omero transfer prepare needs a connection but omero import -f does not #95
Description
omero transfer prepare fails to execute for a simple user if $OMERODIR is not defined or points to a non existing directory.
Creating $OMERODIR even as an empty directory allows omero transfer prepare to run.
omero transfer prepare calls omero import -f in generate_xml through a CLI() instance.
The OMERODIR not found error happens at this line, but further traceback is lost by the subcommand
from omero.cli import CLI
cli = CLI()
cli.loadplugins()
cli.invoke(['logout'])
# import -f works
cli.invoke(['import', '-f', '.'])
# output
"""
Using OMERO.java-5.6.6-ice36
2025-02-13 13:48:43,780 103 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.6.0
2025-02-13 13:48:43,788 111 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 6.11.1 revision: 383bac974cd52e83908b54e4769ebb1e0d0673ee date: 1 December 2022
2025-02-13 13:48:43,826 149 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2025-02-13 13:48:43,976 299 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2025-02-13 13:48:44,099 422 [ main] ERROR loci.formats.ImageReader - File has length 0 and may be corrupt
2025-02-13 13:48:44,109 432 [ main] INFO ome.formats.importer.ImportCandidates - 8 file(s) parsed into 0 group(s) with 8 call(s) to setId in 127ms. (133ms total) [8 unknowns]
"""
# We are not connected, this fails
cli.invoke(['fs', 'images'])
# output
"""
Previously logged in to localhost:4064 as facility0
stdin is not a terminal: cannot request server
"""
# this fails too
cli.invoke(['transfer', 'prepare', '.'])
# output
"""
Previously logged in to localhost:4064 as facility0
stdin is not a terminal: cannot request server
"""
# Now connect
cli.invoke(['login', '-w', 'omero', 'facility0@localhost'])
"""
Previously logged in to localhost:4064 as facility0
Created session for facility0@localhost:4064. Idle timeout: 10 min. Current group: default
"""
Path(os.environ['OMERODIR']).exists()
# output
"""
False
"""
# run transfer prepare while logged in
cli.invoke(['transfer', 'prepare', '.'])
# output
"""
Using session for facility0@localhost:4064. Idle timeout: 10 min. Current group: default
Truncated Traceback (Use C-c C-$ to view full TB):
File ~/miniforge3/envs/quay/lib/python3.10/subprocess.py:1847, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session)
1845 if errno_num != 0:
1846 err_msg = os.strerror(errno_num)
-> 1847 raise child_exception_type(errno_num, err_msg, err_filename)
1848 raise child_exception_type(err_msg)
FileNotFoundError: [Errno 2] No such file or directory: '/home/guillaume/OMERO.server'
"""
# create an empty dir
Path(os.environ["OMERODIR"]).mkdir()
# This succeeds
cli.invoke(['transfer', 'prepare', '.'])
"""
Using session for facility0@localhost:4064. Idle timeout: 10 min. Current group: default
"""