Warning
This document is for an in-development version 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_util.data
"""
Manage tool data tables, which store (at the application level) data that is
used by tools, for example in the generation of dynamic options. Tables are
loaded and stored by names which tools use to refer to them. This allows
users to configure data tables for a local Galaxy instance without needing
to modify the tool configurations.
"""
import errno
import hashlib
import json
import logging
import os
import os.path
import re
import string
import time
from dataclasses import dataclass
from glob import glob
from tempfile import NamedTemporaryFile
from typing import (
Any,
BinaryIO,
Callable,
cast,
Dict,
List,
Optional,
overload,
Set,
Tuple,
Type,
TYPE_CHECKING,
Union,
)
from typing_extensions import (
Protocol,
TypedDict,
)
from galaxy import util
from galaxy.exceptions import MessageException
from galaxy.util import (
Element,
requests,
RW_R__R__,
)
from galaxy.util.compression_utils import decompress_path_to_directory
from galaxy.util.dictifiable import Dictifiable
from galaxy.util.filelock import FileLock
from galaxy.util.path import StrPath
from galaxy.util.renamed_temporary_file import RenamedTemporaryFile
from galaxy.util.template import fill_template
from ._schema import (
ToolDataEntry,
ToolDataEntryList,
)
from .bundles.models import (
DataTableBundle,
DataTableBundleProcessorDescription,
RepoInfo,
)
if TYPE_CHECKING:
from galaxy.tools.data_manager.manager import DataManager
log = logging.getLogger(__name__)
BUNDLE_INDEX_FILE_NAME = "_gx_data_bundle_index.json"
DEFAULT_TABLE_TYPE = "tabular"
TOOL_DATA_TABLE_CONF_XML = """<?xml version="1.0"?>
<tables>
</tables>
"""
# Internally just the first two - but tool shed code (data_manager_manual) will still
# pass DataManager in.
EntrySource = Optional[Union[dict, RepoInfo, "DataManager"]]
class StoresConfigFilePaths(Protocol):
def get(self, key: Any, default: Optional[Any]) -> Optional[Any]: ...
class ToolDataPathFiles:
update_time: float
def __init__(self, tool_data_path):
self.tool_data_path = os.path.abspath(tool_data_path)
self.update_time = 0
@property
def tool_data_path_files(self) -> Set[str]:
if time.time() - self.update_time > 1:
self.update_files()
return self._tool_data_path_files
def update_files(self) -> None:
try:
content = os.walk(self.tool_data_path)
self._tool_data_path_files = set(
filter(
os.path.exists,
[
os.path.join(dirpath, fn)
for dirpath, _, fn_list in content
for fn in fn_list
if fn and fn.endswith(".loc") or fn.endswith(".loc.sample")
],
)
)
self.update_time = time.time()
except Exception:
log.exception("Failed to update _tool_data_path_files")
self._tool_data_path_files = set()
def exists(self, path: str) -> bool:
path = os.path.abspath(path)
if path in self.tool_data_path_files:
return True
else:
return os.path.exists(path)
ErrorListT = List[str]
class FileNameInfoT(TypedDict):
found: bool
filename: str
from_shed_config: bool
tool_data_path: Optional[StrPath]
config_element: Optional[Element]
tool_shed_repository: Optional[Dict[str, Any]]
errors: ErrorListT
LoadInfoT = Tuple[Tuple[Element, Optional[StrPath]], Dict[str, Any]]
[docs]class ToolDataTable(Dictifiable):
type_key: str
data: List[List[str]]
empty_field_value: str
empty_field_values: Dict[Optional[str], str]
filenames: Dict[str, FileNameInfoT]
_load_info: LoadInfoT
_merged_load_info: List[Tuple[Type["ToolDataTable"], LoadInfoT]]
[docs] @classmethod
def from_dict(cls, d):
data_table_class = globals()[d["model_class"]]
data_table = data_table_class.__new__(data_table_class)
for attr, val in d.items():
if not attr == "model_class":
setattr(data_table, attr, val)
data_table._loaded_content_version = 1
return data_table
[docs] def __init__(
self,
config_element: Element,
tool_data_path: Optional[StrPath],
tool_data_path_files: ToolDataPathFiles,
from_shed_config: bool = False,
filename: Optional[StrPath] = None,
other_config_dict: Optional[StoresConfigFilePaths] = None,
) -> None:
name = config_element.get("name")
assert name
self.name = name
self.empty_field_value = config_element.get("empty_field_value", "")
self.empty_field_values: Dict[str, str] = {}
self.allow_duplicate_entries = util.asbool(config_element.get("allow_duplicate_entries", True))
self.here = os.path.dirname(filename) if filename else None
self.filenames: Dict[str, FileNameInfoT] = {}
self.tool_data_path = tool_data_path
self.tool_data_path_files = tool_data_path_files
self.other_config_dict = other_config_dict or {}
self.missing_index_file: Optional[str] = None
# increment this variable any time a new entry is added, or when the table is totally reloaded
# This value has no external meaning, and does not represent an abstract version of the underlying data
self._loaded_content_version = 1
self._load_info = (
(config_element, tool_data_path),
{
"from_shed_config": from_shed_config,
"tool_data_path_files": self.tool_data_path_files,
"other_config_dict": other_config_dict,
"filename": filename,
},
)
self._merged_load_info: List[Tuple[Type[ToolDataTable], Tuple[Tuple[Element, StrPath], Dict[str, Any]]]] = []
def _update_version(self, version: Optional[int] = None) -> int:
if version is not None:
self._loaded_content_version = version
else:
self._loaded_content_version += 1
return self._loaded_content_version
[docs] def get_empty_field_by_name(self, name: Optional[str]) -> str:
return self.empty_field_values.get(name, self.empty_field_value)
def _add_entry(
self,
entry: Union[List[str], Dict[str, str]],
allow_duplicates: bool = True,
persist: bool = False,
entry_source: EntrySource = None,
tool_data_file_path: Optional[str] = None,
