Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.tool_shed.tools.data_table_manager
import logging
import os
import shutil
from typing import List
from galaxy.structured_app import StructuredApp
from galaxy.tool_shed.util import hg_util
from galaxy.util import etree
from galaxy.util.tool_shed import xml_util
log = logging.getLogger(__name__)
[docs]class ShedToolDataTableManager:
[docs] def generate_repository_info_elem(
self, tool_shed: str, repository_name: str, changeset_revision: str, owner: str, parent_elem=None, **kwd
) -> etree.Element:
"""Create and return an ElementTree repository info Element."""
if parent_elem is None:
elem = etree.Element("tool_shed_repository")
else:
elem = etree.SubElement(parent_elem, "tool_shed_repository")
tool_shed_elem = etree.SubElement(elem, "tool_shed")
tool_shed_elem.text = tool_shed
repository_name_elem = etree.SubElement(elem, "repository_name")
repository_name_elem.text = repository_name
repository_owner_elem = etree.SubElement(elem, "repository_owner")
repository_owner_elem.text = owner
changeset_revision_elem = etree.SubElement(elem, "installed_changeset_revision")
changeset_revision_elem.text = changeset_revision
# add additional values
# TODO: enhance additional values to allow e.g. use of dict values that will recurse
for key, value in kwd.items():
new_elem = etree.SubElement(elem, key)
new_elem.text = value
return elem
[docs] def generate_repository_info_elem_from_repository(self, tool_shed_repository, parent_elem=None, **kwd):
return self.generate_repository_info_elem(
tool_shed_repository.tool_shed,
tool_shed_repository.name,
tool_shed_repository.installed_changeset_revision,
tool_shed_repository.owner,
parent_elem=parent_elem,
**kwd,
)
[docs] def get_tool_index_sample_files(self, sample_files: List[str]) -> List[str]:
"""
Try to return the list of all appropriate tool data sample files included
in the repository.
"""
tool_index_sample_files = []
for s in sample_files:
# The problem with this is that Galaxy does not follow a standard naming
# convention for file names.
if s.endswith(".loc.sample") or s.endswith(".xml.sample") or s.endswith(".txt.sample"):
tool_index_sample_files.append(str(s))
return tool_index_sample_files
[docs] def handle_missing_data_table_entry(self, relative_install_dir, tool_path, repository_tools_tups):
"""
Inspect each tool to see if any have input parameters that are dynamically
generated select lists that require entries in the tool_data_table_conf.xml
file. This method is called only from Galaxy (not the tool shed) when a
repository is being installed or reinstalled.
"""
missing_data_table_entry = False
for repository_tools_tup in repository_tools_tups:
tup_path, guid, repository_tool = repository_tools_tup
if repository_tool.params_with_missing_data_table_entry:
missing_data_table_entry = True
break
if missing_data_table_entry:
# The repository must contain a tool_data_table_conf.xml.sample file that includes
# all required entries for all tools in the repository.
sample_tool_data_table_conf = hg_util.get_config_from_disk(
"tool_data_table_conf.xml.sample", relative_install_dir
)
if sample_tool_data_table_conf:
# Add entries to the ToolDataTableManager's in-memory data_tables dictionary.
error, message = self.handle_sample_tool_data_table_conf_file(sample_tool_data_table_conf, persist=True)
if error:
# TODO: Do more here than logging an exception.
log.debug(message)
# Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
self.reset_tool_data_tables()
return repository_tools_tups
[docs] def handle_sample_tool_data_table_conf_file(self, filename, persist=False):
"""
Parse the incoming filename and add new entries to the in-memory
self.app.tool_data_tables dictionary. If persist is True (should
only occur if call is from the Galaxy side, not the tool shed), the
new entries will be appended to Galaxy's shed_tool_data_table_conf.xml
file on disk.
