Merge pull request #14668 from jmchilton/tool_util_cleanup

Cleanup tool_util.py

lib/galaxy/tool_shed/galaxy_install/install_manager.py

@@ -162,7 +162,8 @@ class InstallRepositoryManager:
             )
             sample_files = irmm_metadata_dict.get("sample_files", [])
             tool_index_sample_files = stdtm.get_tool_index_sample_files(sample_files)
-            tool_util.copy_sample_files(self.app, tool_index_sample_files, tool_path=tool_path)
+            tool_data_path = self.app.config.tool_data_path
+            tool_util.copy_sample_files(tool_data_path, tool_index_sample_files, tool_path=tool_path)
             sample_files_copied = [str(s) for s in tool_index_sample_files]
             repository_tools_tups = irmm.get_repository_tools_tups()
             if repository_tools_tups:
@@ -177,7 +178,7 @@ class InstallRepositoryManager:
                 # Copy remaining sample files included in the repository to the ~/tool-data directory of the
                 # local Galaxy instance.
                 tool_util.copy_sample_files(
-                    self.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied
+                    tool_data_path, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied
                 )
                 self.tpm.add_to_tool_panel(
                     repository_name=tool_shed_repository.name,

lib/galaxy/tool_shed/metadata/metadata_generator.py

@@ -313,7 +313,7 @@ class MetadataGenerator:
             # can load tools that depend on them.
             data_table_conf_xml_sample_files = []
             for sample_file in sample_file_copy_paths:
-                tool_util.copy_sample_file(self.app, sample_file, dest_path=work_dir)
+                tool_util.copy_sample_file(self.app.config.tool_data_path, sample_file, dest_path=work_dir)
                 # If the list of sample files includes a tool_data_table_conf.xml.sample file, load
                 # its table elements into memory.
                 relative_path, filename = os.path.split(sample_file)

lib/galaxy/tool_shed/util/tool_util.py

@@ -1,6 +1,7 @@
 import logging
 import os
 import shutil
+from typing import Optional
 
 import galaxy.tools
 from galaxy import util
@@ -39,14 +40,15 @@ def build_tool_panel_section_select_field(app):
     return select_field
 
 
-def copy_sample_file(app, filename, dest_path=None):
+def copy_sample_file(tool_data_path: str, filename: str, dest_path: Optional[str] = None) -> str:
     """
     Copies a sample file at `filename` to `the dest_path`
     directory and strips the '.sample' extensions from `filename`.
     Returns the path to the copied file (with the .sample extension).
     """
     if dest_path is None:
-        dest_path = os.path.abspath(app.config.tool_data_path)
+        dest_path = tool_data_path
+    assert dest_path
     sample_file_name = basic_util.strip_path(filename)
     copied_file = sample_file_name.rsplit(".sample", 1)[0]
     full_source_path = os.path.abspath(filename)
@@ -63,7 +65,13 @@ def copy_sample_file(app, filename, dest_path=None):
     return non_sample_path
 
 
-def copy_sample_files(app, sample_files, tool_path=None, sample_files_copied=None, dest_path=None):
+def copy_sample_files(
+    tool_data_path: str,
+    sample_files,
+    tool_path: Optional[str] = None,
+    sample_files_copied=None,
+    dest_path: Optional[str] = None,
+) -> None:
     """
     Copy all appropriate files to dest_path in the local Galaxy environment that have not
     already been copied.  Those that have been copied are contained in sample_files_copied.
@@ -79,13 +87,18 @@ def copy_sample_files(app, sample_files, tool_path=None, sample_files_copied=Non
             if tool_path:
                 filename = os.path.join(tool_path, filename)
             # Attempt to ensure we're copying an appropriate file.
-            if is_data_index_sample_file(filename):
-                copy_sample_file(app, filename, dest_path=dest_path)
+            if _is_data_index_sample_file(filename):
+                copy_sample_file(tool_data_path, filename, dest_path=dest_path)
 
 
 def generate_message_for_invalid_tools(
-    app, invalid_file_tups, repository, metadata_dict, as_html=True, displaying_invalid_tool=False
-):
+    app,
+    invalid_file_tups: list,
+    repository,
+    metadata_dict: Optional[dict],
+    as_html: bool = True,
+    displaying_invalid_tool: bool = False,
+) -> str:
     if as_html:
         new_line = "<br/>"
         bold_start = "<b>"
@@ -133,23 +146,6 @@ def generate_message_for_invalid_tools(
     return message
 