use_first_file_path: bool = False,
**kwd,
) -> None:
raise NotImplementedError("Abstract method")
[docs] def add_entry(
self,
entry: Union[List[str], Dict[str, str]],
allow_duplicates: bool = True,
persist: bool = False,
entry_source: EntrySource = None,
tool_data_file_path: Optional[str] = None,
use_first_file_path: bool = False,
**kwd,
) -> int:
self._add_entry(
entry,
allow_duplicates=allow_duplicates,
persist=persist,
entry_source=entry_source,
tool_data_file_path=tool_data_file_path,
use_first_file_path=use_first_file_path,
**kwd,
)
return self._update_version()
[docs] def add_entries(
self,
entries: List[List[str]],
allow_duplicates: bool = True,
persist: bool = False,
entry_source: EntrySource = None,
**kwd,
) -> int:
for entry in entries:
try:
self.add_entry(
entry, allow_duplicates=allow_duplicates, persist=persist, entry_source=entry_source, **kwd
)
except MessageException as e:
if e.type == "warning":
log.warning(str(e))
else:
log.error(str(e))
except Exception as e:
log.error(str(e))
return self._loaded_content_version
def _remove_entry(self, values):
raise NotImplementedError("Abstract method")
[docs] def is_current_version(self, other_version):
return self._loaded_content_version == other_version
[docs] def merge_tool_data_table(
self,
other_table: "ToolDataTable",
allow_duplicates: bool = True,
persist: bool = False,
**kwd,
) -> int:
raise NotImplementedError("Abstract method")
[docs] def reload_from_files(self) -> int:
new_version = self._update_version()
merged_info = self._merged_load_info
self.__init__(*self._load_info[0], **self._load_info[1]) # type: ignore[misc]
self._update_version(version=new_version)
for tool_data_table_class, load_info in merged_info:
self.merge_tool_data_table(tool_data_table_class(*load_info[0], **load_info[1]), allow_duplicates=False)
return self._update_version()
[docs]class TabularToolDataTable(ToolDataTable):
"""
Data stored in a tabular / separated value format on disk, allows multiple
files to be merged but all must have the same column definitions:
.. code-block:: xml
<table type="tabular" name="test">
<column name='...' index = '...' />
<file path="..." />
<file path="..." />
</table>
"""
dict_collection_visible_keys = ["name"]
dict_element_visible_keys = ["name", "fields"]
dict_export_visible_keys = ["name", "data", "largest_index", "columns", "missing_index_file"]
type_key = "tabular"
[docs] def __init__(
self,
config_element: Element,
tool_data_path: Optional[StrPath],
tool_data_path_files: ToolDataPathFiles,
from_shed_config: bool = False,
filename: Optional[StrPath] = None,
other_config_dict: Optional[StoresConfigFilePaths] = None,
) -> None:
super().__init__(
config_element,
tool_data_path,
tool_data_path_files,
from_shed_config,
filename,
other_config_dict=other_config_dict,
)
self.config_element = config_element
self.data = []
self.configure_and_load(config_element, tool_data_path, from_shed_config)
[docs] def configure_and_load(
self,
config_element: Element,
tool_data_path: Optional[StrPath],
from_shed_config: bool = False,
url_timeout: float = 10,
) -> None:
"""
Configure and load table from an XML element.
"""
self.separator = config_element.get("separator", "\t")
self.comment_char = config_element.get("comment_char", "#")
# Configure columns
self.parse_column_spec(config_element)
# store repo info if available:
repo_elem = config_element.find("tool_shed_repository")
if repo_elem is not None:
tool_shed_elem = repo_elem.find("tool_shed")
assert tool_shed_elem is not None
repository_name_elem = repo_elem.find("repository_name")
assert repository_name_elem is not None
repository_owner_elem = repo_elem.find("repository_owner")
assert repository_owner_elem is not None
installed_changeset_revision_elem = repo_elem.find("installed_changeset_revision")
assert installed_changeset_revision_elem is not None
repo_info = dict(
tool_shed=tool_shed_elem.text,
name=repository_name_elem.text,
owner=repository_owner_elem.text,
installed_changeset_revision=installed_changeset_revision_elem.text,
)
else:
repo_info = None
# Read every file
for file_element in config_element.findall("file"):
tmp_file = None
filename = file_element.get("path", None)
if filename is None:
# Handle URLs as files
filename = file_element.get("url", None)
if filename:
tmp_file = NamedTemporaryFile(prefix=f"TTDT_URL_{self.name}-", mode="w")
try:
tmp_file.write(requests.get(filename, timeout=url_timeout).text)
except Exception as e:
log.error('Error loading Data Table URL "%s": %s', filename, e)
continue
log.debug('Loading Data Table URL "%s" as filename "%s".', filename, tmp_file.name)
filename = tmp_file.name
tmp_file.flush()
else:
# Pull the filename from a global config
filename = file_element.get("from_config")
if filename:
filename = self.other_config_dict.get(filename, None)
if filename:
filename = _expand_here_template(filename, here=self.here)
found = False
if filename is None:
log.debug(
"Encountered a file element (%s) that does not contain a path value when loading tool data table '%s'.",
util.xml_to_string(file_element),
self.name,
)
continue
# FIXME: splitting on and merging paths from a configuration file when loading is wonky
# Data should exist on disk in the state needed, i.e. the xml configuration should
# point directly to the desired file to load. Munging of the tool_data_tables_conf.xml.sample
# can be done during installing / testing / metadata resetting with the creation of a proper
# tool_data_tables_conf.xml file, containing correct <file path=> attributes. Allowing a
# path.join with a different root should be allowed, but splitting should not be necessary.
if tool_data_path and from_shed_config:
