep in installed_deps:
+                    continue
                 versioned_install(recipe_context, dep, dep_version)
+                installed_deps.append(dep)
             else:
                 # Install latest.
                 dep_to_version[dep] = None
+                if dep in installed_deps:
+                    continue
                 unversioned_install(dep)
         try:
             for dep in deps:
@@ -198,7 +208,16 @@ def versioned_install(recipe_context, package=None, version=None):
                 }
                 deps_metadata.append(dep_metadata)
 
-            brew_execute(["install", package])
+            cellar_root = recipe_context.brew_context.homebrew_cellar
+            cellar_path = recipe_context.cellar_path
+            env_actions = build_env_actions(deps_metadata, cellar_root, cellar_path, custom_only=True)
+            env = EnvAction.build_env(env_actions)
+            args = ["install"]
+            if VERBOSE:
+                args.append("--verbose")
+            args.extend(BREW_ARGS)
+            args.append(package)
+            brew_execute(args, env=env)
             deps = brew_execute(["deps", package])
             deps = [d.strip() for d in deps.split("\n") if d]
             metadata = {
@@ -278,10 +297,10 @@ def attempt_unlink(package):
         pass
 
 
-def brew_execute(args):
+def brew_execute(args, env=None):
     os.environ["HOMEBREW_NO_EMOJI"] = "1"  # simplify brew parsing.
     cmds = ["brew"] + args
-    return execute(cmds)
+    return execute(cmds, env=env)
 
 
 def build_env_statements_from_recipe_context(recipe_context, **kwds):
@@ -290,11 +309,20 @@ def build_env_statements_from_recipe_context(recipe_context, **kwds):
     return env_statements
 
 
-def build_env_statements(cellar_root, cellar_path, relaxed=None):
+def build_env_statements(cellar_root, cellar_path, relaxed=None, custom_only=False):
     deps = load_versioned_deps(cellar_path, relaxed=relaxed)
+    actions = build_env_actions(deps, cellar_root, cellar_path, relaxed, custom_only)
+    env_statements = []
+    for action in actions:
+        env_statements.extend(action.to_statements())
+    return "\n".join(env_statements)
+
+
+def build_env_actions(deps, cellar_root, cellar_path, relaxed=None, custom_only=False):
 
     path_appends = []
     ld_path_appends = []
+    actions = []
 
     def handle_keg(cellar_path):
         bin_path = os.path.join(cellar_path, "bin")
@@ -303,6 +331,14 @@ def build_env_statements(cellar_root, cellar_path, relaxed=None):
         lib_path = os.path.join(cellar_path, "lib")
         if os.path.isdir(lib_path):
             ld_path_appends.append(lib_path)
+        env_path = os.path.join(cellar_path, "platform_environment.json")
+        if os.path.exists(env_path):
+            with open(env_path, "r") as f:
+                env_metadata = json.load(f)
+                if "actions" in env_metadata:
+                    def to_action(desc):
+                        return EnvAction(cellar_path, desc)
+                    actions.extend(map(to_action, env_metadata["actions"]))
 
     for dep in deps:
         package = dep['name']
@@ -311,14 +347,54 @@ def build_env_statements(cellar_root, cellar_path, relaxed=None):
         handle_keg( dep_cellar_path )
 
     handle_keg( cellar_path )
-    env_statements = []
-    if path_appends:
-        env_statements.append("PATH=" + ":".join(path_appends) + ":$PATH")
-        env_statements.append("export PATH")
-    if ld_path_appends:
-        env_statements.append("LD_LIBRARY_PATH=" + ":".join(ld_path_appends) + ":$LD_LIBRARY_PATH")
-        env_statements.append("export LD_LIBRARY_PATH")
-    return "\n".join(env_statements)
+    if not custom_only:
+        if path_appends:
+            actions.append(EnvAction(cellar_path, {"action": "prepend", "variable": "PATH", "value": ":".join(path_appends)}))
+        if ld_path_appends:
+            actions.append(EnvAction(cellar_path, {"action": "prepend", "variable": "LD_LIBRARY_PATH", "value": ":".join(path_appends)}))
+    return actions
+
+
+class EnvAction(object):
+
+    def __init__(self, keg_root, action_description):
+        self.variable = action_description["variable"]
+        self.action = action_description["action"]
+        self.value = string.Template(action_description["value"]).safe_substitute({
+            'KEG_ROOT': keg_root,
+        })
+
+    @staticmethod
+    def build_env(env_actions):
+        new_env = os.environ.copy()
+        map(lambda env_action: env_action.modify_environ(new_env), env_actions)
+        return new_env
+
+    def modify_environ(self, environ):
+        if self.action == "set" or not environ.get(self.variable, ""):
+            environ[self.variable] = self.__eval("${value}")
+        elif self.action == "prepend":
+            environ[self.variable] = self.__eval("${value}:%s" % environ[self.variable])
+        else:
+            environ[self.variable] = self.__eval("%s:${value}" % environ[self.variable])
+
+    def __eval(self, template):
+        return string.Template(template).safe_substitute(
+            variable=self.variable,
+            value=self.value,
+        )
+
+    def to_statements(self):
+        if self.action == "set":
+            template = '''${variable}="${value}"'''
+        elif self.action == "prepend":
+            template = '''${variable}="${value}:$$${variable}"'''
+        else:
+            template = '''${variable}="$$${variable}:${value}"'''
+        return [
+            self.__eval(template),
+            "export %s" % self.variable
+        ]
 
 
 @contextlib.contextmanager
@@ -350,8 +426,15 @@ def git_execute(args):
     return execute(cmds)
 
 
-def execute(cmds):
-    p = subprocess.Popen(cmds, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+def execute(cmds, env=None):
+    subprocess_kwds = dict(
+        shell=False,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+    )
+    if env:
+        subprocess_kwds["env"] = env
+    p = subprocess.Popen(cmds, **subprocess_kwds)
     #log = p.stdout.read()
     global VERBOSE
     stdout, stderr = p.communicate()
@@ -363,7 +446,10 @@ def execute(cmds):
 
 
 def brew_deps(package):
-    stdout = brew_execute(["deps", package])
+    args = ["deps"]
+    args.extend(BREW_ARGS)
+    args.append(package)
+    stdout = brew_execute(args)
     return [p.strip() for p in stdout.split("\n") if p]