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.datatypes.qiime2

import ast
import html
import io
import uuid as _uuid
import zipfile
from typing import (
    Dict,
    List,
    Optional,
)

import yaml

from galaxy.datatypes.binary import CompressedZipArchive
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.protocols import (
    DatasetProtocol,
    HasMetadata,
)
from galaxy.datatypes.sniff import (
    build_sniff_from_prefix,
    FilePrefix,
)
from galaxy.datatypes.tabular import Tabular


class _QIIME2ResultBase(CompressedZipArchive):
    """Base class for QIIME2Artifact and QIIME2Visualization"""

    MetadataElement(name="semantic_type", readonly=True)
    MetadataElement(name="semantic_type_simple", readonly=True, visible=False)
    MetadataElement(name="uuid", readonly=True)
    MetadataElement(name="format", optional=True, no_value="", readonly=True)
    MetadataElement(name="version", readonly=True)

    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
        metadata = _get_metadata_from_archive(dataset.get_file_name())
        for key, value in metadata.items():
            if value:
                setattr(dataset.metadata, key, value)

        dataset.metadata.semantic_type_simple = _strip_properties(dataset.metadata.semantic_type)

    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
        if dataset.metadata.semantic_type == "Visualization":
            dataset.blurb = "QIIME 2 Visualization"
        else:
            dataset.blurb = "QIIME 2 Artifact"

        dataset.peek = "\n".join(map(": ".join, self._peek(dataset)))

    def display_peek(self, dataset: DatasetProtocol) -> str:
        def make_row(pair):
            return f"<tr><th>{pair[0]}</th><td>{html.escape(pair[1])}</td></tr>"

        table = ['<table cellspacing="0" cellpadding="2">']
        table += [make_row(pair) for pair in self._peek(dataset, simple=True)]
        table += ["</table>"]

        return "".join(table)

    def _peek(self, dataset: HasMetadata, simple: bool = False) -> List:
        peek = [("Type", dataset.metadata.semantic_type), ("UUID", dataset.metadata.uuid)]
        if not simple:
            if dataset.metadata.semantic_type != "Visualization":
                peek.append(("Format", dataset.metadata.format))
            peek.append(("Version", dataset.metadata.version))
        return peek

    def _sniff(self, filename: str) -> Optional[Dict]:
        """Helper method for use in inherited datatypes"""
        try:
            if not zipfile.is_zipfile(filename):
                raise Exception()
            return _get_metadata_from_archive(filename)
        except Exception:
            return None