# Must identify with from_shed_config as well, because the
# regular galaxy app has and uses tool_data_path.
# We're loading a tool in the tool shed, so we cannot use the Galaxy tool-data
# directory which is hard-coded into the tool_data_table_conf.xml entries.
filename = os.path.split(filename)[1]
filename = os.path.join(tool_data_path, filename)
if self.tool_data_path_files.exists(filename):
found = True
elif not os.path.isabs(filename):
# Since the path attribute can include a hard-coded path to a specific directory
# (e.g., <file path="tool-data/cg_crr_files.loc" />) which may not be the same value
# as self.tool_data_path, we'll parse the path to get the filename and see if it is
# in self.tool_data_path.
file_path, file_name = os.path.split(filename)
if file_path != self.tool_data_path:
assert self.tool_data_path
corrected_filename = os.path.join(self.tool_data_path, file_name)
if self.tool_data_path_files.exists(corrected_filename):
filename = corrected_filename
found = True
elif not from_shed_config and self.tool_data_path_files.exists(f"{corrected_filename}.sample"):
log.info(f"Could not find tool data {corrected_filename}, reading sample")
filename = f"{corrected_filename}.sample"
found = True
errors: ErrorListT = []
if found:
self.extend_data_with(filename, errors=errors)
self._update_version()
else:
self.missing_index_file = filename
# TODO: some data tables need to exist (even if they are empty)
# for tools to load. In an installed Galaxy environment and the
# default tool_data_table_conf.xml, this will emit spurious
# warnings about missing location files that would otherwise be
# empty and we don't care about unless the admin chooses to
# populate them.
log.warning(f"Cannot find index file '{filename}' for tool data table '{self.name}'")
if filename not in self.filenames or not self.filenames[filename]["found"]:
self.filenames[filename] = dict(
found=found,
filename=filename,
from_shed_config=from_shed_config,
tool_data_path=tool_data_path,
config_element=config_element,
tool_shed_repository=repo_info,
errors=errors,
)
else:
log.debug(
"Filename '%s' already exists in filenames (%s), not adding", filename, list(self.filenames.keys())
)
# Remove URL tmp file
if tmp_file is not None:
tmp_file.close()
[docs] def merge_tool_data_table(self, other_table, allow_duplicates=True, persist=False, **kwd):
assert (
self.columns == other_table.columns
), f"Merging tabular data tables with non matching columns is not allowed: {self.name}:{self.columns} != {other_table.name}:{other_table.columns}"
# merge filename info
for filename, info in other_table.filenames.items():
if filename not in self.filenames:
self.filenames[filename] = info
# save info about table
self._merged_load_info.append((other_table.__class__, other_table._load_info))
# If we are merging in a data table that does not allow duplicates, enforce that upon the data table
if self.allow_duplicate_entries and not other_table.allow_duplicate_entries:
log.debug(
'While attempting to merge tool data table "%s", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries.',
self.name,
)
self.allow_duplicate_entries = False
self._deduplicate_data()
# add data entries and return current data table version
return self.add_entries(other_table.data, allow_duplicates=allow_duplicates, persist=persist, **kwd)
[docs] def handle_found_index_file(self, filename):
self.missing_index_file = None
self.extend_data_with(filename)
# This method is used in tools, so need to keep its API stable
[docs] def get_field(self, value):
rval = None
for i in self.get_named_fields_list():
if i["value"] == value:
rval = TabularToolDataField(i)
return rval
# This method is used in tools, so need to keep its API stable
[docs] def get_named_fields_list(self) -> List[Dict[Union[str, int], str]]:
rval = []
named_columns = self.get_column_name_list()
for fields in self.get_fields():
field_dict = {}
for i, field in enumerate(fields):
if i == len(named_columns):
break
field_name: Optional[Union[str, int]] = named_columns[i]
if field_name is None:
field_name = i # check that this is supposed to be 0 based.
field_dict[field_name] = field
rval.append(field_dict)
return rval
[docs] def parse_column_spec(self, config_element: Element) -> None:
"""
Parse column definitions, which can either be a set of 'column' elements
with a name and index (as in dynamic options config), or a shorthand
comma separated list of names in order as the text of a 'column_names'
element.
A column named 'value' is required.
"""
self.columns: Dict[str, int] = {}
if config_element.find("columns") is not None:
column_names = util.xml_text(config_element.find("columns"))
column_names = [n.strip() for n in column_names.split(",")]
for index, name in enumerate(column_names):
self.columns[name] = index
self.largest_index = index
else:
self.largest_index = 0
for column_elem in config_element.findall("column"):
name = column_elem.get("name")
assert name is not None, "Required 'name' attribute missing from column def"
index_attr = column_elem.get("index")
assert index_attr is not None, "Required 'index' attribute missing from column def"
index = int(index_attr)
self.columns[name] = index
if index > self.largest_index:
self.largest_index = index
empty_field_value = column_elem.get("empty_field_value", None)
if empty_field_value is not None:
self.empty_field_values[name] = empty_field_value
assert "value" in self.columns, "Required 'value' column missing from column def"
if "name" not in self.columns:
self.columns["name"] = self.columns["value"]
[docs] def extend_data_with(self, filename: str, errors: Optional[ErrorListT] = None) -> None:
here = os.path.dirname(os.path.abspath(filename))
self.data.extend(self.parse_file_fields(filename, errors=errors, here=here))
if not self.allow_duplicate_entries:
self._deduplicate_data()
[docs] def parse_file_fields(
self, filename: str, errors: Optional[ErrorListT] = None, here: str = "__HERE__"
) -> List[List[str]]:
"""
Parse separated lines from file and return a list of tuples.