 
-def get_tool_path_install_dir(partial_install_dir, shed_tool_conf_dict, tool_dict, config_elems):
-    for elem in config_elems:
-        if elem.tag == "tool":
-            if elem.get("guid") == tool_dict["guid"]:
-                tool_path = shed_tool_conf_dict["tool_path"]
-                relative_install_dir = os.path.join(tool_path, partial_install_dir)
-                return tool_path, relative_install_dir
-        elif elem.tag == "section":
-            for section_elem in elem:
-                if section_elem.tag == "tool":
-                    if section_elem.get("guid") == tool_dict["guid"]:
-                        tool_path = shed_tool_conf_dict["tool_path"]
-                        relative_install_dir = os.path.join(tool_path, partial_install_dir)
-                        return tool_path, relative_install_dir
-    return None, None
-
-
 def handle_missing_index_file(app, tool_path, sample_files, repository_tools_tups, sample_files_copied):
     """
     Inspect each tool to see if it has any input parameters that are dynamically
@@ -175,7 +171,7 @@ def handle_missing_index_file(app, tool_path, sample_files, repository_tools_tup
     return repository_tools_tups, sample_files_copied
 
 
-def is_data_index_sample_file(file_path):
+def _is_data_index_sample_file(file_path):
     """
     Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when
     a tool shed repository is being installed into a Galaxy instance.
@@ -254,9 +250,7 @@ __all__ = (
     "copy_sample_file",
     "copy_sample_files",
     "generate_message_for_invalid_tools",
-    "get_tool_path_install_dir",
     "handle_missing_index_file",
-    "is_data_index_sample_file",
     "new_state",
     "panel_entry_per_tool",
 )

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -14,20 +14,24 @@ from galaxy.exceptions import ConfigDoesNotAllowException
 from galaxy.tool_shed.galaxy_install import install_manager
 from galaxy.tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
 from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
+from galaxy.tool_shed.util import (
+    hg_util,
+    tool_dependency_util,
+    tool_util,
+)
 from galaxy.tool_util.deps import views
 from galaxy.util import unicodify
+from galaxy.util.tool_shed import (
+    common_util,
+    encoding_util,
+)
 from galaxy.web.form_builder import CheckboxField
 from tool_shed.galaxy_install import dependency_display
 from tool_shed.galaxy_install.grids import admin_toolshed_grids
 from tool_shed.util import (
-    common_util,
-    encoding_util,
-    hg_util,
     readme_util,
     repository_util,
     shed_util_common as suc,
-    tool_dependency_util,
-    tool_util,
 )
 from tool_shed.util.web_util import escape
 from .admin import AdminGalaxy

lib/tool_shed/tools/tool_validator.py

@@ -65,7 +65,7 @@ class ToolValidator(GalaxyToolValidator):
                 for name in files:
                     if name.endswith(".sample"):
                         relative_path = os.path.join(root, name)
-                        tool_util.copy_sample_file(self.app, relative_path, dest_path=dest_path)
+                        tool_util.copy_sample_file(self.app.config.tool_data_path, relative_path, dest_path=dest_path)
                         sample_files.append(name)
         return sample_files
 

lib/tool_shed/util/tool_util.py

@@ -1,25 +1,13 @@
 from galaxy.tool_shed.util.tool_util import (
-    build_shed_tool_conf_select_field,
-    build_tool_panel_section_select_field,
     copy_sample_file,
     copy_sample_files,
     generate_message_for_invalid_tools,
-    get_tool_path_install_dir,
-    handle_missing_index_file,
-    is_data_index_sample_file,
     new_state,
-    panel_entry_per_tool,
 )
 
 __all__ = (
-    "build_shed_tool_conf_select_field",
-    "build_tool_panel_section_select_field",
     "copy_sample_file",
     "copy_sample_files",
     "generate_message_for_invalid_tools",
-    "get_tool_path_install_dir",
-    "handle_missing_index_file",
-    "is_data_index_sample_file",
     "new_state",
-    "panel_entry_per_tool",
 )