mirror of
https://github.com/chanzuckerberg/cellxgene.git
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a593e95ab3
* rename config param label-file * annotations rework - CLI params, file naming and backups * lint * improve cli option error checks * enable session cookies * enable session cookies * add session id * name annotations file in multi-dataset and multi-user safe manner * pass data user hash to front-end * add annotation collection name support to front-end * add constant for annotation data collection name * parameterize annotation collection name; make it sticky in the session * clarify comments * hard wire a temporary data collection name for testing * prettier * test comment * package command * set annotations filename dialog * name and hash are visible * wire up data collection capture
62 lines
1.9 KiB
Python
62 lines
1.9 KiB
Python
"""
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Helpers for user annotations
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"""
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import os
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import os.path
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from datetime import datetime
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import pandas as pd
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def read_labels(fname):
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if fname is not None and os.path.exists(fname) and os.path.getsize(fname) > 0:
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return pd.read_csv(fname, dtype='category', index_col=0, header=0, comment='#')
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else:
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return pd.DataFrame()
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def write_labels(fname, df, header=None, backup_dir=None):
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if backup_dir is not None:
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backup(fname, backup_dir)
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# rotate_fname(fname, backup_dir)
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if not df.empty:
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with open(fname, 'w', newline="") as f:
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if header is not None:
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f.write(header)
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df.to_csv(f)
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else:
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open(fname, 'w').close()
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def backup(fname, backup_dir, max_backups=9):
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"""
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save N backups of file to backup_dir.
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1. fname -> backup_dir/fname-TIME
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2. delete excess files in backup_dir
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"""
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# Make sure there is work to do
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if not os.path.exists(fname):
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return
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# Ensure backup_dir exists
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if not os.path.exists(backup_dir):
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os.mkdir(backup_dir)
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# Save current file to backup_dir
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fname_base = os.path.basename(fname)
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fname_base_root, fname_base_ext = os.path.splitext(fname_base)
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# don't use ISO standard time format, as it contains characters illegal on some filesytems.
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nowish = datetime.now().strftime('%Y-%m-%dT%H-%M-%S')
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backup_fname = os.path.join(backup_dir, f"{fname_base_root}-{nowish}{fname_base_ext}")
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if os.path.exists(backup_fname):
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os.remove(backup_fname)
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os.rename(fname, backup_fname)
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# prune the backup_dir to max number of backup files, keeping the most recent backups
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backups = list(filter(lambda s: s.startswith(fname_base_root), os.listdir(backup_dir)))
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excess_count = len(backups) - max_backups
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if excess_count > 0:
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backups.sort()
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for bu in backups[0:excess_count]:
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os.remove(os.path.join(backup_dir, bu))
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