TODO: Allow named access to fields using the column names.
"""
separator_char = "<TAB>" if self.separator == "\t" else self.separator
rval = []
with open(filename) as fh:
for i, line in enumerate(fh):
if line.lstrip().startswith(self.comment_char):
continue
line = line.rstrip("\n\r")
if line:
line = _expand_here_template(line, here=here)
fields = line.split(self.separator)
if self.largest_index < len(fields):
rval.append(fields)
else:
line_error = (
"Line %i in tool data table '%s' is invalid (HINT: '%s' characters must be used to separate fields):\n%s"
% ((i + 1), self.name, separator_char, line)
)
if errors is not None:
errors.append(line_error)
log.warning(line_error)
log.debug("Loaded %i lines from '%s' for '%s'", len(rval), filename, self.name)
return rval
# This method is used in tools, so need to keep its API stable
[docs] def get_column_name_list(self) -> List[Union[str, None]]:
rval: List[Union[str, None]] = []
for i in range(self.largest_index + 1):
found_column = False
for name, index in self.columns.items():
if index == i:
if not found_column:
rval.append(name)
elif name == "value":
# the column named 'value' always has priority over other named columns
rval[-1] = name
found_column = True
if not found_column:
rval.append(None)
return rval
# This method is used in tools, so need to keep its API stable
[docs] def get_entry(self, query_attr: str, query_val: str, return_attr: str, default: None = None):
"""
Returns table entry associated with a col/val pair.
"""
rval = self.get_entries(query_attr, query_val, return_attr, limit=1)
if rval:
return rval[0]
return default
[docs] def get_entries(self, query_attr: str, query_val: str, return_attr: str, limit=None) -> List:
"""
Returns table entries associated with a col/val pair.
"""
query_col = self.columns.get(query_attr, None)
if query_col is None:
return []
if return_attr is not None:
return_col = self.columns.get(return_attr, None)
if return_col is None:
return []
rval = []
# Look for table entry.
for fields in self.get_fields():
if fields[query_col] == query_val:
if return_attr is None:
field_dict = {}
for i, col_name in enumerate(self.get_column_name_list()):
field_dict[col_name or i] = fields[i]
rval.append(field_dict)
else:
rval.append(fields[return_col])
if limit is not None and len(rval) == limit:
break
return rval
# This method is used in tools, so need to keep its API stable
[docs] def get_filename_for_source(self, source: EntrySource, default: Optional[str] = None) -> Optional[str]:
source_repo_info: Optional[dict] = None
if source:
# if dict, assume is compatible info dict, otherwise call method
if isinstance(source, dict):
source_repo_info = source
else:
source_repo_info_model: Optional[RepoInfo]
if source is None or isinstance(source, RepoInfo):
source_repo_info_model = source
else:
# we have a data manager, use its repo_info method
source_data_manager = cast("DataManager", source)
source_repo_info_model = source_data_manager.repo_info
source_repo_info = source_repo_info_model.model_dump() if source_repo_info_model else None
filename = default
for name, value in self.filenames.items():
repo_info = value.get("tool_shed_repository")
if (not source_repo_info and not repo_info) or (
source_repo_info and repo_info and source_repo_info == repo_info
):
filename = name
break
return filename
def _add_entry(
self,
entry: Union[List[str], Dict[str, str]],
allow_duplicates: bool = True,
persist: bool = False,
entry_source: EntrySource = None,
tool_data_file_path: Optional[str] = None,
use_first_file_path: bool = False,
**kwd,
) -> None:
# accepts dict or list of columns
if isinstance(entry, dict):
fields = []
for column_name in self.get_column_name_list():
if column_name not in entry:
log.debug(
"Using default column value for column '%s' when adding data table entry (%s) to table '%s'.",
column_name,
entry,
self.name,
)
field_value = self.get_empty_field_by_name(column_name)
else:
field_value = entry[column_name]
fields.append(field_value)
else:
fields = entry
if self.largest_index < len(fields):
fields = self._replace_field_separators(fields)
if (allow_duplicates and self.allow_duplicate_entries) or fields not in self.get_fields():
self.data.append(fields)
else:
raise MessageException(
f"Attempted to add fields ({fields}) to data table '{self.name}', but this entry already exists and allow_duplicates is False.",
type="warning",
)
else:
raise MessageException(
f"Attempted to add fields ({fields}) to data table '{self.name}', but there were not enough fields specified ( {len(fields)} < {self.largest_index + 1} )."
)
filename = None
if persist:
if tool_data_file_path is not None:
filename = tool_data_file_path
if os.path.realpath(filename) not in [os.path.realpath(n) for n in self.filenames]:
raise MessageException(f"Path '{tool_data_file_path}' is not a known data table file path.")
elif not use_first_file_path:
filename = self.get_filename_for_source(entry_source)
else:
for name in self.filenames:
filename = name
break
if filename is None:
# If we reach this point, there is no data table with a corresponding .loc file.
raise MessageException(
f"Unable to determine filename for persisting data table '{self.name}' values: '{fields}'."
