Source code for ocrd.cli.workspace

"""
OCR-D CLI: workspace management

.. click:: ocrd.cli.workspace:workspace_cli
    :prog: ocrd workspace
    :nested: full
"""
import os
from os import getcwd
from os.path import relpath, exists, join, isabs, dirname, basename, abspath
from pathlib import Path
from json import loads
import sys
from glob import glob   # XXX pathlib.Path.glob does not support absolute globs
import re

import click

from ocrd import Resolver, Workspace, WorkspaceValidator, WorkspaceBackupManager
from ocrd_utils import getLogger, initLogging, pushd_popd, EXT_TO_MIME
from ocrd.decorators import mets_find_options
from . import command_with_replaced_help


[docs]class WorkspaceCtx(): def __init__(self, directory, mets_url, mets_basename, automatic_backup): self.log = getLogger('ocrd.cli.workspace') if mets_basename and mets_url: raise ValueError("Use either --mets or --mets-basename, not both") if mets_basename and not mets_url: self.log.warning(DeprecationWarning("--mets-basename is deprecated. Use --mets/--directory instead")) mets_basename = mets_basename if mets_basename else 'mets.xml' if directory and mets_url: directory = abspath(directory) if not abspath(mets_url).startswith(directory): raise ValueError("--mets has a directory part inconsistent with --directory") elif not directory and mets_url: if mets_url.startswith('http') or mets_url.startswith('https:'): raise ValueError("--mets is an http(s) URL but no --directory was given") directory = dirname(abspath(mets_url)) or getcwd() elif directory and not mets_url: directory = abspath(directory) mets_url = join(directory, mets_basename) else: directory = getcwd() mets_url = join(directory, mets_basename) self.directory = directory self.resolver = Resolver() self.mets_url = mets_url self.automatic_backup = automatic_backup
pass_workspace = click.make_pass_decorator(WorkspaceCtx) # ---------------------------------------------------------------------- # ocrd workspace # ---------------------------------------------------------------------- @click.group("workspace") @click.option('-d', '--directory', envvar='WORKSPACE_DIR', type=click.Path(file_okay=False), metavar='WORKSPACE_DIR', help='Changes the workspace folder location [default: METS_URL directory or .]"') @click.option('-M', '--mets-basename', default=None, help='METS file basename. Deprecated, use --mets/--directory') @click.option('-m', '--mets', default=None, help='The path/URL of the METS file [default: WORKSPACE_DIR/mets.xml]', metavar="METS_URL") @click.option('--backup', default=False, help="Backup mets.xml whenever it is saved.", is_flag=True) @click.pass_context def workspace_cli(ctx, directory, mets, mets_basename, backup): """ Working with workspace """ initLogging() ctx.obj = WorkspaceCtx(directory, mets_url=mets, mets_basename=mets_basename, automatic_backup=backup) # ---------------------------------------------------------------------- # ocrd workspace validate # ---------------------------------------------------------------------- @workspace_cli.command('validate', cls=command_with_replaced_help( (r' \[METS_URL\]', ''))) # XXX deprecated argument @pass_workspace @click.option('-a', '--download', is_flag=True, help="Download all files") @click.option('-s', '--skip', help="Tests to skip", default=[], multiple=True, type=click.Choice(['imagefilename', 'dimension', 'mets_unique_identifier', 'mets_file_group_names', 'mets_files', 'pixel_density', 'page', 'page_xsd', 'mets_xsd', 'url'])) @click.option('--page-textequiv-consistency', '--page-strictness', help="How strict to check PAGE multi-level textequiv consistency", type=click.Choice(['strict', 'lax', 'fix', 'off']), default='strict') @click.option('--page-coordinate-consistency', help="How fierce to check PAGE multi-level coordinate consistency", type=click.Choice(['poly', 'baseline', 'both', 'off']), default='poly') @click.argument('mets_url', default=None, required=False) def workspace_validate(ctx, mets_url, download, skip, page_textequiv_consistency, page_coordinate_consistency): """ Validate a workspace METS_URL can be a URL, an absolute path or a path relative to $PWD. If not given, use --mets accordingly. Check that the METS and its referenced file contents abide by the OCR-D specifications. """ LOG = getLogger('ocrd.cli.workspace.validate') if mets_url: LOG.warning(DeprecationWarning("Use 'ocrd workspace --mets METS init' instead of argument 'METS_URL' ('%s')" % mets_url)) else: mets_url = ctx.mets_url report = WorkspaceValidator.validate( ctx.resolver, mets_url, src_dir=ctx.directory, skip=skip, download=download, page_strictness=page_textequiv_consistency, page_coordinate_consistency=page_coordinate_consistency ) print(report.to_xml()) if not report.is_valid: sys.exit(128) # ---------------------------------------------------------------------- # ocrd