Merge pull request #14615 from jmchilton/ts_cleanup_3

More Tool Shed Cleanup

lib/galaxy/model/tool_shed_install/__init__.py

@@ -727,13 +727,6 @@ class ToolDependency(Base, _HasTable):
             self.installation_status.UNINSTALLED,
         ]
 
-    def get_env_shell_file_path(self, app):
-        installation_directory = self.installation_directory(app)
-        file_path = os.path.join(installation_directory, "env.sh")
-        if os.path.exists(file_path):
-            return file_path
-        return None
-
     @property
     def in_error_state(self):
         return self.status == self.installation_status.ERROR

lib/galaxy/tool_shed/galaxy_install/install_manager.py

@@ -42,7 +42,7 @@ class InstallRepositoryManager:
         else:
             self.tpm = tpm
 
-    def get_repository_components_for_installation(
+    def _get_repository_components_for_installation(
         self, encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys
     ):
         """
@@ -468,7 +468,7 @@ class InstallRepositoryManager:
                 self.install_model.ToolShedRepository.installation_status.UNINSTALLED,
             ]:
                 repositories_for_installation.append(repository)
-                repo_info_dict, tool_panel_section_key = self.get_repository_components_for_installation(
+                repo_info_dict, tool_panel_section_key = self._get_repository_components_for_installation(
                     tsr_id, ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys
                 )
                 filtered_repo_info_dicts.append(repo_info_dict)
@@ -797,7 +797,7 @@ class InstallRepositoryManager:
                         (
                             prior_repo_info_dict,
                             prior_tool_panel_section_key,
-                        ) = self.get_repository_components_for_installation(
+                        ) = self._get_repository_components_for_installation(
                             prior_install_required_id,
                             tsr_ids,
                             repo_info_dicts,
@@ -806,7 +806,7 @@ class InstallRepositoryManager:
                         ordered_tsr_ids.append(prior_install_required_id)
                         ordered_repo_info_dicts.append(prior_repo_info_dict)
                         ordered_tool_panel_section_keys.append(prior_tool_panel_section_key)
-                repo_info_dict, tool_panel_section_key = self.get_repository_components_for_installation(
+                repo_info_dict, tool_panel_section_key = self._get_repository_components_for_installation(
                     tsr_id, tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys
                 )
                 if tsr_id not in ordered_tsr_ids:

lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py

@@ -594,40 +594,6 @@ class InstalledRepositoryManager:
                 return relative_path
         return None
 
-    def get_runtime_dependent_tool_dependency_tuples(self, tool_dependency, status=None):
-        """
-        Return the list of tool dependency objects that require the received tool dependency at run time.  The returned
-        list will be filtered by the received status if it is not None.  This method is called only from Galaxy.
-        """
-        runtime_dependent_tool_dependency_tups = []
-        required_env_shell_file_path = tool_dependency.get_env_shell_file_path(self.app)
-        if required_env_shell_file_path:
-            required_env_shell_file_path = os.path.abspath(required_env_shell_file_path)
-        if required_env_shell_file_path is not None:
-            for td in self.app.install_model.context.query(self.app.install_model.ToolDependency):
-                if status is None or td.status == status:
-                    env_shell_file_path = td.get_env_shell_file_path(self.app)
-                    if env_shell_file_path is not None:
-                        try:
-                            contents = open(env_shell_file_path).read()
-                        except Exception as e:
-                            contents = None
-                            log.debug(
-                                "Error reading file %s, so cannot determine if package %s requires package %s at run time: %s"
-                                % (str(env_shell_file_path), str(td.name), str(tool_dependency.name), str(e))
-                            )
-                        if contents is not None and contents.find(required_env_shell_file_path) >= 0:
-                            td_tuple = self.get_tool_dependency_tuple_for_installed_repository_manager(td)
-                            runtime_dependent_tool_dependency_tups.append(td_tuple)
-        return runtime_dependent_tool_dependency_tups
-
-    def get_tool_dependency_tuple_for_installed_repository_manager(self, tool_dependency):
-        if tool_dependency.type is None:
-            type = None
-        else:
-            type = str(tool_dependency.type)
-        return (tool_dependency.tool_shed_repository_id, str(tool_dependency.name), str(tool_dependency.version), type)
-
     def handle_existing_tool_dependencies_that_changed_in_update(
         self, repository, original_dependency_dict, new_dependency_dict
     ):

lib/galaxy/tool_shed/metadata/metadata_generator.py

@@ -120,7 +120,7 @@ class MetadataGenerator:
             suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME,
         ]
 
-    def generate_data_manager_metadata(
+    def _generate_data_manager_metadata(
         self, repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None
     ):
         """
@@ -415,7 +415,7 @@ class MetadataGenerator:
                                     )
         # Handle any data manager entries
         data_manager_config = get_config_from_disk(suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir)
-        metadata_dict = self.generate_data_manager_metadata(
+        metadata_dict = self._generate_data_manager_metadata(
             files_dir, data_manager_config, metadata_dict, shed_config_dict=self.shed_config_dict
         )
 

lib/galaxy/util/tool_shed/xml_util.py

@@ -1,6 +1,10 @@
 import logging
 import os
 import tempfile
+from typing import (
+    Optional,
+    Tuple,
+)
 
 from galaxy.util import (
     etree,
@@ -21,51 +25,7 @@ def create_and_write_tmp_file(elem):
     return tmp_filename
 