)
else:
log.debug("Persisting changes to file: %s", filename)
data_table_fh: BinaryIO
with FileLock(filename):
try:
if os.path.exists(filename):
data_table_fh = open(filename, "r+b")
if os.stat(filename).st_size > 0:
# ensure last existing line ends with new line
data_table_fh.seek(-1, 2) # last char in file
last_char = data_table_fh.read(1)
if last_char not in [b"\n", b"\r"]:
data_table_fh.write(b"\n")
else:
data_table_fh = open(filename, "wb")
except OSError as e:
log.exception("Error opening data table file (%s): %s", filename, e)
raise
fields_collapsed = f"{self.separator.join(fields)}\n"
data_table_fh.write(fields_collapsed.encode("utf-8"))
def _remove_entry(self, values):
# update every file
for filename in self.filenames:
if os.path.exists(filename):
values = self._replace_field_separators(values)
self.filter_file_fields(filename, values)
else:
log.warning(f"Cannot find index file '{filename}' for tool data table '{self.name}'")
self.reload_from_files()
[docs] def filter_file_fields(self, loc_file, values):
"""
Reads separated lines from file and print back only the lines that pass a filter.
"""
with open(loc_file) as reader:
rval = ""
for line in reader:
if line.lstrip().startswith(self.comment_char):
rval += line
else:
line_s = line.rstrip("\n\r")
if line_s:
fields = line_s.split(self.separator)
if fields != values:
rval += line
with open(loc_file, "w") as writer:
writer.write(rval)
return rval
def _replace_field_separators(self, fields, separator=None, replace=None, comment_char=None):
# make sure none of the fields contain separator
# make sure separator replace is different from comment_char,
# due to possible leading replace
if separator is None:
separator = self.separator
if replace is None:
if separator == " ":
if comment_char == "\t":
replace = "_"
else:
replace = "\t"
else:
if comment_char == " ":
replace = "_"
else:
replace = " "
return [x.replace(separator, replace) for x in fields]
def _deduplicate_data(self):
# Remove duplicate entries, without recreating self.data object
dup_lines = []
hash_set = set()
for i, fields in enumerate(self.data):
fields_hash = hash(self.separator.join(fields))
if fields_hash in hash_set:
dup_lines.append(i)
log.debug(
'Found duplicate entry in tool data table "%s", but duplicates are not allowed, removing additional entry for: "%s"',
self.name,
fields,
)
else:
hash_set.add(fields_hash)
for i in reversed(dup_lines):
self.data.pop(i)
@property
def xml_string(self):
return util.xml_to_string(self.config_element)
[docs] def to_dict(self, view: str = "collection", value_mapper: Optional[Dict[str, Callable]] = None) -> Dict[str, Any]:
rval = super().to_dict(view, value_mapper)
if view == "element":
rval["columns"] = sorted(self.columns.keys(), key=lambda x: self.columns[x])
rval["fields"] = self.get_fields()
return rval
[docs]class TabularToolDataField(Dictifiable):
dict_collection_visible_keys: List[str] = []
def __getitem__(self, key):
return self.data[key]
[docs] def get_base_dir(self):
path = self.get_base_path()
if not os.path.isdir(path):
path = os.path.dirname(path)
return path
[docs] def get_filesize_map(self, rm_base_dir=False):
out = {}
for path in self.get_files():
if rm_base_dir:
out[self.clean_base_dir(path)] = os.path.getsize(path)
else:
out[path] = os.path.getsize(path)
return out
[docs] def get_fingerprint(self):
sha1 = hashlib.sha1()
fmap = self.get_filesize_map(True)
for k in sorted(fmap.keys()):
sha1.update(util.smart_str(k))
sha1.update(util.smart_str(fmap[k]))
return sha1.hexdigest()
[docs] def to_dict(self, view: str = "collection", value_mapper: Optional[Dict[str, Callable]] = None) -> Dict[str, Any]:
rval = super().to_dict(view, value_mapper)
rval["name"] = self.data["value"]
rval["fields"] = self.data
rval["base_dir"] = (self.get_base_dir(),)
rval["files"] = self.get_filesize_map(True)
rval["fingerprint"] = self.get_fingerprint()
return rval
@overload
def _expand_here_template(content: str, here: Optional[str]) -> str: ...
@overload
def _expand_here_template(content: None, here: Optional[str]) -> None: ...
def _expand_here_template(content: Optional[str], here: Optional[str]) -> Optional[str]:
if here and content:
content = string.Template(content).safe_substitute({"__HERE__": here})
return content
# Registry of tool data types by type_key
tool_data_table_types_list: List[Type[ToolDataTable]] = [TabularToolDataTable]
class HasExtraFiles(Protocol):
extra_files_path: str
def extra_files_path_exists(self) -> bool: ...
class DirectoryAsExtraFiles(HasExtraFiles):
def __init__(self, directory):
self.extra_files_path = directory
def extra_files_path_exists(self) -> bool:
return True
class OutputDataset(HasExtraFiles, Protocol):
ext: str
def get_file_name(self, sync_cache=True) -> str: ...
class ToolDataTableManager(Dictifiable):
"""Manages a collection of tool data tables"""
data_tables: Dict[str, ToolDataTable]
tool_data_table_types = {cls.type_key: cls for cls in tool_data_table_types_list}
def __init__(
self,
tool_data_path: str,
config_filename: Optional[Union[StrPath, List[StrPath]]] = None,
tool_data_table_config_path_set=None,
other_config_dict: Optional[StoresConfigFilePaths] = None,
) -> None:
self.tool_data_path = tool_data_path
# This stores all defined data table entries from both the tool_data_table_conf.xml file and the shed_tool_data_table_conf.xml file
# at server startup. If tool shed repositories are installed that contain a valid file named tool_data_table_conf.xml.sample, entries