workspace clone # ---------------------------------------------------------------------- @workspace_cli.command('clone', cls=command_with_replaced_help( (r' \[WORKSPACE_DIR\]', ''))) # XXX deprecated argument @click.option('-f', '--clobber-mets', help="Overwrite existing METS file", default=False, is_flag=True) @click.option('-a', '--download', is_flag=True, help="Download all files and change location in METS file after cloning") @click.argument('mets_url') # XXX deprecated @click.argument('workspace_dir', default=None, required=False) @pass_workspace def workspace_clone(ctx, clobber_mets, download, mets_url, workspace_dir): """ Create a workspace from METS_URL and return the directory METS_URL can be a URL, an absolute path or a path relative to $PWD. If METS_URL is not provided, use --mets accordingly. METS_URL can also be an OAI-PMH GetRecord URL wrapping a METS file. """ LOG = getLogger('ocrd.cli.workspace.clone') if workspace_dir: LOG.warning(DeprecationWarning("Use 'ocrd workspace --directory DIR clone' instead of argument 'WORKSPACE_DIR' ('%s')" % workspace_dir)) ctx.directory = workspace_dir workspace = ctx.resolver.workspace_from_url( mets_url, dst_dir=os.path.abspath(ctx.directory), mets_basename=basename(ctx.mets_url), clobber_mets=clobber_mets, download=download, ) workspace.save_mets() print(workspace.directory) # ---------------------------------------------------------------------- # ocrd workspace init # ---------------------------------------------------------------------- @workspace_cli.command('init', cls=command_with_replaced_help( (r' \[DIRECTORY\]', ''))) # XXX deprecated argument @click.option('-f', '--clobber-mets', help="Clobber mets.xml if it exists", is_flag=True, default=False) # XXX deprecated @click.argument('directory', default=None, required=False) @pass_workspace def workspace_init(ctx, clobber_mets, directory): """ Create a workspace with an empty METS file in --directory. """ LOG = getLogger('ocrd.cli.workspace.init') if directory: LOG.warning(DeprecationWarning("Use 'ocrd workspace --directory DIR init' instead of argument 'DIRECTORY' ('%s')" % directory)) ctx.directory = directory workspace = ctx.resolver.workspace_from_nothing( directory=os.path.abspath(ctx.directory), mets_basename=basename(ctx.mets_url), clobber_mets=clobber_mets ) workspace.save_mets() print(workspace.directory) # ---------------------------------------------------------------------- # ocrd workspace add # ---------------------------------------------------------------------- @workspace_cli.command('add') @click.option('-G', '--file-grp', help="fileGrp USE", required=True, metavar='FILE_GRP') @click.option('-i', '--file-id', help="ID for the file", required=True, metavar='FILE_ID') @click.option('-m', '--mimetype', help="Media type of the file. Guessed from extension if not provided", required=False, metavar='TYPE') @click.option('-g', '--page-id', help="ID of the physical page", metavar='PAGE_ID') @click.option('-C', '--check-file-exists', help="Whether to ensure FNAME exists", is_flag=True, default=False) @click.option('--ignore', help="Do not check whether file exists.", default=False, is_flag=True) @click.option('--force', help="If file with ID already exists, replace it. No effect if --ignore is set.", default=False, is_flag=True) @click.argument('fname', required=True) @pass_workspace def workspace_add_file(ctx, file_grp, file_id, mimetype, page_id, ignore, check_file_exists, force, fname): """ Add a file or http(s) URL FNAME to METS in a workspace. If FNAME is not an http(s) URL and is not a workspace-local existing file, try to copy to workspace. """ workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url), automatic_backup=ctx.automatic_backup) log = getLogger('ocrd.cli.workspace.add') if not mimetype: try: mimetype = EXT_TO_MIME[Path(fname).suffix] log.info("Guessed mimetype to be %s" % mimetype) except KeyError: log.error("Cannot guess mimetype from extension '%s' for '%s'. Set --mimetype explicitly" % (Path(fname).suffix, fname)) kwargs = {'fileGrp': file_grp, 'ID': file_id, 'mimetype': mimetype, 'pageId': page_id, 'force': force, 'ignore': ignore} log.debug("Adding '%s' (%s)", fname, kwargs) if not (fname.startswith('http://') or fname.startswith('https://')): if not fname.startswith(ctx.directory): if not isabs(fname) and exists(join(ctx.directory, fname)): fname = join(ctx.directory, fname) else: log.debug("File '%s' is not in workspace, copying", fname) try: fname = ctx.resolver.download_to_directory(ctx.directory, fname, subdir=file_grp) except FileNotFoundError: if check_file_exists: log.error("File '%s' does not exist, halt execution!" % fname) sys.exit(1) if check_file_exists and not exists(fname): log.error("File '%s' does not exist, halt