diff env/lib/python3.9/site-packages/galaxy/tool_util/verify/test_data.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/tool_util/verify/test_data.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,122 @@
+import hashlib
+import os
+import re
+import subprocess
+from string import Template
+
+from galaxy.util import (
+    asbool,
+    in_directory,
+    smart_str
+)
+
+UPDATE_TEMPLATE = Template(
+    "git --work-tree $dir --git-dir $dir/.git fetch && "
+    "git --work-tree $dir --git-dir $dir/.git merge origin/master"
+)
+
+UPDATE_FAILED_TEMPLATE = Template(
+    "Warning failed to update test repository $dir - "
+    "update stdout was [$stdout] and stderr was [$stderr]."
+)
+
+
+LIST_SEP = re.compile(r"\s*,\s*")
+
+
+class TestDataResolver:
+
+    def __init__(self, file_dirs=None, env_var='GALAXY_TEST_FILE_DIR', environ=os.environ):
+        if file_dirs is None:
+            file_dirs = environ.get(env_var, None)
+        if file_dirs is None:
+            file_dirs = "test-data,https://github.com/galaxyproject/galaxy-test-data.git"
+        if file_dirs:
+            self.resolvers = [build_resolver(u, environ) for u in LIST_SEP.split(file_dirs)]
+        else:
+            self.resolvers = []
+
+    def get_filename(self, name):
+        for resolver in self.resolvers or []:
+            if not resolver.exists(name):
+                continue
+            filename = resolver.path(name)
+            if filename:
+                return os.path.abspath(filename)
+
+    def get_filecontent(self, name):
+        filename = self.get_filename(name=name)
+        with open(filename, mode='rb') as f:
+            return f.read()
+
+    def get_directory(self, name):
+        return self.get_filename(name=name)
+
+
+def build_resolver(uri, environ):
+    if uri.startswith("http") and uri.endswith(".git"):
+        return GitDataResolver(uri, environ)
+    else:
+        return FileDataResolver(uri)
+
+
+class FileDataResolver:
+
+    def __init__(self, file_dir):
+        self.file_dir = file_dir
+
+    def exists(self, filename):
+        path = os.path.abspath(self.path(filename))
+        return os.path.exists(path) and in_directory(path, self.file_dir)
+
+    def path(self, filename):
+        return os.path.join(self.file_dir, filename)
+
+
+class GitDataResolver(FileDataResolver):
+
+    def __init__(self, repository, environ):
+        self.repository = repository
+        self.updated = False
+        repo_cache = environ.get("GALAXY_TEST_DATA_REPO_CACHE", "test-data-cache")
+        m = hashlib.md5()
+        m.update(smart_str(repository))
+        repo_path = os.path.join(repo_cache, m.hexdigest())
+        super().__init__(repo_path)
+        # My preference would be for this to be false, but for backward compat
+        # will leave it as true for now.
+        self.fetch_data = asbool(environ.get("GALAXY_TEST_FETCH_DATA", "true"))
+
+    def exists(self, filename):
+        exists_now = super().exists(filename)
+        if exists_now or not self.fetch_data or self.updated:
+            return exists_now
+        self.update_repository()
+        return super().exists(filename)
+
+    def update_repository(self):
+        self.updated = True
+        if not os.path.exists(self.file_dir):
+            parent_dir = os.path.dirname(self.file_dir)
+            if not os.path.exists(parent_dir):
+                os.makedirs(parent_dir)
+            self.execute(f"git clone '{self.repository}' '{self.file_dir}'")
+        update_command = UPDATE_TEMPLATE.safe_substitute(dir=self.file_dir)
+        self.execute(update_command)
+
+    def execute(self, cmd):
+        subprocess_kwds = dict(
+            shell=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+        print("Executing %s" % cmd)
+        p = subprocess.Popen(cmd, **subprocess_kwds)
+        stdout, stderr = p.communicate()
+        if p.returncode != 0:
+            kwds = {
+                'dir': self.file_dir,
+                'stdout': stdout,
+                'stderr': stderr,
+            }
+            print(UPDATE_FAILED_TEMPLATE.substitute(**kwds))