# from that file are inserted into this dict at the time of installation.
self.data_tables = {}
self.tool_data_path_files = ToolDataPathFiles(self.tool_data_path)
self.other_config_dict = other_config_dict or {}
for single_config_filename in util.listify(config_filename):
if not single_config_filename:
continue
self.load_from_config_file(single_config_filename, self.tool_data_path, from_shed_config=False)
def index(self) -> ToolDataEntryList:
data_tables = [ToolDataEntry(**table.to_dict()) for table in self.data_tables.values()]
return ToolDataEntryList.model_construct(root=data_tables)
def __getitem__(self, key: str) -> ToolDataTable:
return self.data_tables.__getitem__(key)
def __setitem__(self, key: str, value) -> None:
return self.data_tables.__setitem__(key, value)
def __contains__(self, key: str) -> bool:
return self.data_tables.__contains__(key)
def get(self, name: str, default=None):
try:
return self[name]
except KeyError:
return default
def set(self, name: str, value: ToolDataTable) -> None:
self[name] = value
def get_tables(self) -> Dict[str, "ToolDataTable"]:
return self.data_tables
def to_dict(
self, view: str = "collection", value_mapper: Optional[Dict[str, Callable]] = None
) -> Dict[str, Dict[str, Any]]:
return {
name: data_table.to_dict(view="export", value_mapper=value_mapper)
for name, data_table in self.data_tables.items()
}
def to_json(self, path: StrPath) -> None:
with open(path, "w") as out:
out.write(json.dumps(self.to_dict()))
def load_from_config_file(
self, config_filename: StrPath, tool_data_path: Optional[StrPath], from_shed_config: bool = False
) -> List[Element]:
"""
This method is called under 3 conditions:
1. When the ToolDataTableManager is initialized (see __init__ above).
2. Just after the ToolDataTableManager is initialized and the additional entries defined by shed_tool_data_table_conf.xml
are being loaded into the ToolDataTableManager.data_tables.
3. When a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local
Galaxy instance. In this case, we have 2 entry types to handle, files whose root tag is <tables>, for example:
"""
table_elems = []
tree = util.parse_xml(config_filename)
root = tree.getroot()
for table_elem in root.findall("table"):
table = self.from_elem(
table_elem,
tool_data_path,
from_shed_config,
filename=config_filename,
tool_data_path_files=self.tool_data_path_files,
other_config_dict=self.other_config_dict,
)
table_elems.append(table_elem)
if table.name not in self.data_tables:
self.data_tables[table.name] = table
log.debug("Loaded tool data table '%s' from file '%s'", table.name, config_filename)
else:
log.debug(
"Loading another instance of data table '%s' from file '%s', attempting to merge content.",
table.name,
config_filename,
)
self.data_tables[table.name].merge_tool_data_table(
table, allow_duplicates=False
) # only merge content, do not persist to disk, do not allow duplicate rows when merging
# FIXME: This does not account for an entry with the same unique build ID, but a different path.
return table_elems
def from_elem(
self,
table_elem: Element,
tool_data_path: Optional[StrPath],
from_shed_config: bool,
filename: StrPath,
tool_data_path_files: ToolDataPathFiles,
other_config_dict: Optional[StoresConfigFilePaths] = None,
) -> ToolDataTable:
table_type = table_elem.get("type", "tabular")
assert table_type in self.tool_data_table_types, f"Unknown data table type '{table_type}'"
return self.tool_data_table_types[table_type](
table_elem,
tool_data_path,
tool_data_path_files=tool_data_path_files,
from_shed_config=from_shed_config,
filename=filename,
other_config_dict=other_config_dict,
)
def add_new_entries_from_config_file(
self,
config_filename: StrPath,
tool_data_path: Optional[StrPath],
shed_tool_data_table_config: StrPath,
persist: bool = False,
) -> Tuple[List[Element], str]:
"""
This method is called when a tool shed repository that includes a tool_data_table_conf.xml.sample file is being
installed into a local galaxy instance. We have 2 cases to handle, files whose root tag is <tables>, for example::
<tables>
<!-- Location of Tmap files -->
<table name="tmap_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/tmap_index.loc" />
</table>
</tables>
and files whose root tag is <table>, for example::
<!-- Location of Tmap files -->
<table name="tmap_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/tmap_index.loc" />
</table>
"""
error_message = ""
try:
table_elems = self.load_from_config_file(
config_filename=config_filename, tool_data_path=tool_data_path, from_shed_config=True
)
except Exception as e:
error_message = (
f"Error attempting to parse file {str(os.path.split(config_filename)[1])}: {util.unicodify(e)}"
)
log.debug(error_message, exc_info=True)
table_elems = []
if persist:
# Persist Galaxy's version of the changed tool_data_table_conf.xml file.
self.to_xml_file(shed_tool_data_table_config, table_elems)
return table_elems, error_message
def to_xml_file(
self,
shed_tool_data_table_config: StrPath,
new_elems: Optional[List[Element]] = None,
remove_elems: Optional[List[Element]] = None,
) -> None:
"""
Write the current in-memory version of the shed_tool_data_table_conf.xml file to disk.
remove_elems are removed before new_elems are added.