[docs]class QIIME2Artifact(_QIIME2ResultBase): file_ext = "qza"
[docs] def sniff(self, filename: str) -> bool: metadata = self._sniff(filename) return bool(metadata) and metadata["semantic_type"] != "Visualization" # type: ignore[index]
[docs]class QIIME2Visualization(_QIIME2ResultBase): file_ext = "qzv"
[docs] def sniff(self, filename: str) -> bool: metadata = self._sniff(filename) return bool(metadata) and metadata["semantic_type"] == "Visualization" # type: ignore[index]
[docs]@build_sniff_from_prefix class QIIME2Metadata(Tabular): """ QIIME 2 supports overriding the type of a column to Categorical when a specific directive `#q2:types` is present under the ID row. Galaxy already understands column types quite well, however we sometimes want to override its inferred type. For Galaxy, we are going to require that if a directive occurs, it happens on the second line (after the header). This is the most typical location and interacts best with the current implementation of Tabular. """ file_ext = "qiime2.tabular" _TYPES_DIRECTIVE = "#q2:types" _search_lines = 2
[docs] def get_column_names(self, first_line: str) -> Optional[List[str]]: return first_line.strip().split("\t")
[docs] def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None: """ Let Galaxy's Tabular format handle most of this. We will just jump in at the last minute to (potentially) override some column types. """ super().set_meta(dataset, overwrite=overwrite, **kwd) if dataset.has_data(): with open(dataset.get_file_name()) as dataset_fh: line = None for line, _ in zip(dataset_fh, range(self._search_lines)): if line.startswith(self._TYPES_DIRECTIVE): break if line is None: return q2_types = line.strip().split("\t") # The first column (q2:types) is always the IDs q2_types[0] = "index" if len(q2_types) < dataset.metadata.columns: # this is probably malformed, but easy to fix q2_types.extend([""] * (dataset.metadata.columns - len(q2_types))) for idx, (q2_type, col_type) in enumerate(zip(q2_types, dataset.metadata.column_types)): if q2_type == "": if col_type in ("float", "int"): q2_types[idx] = "numeric" else: q2_types[idx] = "categorical" else: if q2_type == "categorical" and col_type in ("float", "int", "list"): dataset.metadata.column_types[idx] = "str"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool: for _, line in zip(range(self._search_lines), file_prefix.line_iterator()): if line.startswith(self._TYPES_DIRECTIVE): return True return False
############################################################################## # Helpers ############################################################################## def _strip_properties(expression): # This is necessary because QIIME 2's semantic types include a limited # form of intersection type, which means that `A & B` is a subtype of `A` # as well as a subtype of `B`. This means it is not generally speaking # possible or practical to enumerate all valid subtypes and then do an # exact match using <options options_filter_attribute="Some[Type]"> # So instead filter out 90% of the invalid inputs and let QIIME 2 raise an # error on the finer details such as these "properties". try: expression_tree = ast.parse(expression) reconstructer = _PredicateRemover() reconstructer.visit(expression_tree) return reconstructer.expression # If we have any problems stripping properties just use the full expression # this punts the error off to q2galaxy so if we error we do so there and # not here except Exception: return expression # Python 3.9 has a built in unparse. We can probably use this in the future # when we are using 3.9 # https://docs.python.org/3.9/library/ast.html#ast.unparse class _PredicateRemover(ast.NodeVisitor): binops = { ast.Add: " + ", ast.Sub: " - ", ast.Mult: " * ", ast.Div: " / ", ast.FloorDiv: " // ", ast.Pow: " ** ", ast.LShift: " << ", ast.RShift: " >> ", ast.BitOr: " | ", ast.BitXor: " ^ ", ast.BitAnd: " & ", ast.MatMult: " @ ", } def __init__(self): self.expression = "" def visit_Name(self, node): self.expression += node.id def visit_Subscript(self, node): self.visit(node.value) self.expression += "[" self.visit(node.slice) self.expression += "]" def visit_Tuple(self, node): trailing_comma = "" for n in node.elts: self.expression += trailing_comma self.visit(n) trailing_comma = ", " def visit_BinOp(self, node): self.visit(node.left) if not isinstance(node.op, ast.Mod): self.expression += self.binops[node.op.__class__] self.visit(node.right) def _get_metadata_from_archive(archive): uuid = _get_uuid(archive) archive_version, framework_version = _get_versions(archive, uuid) metadata_contents = _get_metadata_contents(archive, uuid) return { "uuid": uuid, "version": framework_version, "semantic_type": metadata_contents["type"], "format": metadata_contents["format"] or "", } def _get_metadata_contents(path, uuid): with _open_file_in_archive(path, "metadata.yaml", uuid) as fh: return yaml.safe_load(fh.read()) def _get_uuid(path): roots = set() for relpath in _iter_zip_root(path): if not relpath.startswith("."): roots.add(relpath) if len(roots) == 0: raise ValueError("Archive does not have a visible root directory.") if len(roots) > 1: raise ValueError("Archive has multiple root directories: %r" % roots) uuid = roots.pop() if not _is_uuid4(uuid): raise ValueError("Archive root directory name %r is not a valid version 4 " "UUID." % uuid) return uuid def _get_versions(path, uuid): try: with _open_file_in_archive(path, "VERSION", uuid) as fh: header, version_line, framework_version_line, eof = fh.read().split("\n") if header.strip() != "QIIME 2": raise Exception() # GOTO except Exception version = version_line.split(":")[1].strip() framework_version = framework_version_line.split(":")[1].strip() return version, framework_version except Exception: raise ValueError("Archive does not contain a correctly formatted" " VERSION file.") def _open_file_in_archive(zip_path, path, uuid): relpath = "/".join([uuid, path]) with zipfile.ZipFile(zip_path, mode="r") as zf: return io.TextIOWrapper(zf.open(relpath)) def _iter_zip_root(path): seen = set() with zipfile.ZipFile(path, mode="r") as zf: for name in zf.namelist(): parts = name.split("/") # zip is always / for seperators if len(parts) > 0: result = parts[0] if result not in seen: seen.add(result) yield result def _is_uuid4(uuid_str): # Adapted from https://gist.github.com/ShawnMilo/7777304 try: uuid = _uuid.UUID(hex=uuid_str, version=4) except ValueError: # The string is not a valid hex code for a UUID. return False # If uuid_str is a valid hex code, but an invalid uuid4, UUID.__init__ # will convert it to a valid uuid4. return str(uuid) == uuid_str