execution!" % fname) sys.exit(1) if fname.startswith(ctx.directory): fname = relpath(fname, ctx.directory) kwargs['local_filename'] = fname kwargs['url'] = fname if not page_id: log.warning("You did not provide '--page-id/-g', so the file you added is not linked to a specific page.") workspace.mets.add_file(**kwargs) workspace.save_mets() # ---------------------------------------------------------------------- # ocrd workspace add-bulk # ---------------------------------------------------------------------- # pylint: disable=broad-except @workspace_cli.command('bulk-add') @click.option('-r', '--regex', help="Regular expression matching the FILE_GLOB filesystem paths to define named captures usable in the other parameters", required=True) @click.option('-m', '--mimetype', help="Media type of the file. If not provided, guess from filename", required=False) @click.option('-g', '--page-id', help="physical page ID of the file", required=False) @click.option('-i', '--file-id', help="ID of the file", required=True) @click.option('-u', '--url', help="local filesystem path in the workspace directory (copied from source file if different)", required=True) @click.option('-G', '--file-grp', help="File group USE of the file", required=True) @click.option('-n', '--dry-run', help="Don't actually do anything to the METS or filesystem, just preview", default=False, is_flag=True) @click.option('-I', '--ignore', help="Disable checking for existing file entries (faster)", default=False, is_flag=True) @click.option('-f', '--force', help="Replace existing file entries with the same ID (no effect when --ignore is set, too)", default=False, is_flag=True) @click.option('-s', '--skip', help="Skip files not matching --regex (instead of failing)", default=False, is_flag=True) @click.argument('file_glob', nargs=-1, required=True) @pass_workspace def workspace_cli_bulk_add(ctx, regex, mimetype, page_id, file_id, url, file_grp, dry_run, file_glob, ignore, force, skip): r""" Add files in bulk to an OCR-D workspace. FILE_GLOB can either be a shell glob expression or a list of files. --regex is applied to the absolute path of every file in FILE_GLOB and can define named groups that can be used in --page-id, --file-id, --mimetype, --url and --file-grp by referencing the named group 'grp' in the regex as '{{ grp }}'. \b Example: ocrd workspace bulk-add \\ --regex '^.*/(?P<fileGrp>[^/]+)/page_(?P<pageid>.*)\.(?P<ext>[^\.]*)$' \\ --file-id 'FILE_{{ fileGrp }}_{{ pageid }}' \\ --page-id 'PHYS_{{ pageid }}' \\ --file-grp "{{ fileGrp }}" \\ --url '{{ fileGrp }}/FILE_{{ pageid }}.{{ ext }}' \\ path/to/files/*/*.* """ log = getLogger('ocrd.cli.workspace.bulk-add') # pylint: disable=redefined-outer-name workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url), automatic_backup=ctx.automatic_backup) try: pat = re.compile(regex) except Exception as e: log.error("Invalid regex: %s" % e) sys.exit(1) file_paths = [] for fglob in file_glob: file_paths += [Path(x).resolve() for x in glob(fglob)] for i, file_path in enumerate(file_paths): log.info("[%4d/%d] %s" % (i, len(file_paths), file_path)) # match regex m = pat.match(str(file_path)) if not m: if skip: continue log.error("File not matched by regex: '%s'" % file_path) sys.exit(1) group_dict = m.groupdict() # set up file info file_dict = {'url': url, 'mimetype': mimetype, 'ID': file_id, 'pageId': page_id, 'fileGrp': file_grp} # guess mime type if not file_dict['mimetype']: try: file_dict['mimetype'] = EXT_TO_MIME[file_path.suffix] except KeyError: log.error("Cannot guess mimetype from extension '%s' for '%s'. Set --mimetype explicitly" % (file_path.suffix, file_path)) # expand templates for param_name in file_dict: for group_name in group_dict: file_dict[param_name] = file_dict[param_name].replace('{{ %s }}' % group_name, group_dict[group_name]) # copy files if file_dict['url']: urlpath = Path(workspace.directory, file_dict['url']) if not urlpath.exists(): log.info("cp '%s' '%s'", file_path, urlpath) if not dry_run: if not urlpath.parent.is_dir(): urlpath.parent.mkdir() urlpath.write_bytes(file_path.read_bytes()) # Add to workspace (or not) fileGrp = file_dict.pop('fileGrp') if dry_run: log.info('workspace.add_file(%s)' % file_dict) else: workspace.add_file(fileGrp, ignore=ignore, force=force, **file_dict) # save changes to disk workspace.save_mets() # ---------------------------------------------------------------------- # ocrd workspace find # ---------------------------------------------------------------------- @workspace_cli.command('find') @mets_find_options @click.option('-k', '--output-field', help="Output field. Repeat for multiple fields, will be joined with tab", default=['url'], multiple=True, type=click.Choice([ 'url', 'mimetype', 'pageId', 'ID', 'fileGrp', 'basename', 'basename_without_extension', 