"""
if not (new_elems or remove_elems):
log.debug("ToolDataTableManager.to_xml_file called without any elements to add or remove.")
return # no changes provided, no need to persist any changes
if not new_elems:
new_elems = []
if not remove_elems:
remove_elems = []
full_path = os.path.abspath(shed_tool_data_table_config)
# FIXME: we should lock changing this file by other threads / head nodes
try:
try:
tree = util.parse_xml(full_path)
except OSError as e:
if e.errno == errno.ENOENT:
with open(full_path, "w") as fh:
fh.write(TOOL_DATA_TABLE_CONF_XML)
tree = util.parse_xml(full_path)
else:
raise
root = tree.getroot()
out_elems = list(root)
except Exception as e:
out_elems = []
log.debug("Could not parse existing tool data table config, assume no existing elements: %s", e)
out_elems = [elem for elem in out_elems if elem not in remove_elems]
# add new elems
out_elems.extend(new_elems)
out_path_is_new = not os.path.exists(full_path)
root = util.parse_xml_string('<?xml version="1.0"?>\n<tables></tables>')
for elem in out_elems:
root.append(elem)
with RenamedTemporaryFile(full_path, mode="w") as out:
out.write(util.xml_to_string(root, pretty=True))
os.chmod(full_path, RW_R__R__)
if out_path_is_new:
self.tool_data_path_files.update_files()
def reload_tables(
self, table_names: Optional[Union[List[str], str]] = None, path: Optional[str] = None
) -> List[str]:
"""
Reload tool data tables. If neither table_names nor path is given, reloads all tool data tables.
"""
tables = self.get_tables()
if not table_names:
if path:
table_names = self.get_table_names_by_path(path)
else:
table_names = list(tables.keys())
elif not isinstance(table_names, list):
table_names = [table_names]
for table_name in table_names:
tables[table_name].reload_from_files()
log.debug("Reloaded tool data table '%s' from files.", table_name)
return table_names
def get_table_names_by_path(self, path: str) -> List[str]:
"""Returns a list of table names given a path"""
table_names = set()
for name, data_table in self.data_tables.items():
if path in data_table.filenames:
table_names.add(name)
return list(table_names)
def process_bundle(
self,
out_data: Dict[str, OutputDataset],
bundle_description: DataTableBundleProcessorDescription,
repo_info: Optional[RepoInfo],
options: "BundleProcessingOptions",
) -> List[str]:
data_manager_dict: Dict[str, Any] = _data_manager_dict(out_data)
bundle = DataTableBundle(
processor_description=bundle_description,
data_tables=data_manager_dict.get("data_tables", {}),
repo_info=repo_info,
)
return _process_bundle(out_data, bundle, options, self)
def import_bundle(
self,
target: str,
options: "BundleProcessingOptions",
) -> List[str]:
if not os.path.isdir(target):
target_directory = decompress_path_to_directory(target)
else:
target_directory = target
index_json = os.path.join(target_directory, BUNDLE_INDEX_FILE_NAME)
with open(index_json) as f:
index = json.load(f)
bundle = DataTableBundle(**index)
assert bundle.output_name
out_data = {bundle.output_name: DirectoryAsExtraFiles(target_directory)}
return _process_bundle(out_data, bundle, options, self)
def write_bundle(
self,
out_data: Dict[str, OutputDataset],
bundle_description: DataTableBundleProcessorDescription,
repo_info: Optional[RepoInfo],
) -> Dict[str, OutputDataset]:
"""Writes bundle and returns bundle path."""
data_manager_dict = _data_manager_dict(out_data, ensure_single_output=True)
bundle_datasets: Dict[str, OutputDataset] = {}
for output_name, dataset in out_data.items():
if dataset.ext != "data_manager_json":
continue
bundle = DataTableBundle(
data_tables=data_manager_dict.get("data_tables", {}),
output_name=output_name,
processor_description=bundle_description,
repo_info=repo_info,
)
extra_files_path = dataset.extra_files_path
bundle_path = os.path.join(extra_files_path, BUNDLE_INDEX_FILE_NAME)
with open(bundle_path, "w") as fw:
fw.write(bundle.model_dump_json())
bundle_datasets[bundle_path] = dataset
return bundle_datasets
SUPPORTED_DATA_TABLE_TYPES = TabularToolDataTable
@dataclass
class BundleProcessingOptions:
what: str
data_manager_path: str
target_config_file: str
tool_data_file_path: Optional[str] = None
def _data_manager_dict(out_data: Dict[str, OutputDataset], ensure_single_output: bool = False) -> Dict[str, Any]:
data_manager_dict: Dict[str, Any] = {}
found_output = False
for output_name, output_dataset in out_data.items():
if output_dataset.ext != "data_manager_json":
continue
if found_output and ensure_single_output:
raise Exception("Galaxy can only write bundles for data managers with a single output data_manager_json.")
found_output = True
try:
output_dict = json.loads(open(output_dataset.get_file_name()).read())
except Exception as e:
log.warning(f'Error reading DataManagerTool json for "{output_name}": {e}')
continue
for key, value in output_dict.items():
if key not in data_manager_dict:
data_manager_dict[key] = {}
data_manager_dict[key].update(value)
data_manager_dict.update(output_dict)
return data_manager_dict
from typing import Mapping
def _process_bundle(
out_data: Mapping[str, HasExtraFiles],
bundle: DataTableBundle,
options: BundleProcessingOptions,
tool_data_tables: ToolDataTableManager,
):
updated_data_tables = []
data_tables_dict = bundle.data_tables
bundle_description = bundle.processor_description
for data_table_name in bundle_description.data_table_names:
data_table_values = data_tables_dict.pop(data_table_name, None)
if not data_table_values:
log.warning(f'No values for data table "{data_table_name}" were returned by "{options.what}".')
continue # next data table
data_table_remove_values = None
if isinstance(data_table_values, dict):
values_to_add = data_table_values.get("add")
data_table_remove_values = data_table_values.get("remove")
if values_to_add or data_table_remove_values:
# We don't have an old style data table definition
data_table_values = values_to_add
data_table = tool_data_tables.get(data_table_name, None)
if data_table is None:
log.error(
f'Processing by {options.what} returned an unknown data table "{data_table_name}" with new entries "{data_table_values}". These entries will not be created. Please confirm that an entry for "{data_table_name}" exists in your "tool_data_table_conf.xml" file.'