"""
error = False
try:
new_table_elems, message = self.app.tool_data_tables.add_new_entries_from_config_file(
config_filename=filename,
tool_data_path=self.app.config.shed_tool_data_path,
shed_tool_data_table_config=self.app.config.shed_tool_data_table_config,
persist=persist,
)
if message:
error = True
except Exception as e:
message = str(e)
error = True
return error, message
[docs] def get_target_install_dir(self, tool_shed_repository):
tool_path, relative_target_dir = tool_shed_repository.get_tool_relative_path(self.app)
# This is where index files will reside on a per repo/installed version basis.
target_dir = os.path.join(self.app.config.shed_tool_data_path, relative_target_dir)
if not os.path.exists(target_dir):
os.makedirs(target_dir)
return target_dir, tool_path, relative_target_dir
[docs] def install_tool_data_tables(self, tool_shed_repository, tool_index_sample_files):
TOOL_DATA_TABLE_FILE_NAME = "tool_data_table_conf.xml"
TOOL_DATA_TABLE_FILE_SAMPLE_NAME = f"{TOOL_DATA_TABLE_FILE_NAME}.sample"
SAMPLE_SUFFIX = ".sample"
SAMPLE_SUFFIX_OFFSET = -len(SAMPLE_SUFFIX)
target_dir, tool_path, relative_target_dir = self.get_target_install_dir(tool_shed_repository)
for sample_file in tool_index_sample_files:
path, filename = os.path.split(sample_file)
target_filename = filename
if target_filename.endswith(SAMPLE_SUFFIX):
target_filename = target_filename[:SAMPLE_SUFFIX_OFFSET]
source_file = os.path.join(tool_path, sample_file)
# We're not currently uninstalling index files, do not overwrite existing files.
target_path_filename = os.path.join(target_dir, target_filename)
if not os.path.exists(target_path_filename) or target_filename == TOOL_DATA_TABLE_FILE_NAME:
shutil.copy2(source_file, target_path_filename)
else:
log.debug(
"Did not copy sample file '%s' to install directory '%s' because file already exists.",
filename,
target_dir,
)
# For provenance and to simplify introspection, let's keep the original data table sample file around.
if filename == TOOL_DATA_TABLE_FILE_SAMPLE_NAME:
shutil.copy2(source_file, os.path.join(target_dir, filename))
tool_data_table_conf_filename = os.path.join(target_dir, TOOL_DATA_TABLE_FILE_NAME)
elems = []
if os.path.exists(tool_data_table_conf_filename):
tree, error_message = xml_util.parse_xml(tool_data_table_conf_filename)
if tree:
for elem in tree.getroot():
# Append individual table elems or other elemes, but not tables elems.
if elem.tag == "tables":
# TODO: this code need to be revised
for _table_elem in elems:
elems.append(elem)
else:
elems.append(elem)
else:
log.debug(
"The '%s' data table file was not found, but was expected to be copied from '%s' during repository installation.",
tool_data_table_conf_filename,
TOOL_DATA_TABLE_FILE_SAMPLE_NAME,
)
for elem in elems:
if elem.tag == "table":
for file_elem in elem.findall("file"):
path = file_elem.get("path", None)
if path:
file_elem.set("path", os.path.normpath(os.path.join(target_dir, os.path.split(path)[1])))
# Store repository info in the table tag set for trace-ability.
self.generate_repository_info_elem_from_repository(tool_shed_repository, parent_elem=elem)
if elems:
# Remove old data_table
os.unlink(tool_data_table_conf_filename)
# Persist new data_table content.
self.app.tool_data_tables.to_xml_file(tool_data_table_conf_filename, elems)
return tool_data_table_conf_filename, elems
[docs] def reset_tool_data_tables(self):
# Reset the tool_data_tables to an empty dictionary.
self.app.tool_data_tables.data_tables = {}
# For backwards compatibility with exisiting data managers
ToolDataTableManager = ShedToolDataTableManager
__all__ = (
"ToolDataTableManager",
"ShedToolDataTableManager",
)