'local_filename', ])) @click.option('--download', is_flag=True, help="Download found files to workspace and change location in METS file ") @pass_workspace def workspace_find(ctx, file_grp, mimetype, page_id, file_id, output_field, download): """ Find files. (If any ``FILTER`` starts with ``//``, then its remainder will be interpreted as a regular expression.) """ modified_mets = False ret = list() workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url)) for f in workspace.mets.find_files( ID=file_id, fileGrp=file_grp, mimetype=mimetype, pageId=page_id, ): if download and not f.local_filename: workspace.download_file(f) modified_mets = True ret.append([f.ID if field == 'pageId' else getattr(f, field) or '' for field in output_field]) if modified_mets: workspace.save_mets() if 'pageId' in output_field: idx = output_field.index('pageId') fileIds = list(map(lambda fields: fields[idx], ret)) pages = workspace.mets.get_physical_pages(for_fileIds=fileIds) for fields, page in zip(ret, pages): fields[idx] = page or '' for fields in ret: print('\t'.join(fields)) # ---------------------------------------------------------------------- # ocrd workspace remove # ---------------------------------------------------------------------- @workspace_cli.command('remove') @click.option('-k', '--keep-file', help="Do not delete file from file system", default=False, is_flag=True) @click.option('-f', '--force', help="Continue even if mets:file or file on file system does not exist", default=False, is_flag=True) @click.argument('ID', nargs=-1) @pass_workspace def workspace_remove_file(ctx, id, force, keep_file): # pylint: disable=redefined-builtin """ Delete files (given by their ID attribute ``ID``). (If any ``ID`` starts with ``//``, then its remainder will be interpreted as a regular expression.) """ workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url), automatic_backup=ctx.automatic_backup) for i in id: workspace.remove_file(i, force=force, keep_file=keep_file) workspace.save_mets() # ---------------------------------------------------------------------- # ocrd workspace rename-group # ---------------------------------------------------------------------- @workspace_cli.command('rename-group') @click.argument('OLD', nargs=1) @click.argument('NEW', nargs=1) @pass_workspace def rename_group(ctx, old, new): """ Rename fileGrp (USE attribute ``NEW`` to ``OLD``). """ workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url)) workspace.rename_file_group(old, new) workspace.save_mets() # ---------------------------------------------------------------------- # ocrd workspace remove-group # ---------------------------------------------------------------------- @workspace_cli.command('remove-group') @click.option('-r', '--recursive', help="Delete any files in the group before the group itself", default=False, is_flag=True) @click.option('-f', '--force', help="Continue removing even if group or containing files not found in METS", default=False, is_flag=True) @click.option('-k', '--keep-files', help="Do not delete files from file system", default=False, is_flag=True) @click.argument('GROUP', nargs=-1) @pass_workspace def remove_group(ctx, group, recursive, force, keep_files): """ Delete fileGrps (given by their USE attribute ``GROUP``). (If any ``GROUP`` starts with ``//``, then its remainder will be interpreted as a regular expression.) """ workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url)) for g in group: workspace.remove_file_group(g, recursive=recursive, force=force, keep_files=keep_files) workspace.save_mets() # ---------------------------------------------------------------------- # ocrd workspace prune-files # ---------------------------------------------------------------------- @workspace_cli.command('prune-files') @click.option('-G', '--file-grp', help="fileGrp USE", metavar='FILTER') @click.option('-m', '--mimetype', help="Media type to look for", metavar='FILTER') @click.option('-g', '--page-id', help="Page ID", metavar='FILTER') @click.option('-i', '--file-id', help="ID", metavar='FILTER') @pass_workspace def prune_files(ctx, file_grp, mimetype, page_id, file_id): """ Removes mets:files that point to non-existing local files (If any ``FILTER`` starts with ``//``, then its remainder will be interpreted as a regular expression.) """ workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url), automatic_backup=ctx.automatic_backup) with pushd_popd(workspace.directory): for f in workspace.mets.find_files( ID=file_id, fileGrp=file_grp, mimetype=mimetype, pageId=page_id, ): try: if not f.local_filename or not exists(f.local_filename): workspace.mets.remove_file(f.ID) except Exception as e: ctx.log.exception("Error removing %f: %s", f, e) raise(e) workspace.save_mets() # ---------------------------------------------------------------------- # ocrd