)
continue # next table name
if not isinstance(data_table, SUPPORTED_DATA_TABLE_TYPES):
log.error(
f'Processing by {options.what} returned an unsupported data table "{data_table_name}" with type "{type(data_table)}" with new entries "{data_table_values}". These entries will not be created. Please confirm that the data table is of a supported type ({SUPPORTED_DATA_TABLE_TYPES}).'
)
continue # next table name
output_ref_values = {}
output_ref_by_data_table = bundle_description.output_ref_by_data_table
if data_table_name in output_ref_by_data_table:
for data_table_column, output_ref in output_ref_by_data_table[data_table_name].items():
output_ref_dataset = out_data.get(output_ref, None)
assert output_ref_dataset is not None, "Referenced output was not found."
output_ref_values[data_table_column] = output_ref_dataset
if not isinstance(data_table_values, list):
data_table_values = [data_table_values] if data_table_values else []
if not isinstance(data_table_remove_values, list):
data_table_remove_values = [data_table_remove_values] if data_table_remove_values else []
for data_table_row in data_table_values:
data_table_value = dict(**data_table_row) # keep original values here
for (
name
) in (
data_table_row.keys()
): # FIXME: need to loop through here based upon order listed in data_manager config
if name in output_ref_values:
_process_move(
data_table_name,
name,
output_ref_values[name].extra_files_path,
bundle_description,
options,
**data_table_value,
)
data_table_value[name] = _process_value_translations(
data_table_name, name, bundle_description, options, **data_table_value
)
data_table.add_entry(
data_table_value,
persist=True,
entry_source=bundle.repo_info,
tool_data_file_path=options.tool_data_file_path,
use_first_file_path=True,
)
# Removes data table entries
for data_table_row in data_table_remove_values:
data_table_value = dict(**data_table_row) # keep original values here
data_table.remove_entry(list(data_table_value.values()))
updated_data_tables.append(data_table_name)
if bundle_description.undeclared_tables and data_tables_dict:
# We handle the data move, by just moving all the data out of the extra files path
# moving a directory and the target already exists, we move the contents instead
log.debug("Attempting to add entries for undeclared tables: %s.", ", ".join(data_tables_dict.keys()))
for ref_file in out_data.values():
if ref_file.extra_files_path_exists():
util.move_merge(ref_file.extra_files_path, options.data_manager_path)
path_column_names = ["path"]
for data_table_name, data_table_values in data_tables_dict.items():
data_table = tool_data_tables.get(data_table_name, None)
if not isinstance(data_table_values, list):
data_table_values = [data_table_values]
for data_table_row in data_table_values:
data_table_value = dict(**data_table_row) # keep original values here
for name, value in data_table_row.items():
if name in path_column_names:
data_table_value[name] = os.path.abspath(os.path.join(options.data_manager_path, value))
data_table.add_entry(data_table_value, persist=True, entry_source=bundle.repo_info)
updated_data_tables.append(data_table_name)
else:
for data_table_name, data_table_values in data_tables_dict.items():
# tool returned extra data table entries, but data table was not declared in data manager
# do not add these values, but do provide messages
log.warning(
f'Processing by {options.what} returned an undeclared data table "{data_table_name}" with new entries "{data_table_values}". These entries will not be created. Please confirm that an entry for "{data_table_name}" exists in your "{options.target_config_file}" file.'
)
return updated_data_tables
def _process_move(
data_table_name: str,
column_name: str,
source_base_path: str,
bundle_description: DataTableBundleProcessorDescription,
options: BundleProcessingOptions,
**kwd,
):
move_by_data_table_column = bundle_description.move_by_data_table_column
if data_table_name in move_by_data_table_column and column_name in move_by_data_table_column[data_table_name]:
move = move_by_data_table_column[data_table_name][column_name]
source = move.source_base
if source is None:
source = source_base_path
else:
source = fill_template(
source,
GALAXY_DATA_MANAGER_DATA_PATH=options.data_manager_path,
**kwd,
).strip()
assert source
if move.source_value:
source = os.path.join(
source,
fill_template(
move.source_value,
GALAXY_DATA_MANAGER_DATA_PATH=options.data_manager_path,
**kwd,
).strip(),
)
target = move.target_base
if target is None:
target = options.data_manager_path
else:
target = fill_template(
target,
GALAXY_DATA_MANAGER_DATA_PATH=options.data_manager_path,
**kwd,
).strip()
assert target
if move.target_value:
target = os.path.join(
target,
fill_template(
move.target_value,
GALAXY_DATA_MANAGER_DATA_PATH=options.data_manager_path,
**kwd,
).strip(),
)
if move.type == "file":
dirs = os.path.split(target)[0]
try:
os.makedirs(dirs)
except OSError as e:
if e.errno != errno.EEXIST:
raise e
# moving a directory and the target already exists, we move the contents instead
if os.path.exists(source):
util.move_merge(source, target)
if move.relativize_symlinks:
util.relativize_symlinks(target)
return True
return False
def _process_value_translations(
data_table_name: str,
column_name: str,
bundle_description: DataTableBundleProcessorDescription,
options: BundleProcessingOptions,
**kwd,
) -> str:
value_translation_by_data_table_column = bundle_description.value_translation_by_data_table_column
value = kwd.get(column_name)
if (
data_table_name in value_translation_by_data_table_column
and column_name in value_translation_by_data_table_column[data_table_name]
):
for value_translation in value_translation_by_data_table_column[data_table_name][column_name]:
if isinstance(value_translation, str):
value = fill_template(
value_translation,
GALAXY_DATA_MANAGER_DATA_PATH=options.data_manager_path,
**kwd,
).strip()
else:
value = value_translation(value)
assert value
return value