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Source code for galaxy.tool_shed.tools.data_table_manager
import logging
import os
import shutil
from typing import (
List,
TYPE_CHECKING,
Union,
)
from galaxy.tool_shed.galaxy_install.client import InstallationTarget
from galaxy.tool_shed.util import hg_util
from galaxy.util import etree
from galaxy.util.tool_shed import xml_util
if TYPE_CHECKING:
from galaxy.structured_app import BasicSharedApp
log = logging.getLogger(__name__)
RequiredAppT = Union["BasicSharedApp", InstallationTarget]
[docs]class ShedToolDataTableManager:
app: RequiredAppT
[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",
)