workspace list-group # ---------------------------------------------------------------------- @workspace_cli.command('list-group') @pass_workspace def list_groups(ctx): """ List fileGrp USE attributes """ workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url)) print("\n".join(workspace.mets.file_groups)) # ---------------------------------------------------------------------- # ocrd workspace list-pages # ---------------------------------------------------------------------- @workspace_cli.command('list-page') @pass_workspace def list_pages(ctx): """ List physical page IDs """ workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url)) print("\n".join(workspace.mets.physical_pages)) # ---------------------------------------------------------------------- # ocrd workspace get-id # ---------------------------------------------------------------------- @workspace_cli.command('get-id') @pass_workspace def get_id(ctx): """ Get METS id if any """ workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url)) ID = workspace.mets.unique_identifier if ID: print(ID) # ---------------------------------------------------------------------- # ocrd workspace set-id # ---------------------------------------------------------------------- @workspace_cli.command('set-id') @click.argument('ID') @pass_workspace def set_id(ctx, id): # pylint: disable=redefined-builtin """ Set METS ID. If one of the supported identifier mechanisms is used, will set this identifier. Otherwise will create a new <mods:identifier type="purl">{{ ID }}</mods:identifier>. """ workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url), automatic_backup=ctx.automatic_backup) workspace.mets.unique_identifier = id workspace.save_mets() # ---------------------------------------------------------------------- # ocrd workspace merge # ---------------------------------------------------------------------- @workspace_cli.command('merge') @click.argument('METS_PATH') @click.option('--copy-files', is_flag=True, help="Copy files as well", default=True) @click.option('--fileGrp-mapping', help="JSON object mapping src to dest fileGrp") @mets_find_options @pass_workspace def merge(ctx, copy_files, filegrp_mapping, filegrp, file_id, page_id, mimetype, mets_path): # pylint: disable=redefined-builtin """ Merges this workspace with the workspace that contains ``METS_PATH`` The ``--file-id``, ``--page-id``, ``--mimetype`` and ``--fileGrp`` options have the same semantics as in ``ocrd workspace find``, see ``ocrd workspace find --help`` for an explanation. """ mets_path = Path(mets_path) if filegrp_mapping: filegrp_mapping = loads(filegrp_mapping) workspace = Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url), automatic_backup=ctx.automatic_backup) other_workspace = Workspace(ctx.resolver, directory=str(mets_path.parent), mets_basename=str(mets_path.name)) workspace.merge( other_workspace, copy_files=copy_files, fileGrp_mapping=filegrp_mapping, fileGrp=filegrp, ID=file_id, pageId=page_id, mimetype=mimetype, ) workspace.save_mets() # ---------------------------------------------------------------------- # ocrd workspace backup # ---------------------------------------------------------------------- @workspace_cli.group('backup') @click.pass_context def workspace_backup_cli(ctx): # pylint: disable=unused-argument """ Backing and restoring workspaces - dev edition """ @workspace_backup_cli.command('add') @pass_workspace def workspace_backup_add(ctx): """ Create a new backup """ backup_manager = WorkspaceBackupManager(Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url), automatic_backup=ctx.automatic_backup)) backup_manager.add() @workspace_backup_cli.command('list') @pass_workspace def workspace_backup_list(ctx): """ List backups """ backup_manager = WorkspaceBackupManager(Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url), automatic_backup=ctx.automatic_backup)) for b in backup_manager.list(): print(b) @workspace_backup_cli.command('restore') @click.option('-f', '--choose-first', help="Restore first matching version if more than one", is_flag=True) @click.argument('bak') #, type=click.Path(dir_okay=False, readable=True, resolve_path=True)) @pass_workspace def workspace_backup_restore(ctx, choose_first, bak): """ Restore backup BAK """ backup_manager = WorkspaceBackupManager(Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url), automatic_backup=ctx.automatic_backup)) backup_manager.restore(bak, choose_first) @workspace_backup_cli.command('undo') @pass_workspace def workspace_backup_undo(ctx): """ Restore the last backup """ backup_manager = WorkspaceBackupManager(Workspace(ctx.resolver, directory=ctx.directory, mets_basename=basename(ctx.mets_url), automatic_backup=ctx.automatic_backup)) backup_manager.undo()