 
-def create_element(tag, attributes=None, sub_elements=None):
-    """
-    Create a new element whose tag is the value of the received tag, and whose attributes are all
-    key / value pairs in the received attributes and sub_elements.
-    """
-    if tag:
-        elem = etree.Element(tag)
-        if attributes:
-            # The received attributes is an odict to preserve ordering.
-            for k, v in attributes.items():
-                elem.set(k, v)
-        if sub_elements:
-            # The received attributes is an odict.  These handle information that tends to be
-            # long text including paragraphs (e.g., description and long_description.
-            for k, v in sub_elements.items():
-                # Don't include fields that are blank.
-                if v:
-                    if k == "packages":
-                        # The received sub_elements is an odict whose key is 'packages' and whose
-                        # value is a list of ( name, version ) tuples.
-                        for v_tuple in v:
-                            sub_elem = etree.SubElement(elem, "package")
-                            sub_elem_name, sub_elem_version = v_tuple
-                            sub_elem.set("name", sub_elem_name)
-                            sub_elem.set("version", sub_elem_version)
-                    elif isinstance(v, list):
-                        sub_elem = etree.SubElement(elem, k)
-                        # If v is a list, then it must be a list of tuples where the first
-                        # item is the tag and the second item is the text value.
-                        for v_tuple in v:
-                            if len(v_tuple) == 2:
-                                v_tag = v_tuple[0]
-                                v_text = v_tuple[1]
-                                # Don't include fields that are blank.
-                                if v_text:
-                                    v_elem = etree.SubElement(sub_elem, v_tag)
-                                    v_elem.text = v_text
-                    else:
-                        sub_elem = etree.SubElement(elem, k)
-                        sub_elem.text = v
-        return elem
-    return None
-
-
-def parse_xml(file_name, check_exists=True):
+def parse_xml(file_name, check_exists=True) -> Tuple[Optional[etree.ElementTree], str]:
     """Returns a parsed xml tree with comments intact."""
     error_message = ""
     if check_exists and not os.path.exists(file_name):
@@ -83,6 +43,5 @@ def parse_xml(file_name, check_exists=True):
 
 __all__ = (
     "create_and_write_tmp_file",
-    "create_element",
     "parse_xml",
 )

lib/tool_shed/dependencies/attribute_handlers.py

@@ -1,7 +1,16 @@
 import copy
 import logging
+from typing import (
+    Dict,
+    List,
+    Optional,
+    Tuple,
+)
 
-from galaxy.util import asbool
+from galaxy.util import (
+    asbool,
+    etree,
+)
 from galaxy.web import url_for
 from tool_shed.dependencies.tool import tag_attribute_handler
 from tool_shed.repository_types.util import (
@@ -96,7 +105,7 @@ class RepositoryDependencyAttributeHandler:
                 prior_installation_required = elem.get("prior_installation_required")
                 if asbool(prior_installation_required):
                     attributes["prior_installation_required"] = "True"
-                new_elem = xml_util.create_element("repository", attributes=attributes, sub_elements=sub_elements)
+                new_elem = _create_element("repository", attributes=attributes, sub_elements=sub_elements)
                 altered = True
             return altered, new_elem, error_message
         # From here on we're populating the toolshed and changeset_revision attributes if necessary.
@@ -200,3 +209,51 @@ class ToolDependencyAttributeHandler:
         root = tree.getroot()
         altered, new_root, error_message = tah.process_config(root, skip_actions_tags=False)
         return altered, new_root, error_message
+
+
+def _create_element(
+    tag: str,
+    attributes: Optional[Dict[str, str]] = None,
+    sub_elements: Optional[Dict[str, List[Tuple[str, str]]]] = None,
+) -> Optional[etree.Element]:
+    """
+    Create a new element whose tag is the value of the received tag, and whose attributes are all
+    key / value pairs in the received attributes and sub_elements.
+    """
+    if tag:
+        elem = etree.Element(tag)
+        if attributes:
+            # The received attributes is an odict to preserve ordering.
+            for k, attribute_value in attributes.items():
+                elem.set(k, attribute_value)
+        if sub_elements:
+            # The received attributes is an odict.  These handle information that tends to be
+            # long text including paragraphs (e.g., description and long_description.
+            for k, v in sub_elements.items():
+                # Don't include fields that are blank.
+                if v:
+                    if k == "packages":
+                        # The received sub_elements is an odict whose key is 'packages' and whose
+                        # value is a list of ( name, version ) tuples.
+                        for v_tuple in v:
+                            sub_elem = etree.SubElement(elem, "package")
+                            sub_elem_name, sub_elem_version = v_tuple
+                            sub_elem.set("name", sub_elem_name)
+                            sub_elem.set("version", sub_elem_version)
+                    elif isinstance(v, list):
+                        sub_elem = etree.SubElement(elem, k)
+                        # If v is a list, then it must be a list of tuples where the first
+                        # item is the tag and the second item is the text value.
+                        for v_tuple in v:
+                            if len(v_tuple) == 2:
+                                v_tag = v_tuple[0]
+                                v_text = v_tuple[1]
+                                # Don't include fields that are blank.
+                                if v_text:
+                                    v_elem = etree.SubElement(sub_elem, v_tag)
+                                    v_elem.text = v_text
+                    else:
+                        sub_elem = etree.SubElement(elem, k)
+                        sub_elem.text = v
+        return elem
+    return None

lib/tool_shed/util/xml_util.py

@@ -1,11 +1,9 @@
 from galaxy.util.tool_shed.xml_util import (
     create_and_write_tmp_file,
-    create_element,
     parse_xml,
 )
 
 __all__ = (
     "create_and_write_tmp_file",
-    "create_element",
     "parse_xml",
 )