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Use the link below to download emen2client.py:
emen2client.py serves several functions.
1. Provides a simple command-line interface for bulk upload and download from the database.
2. Contains a number of classes that are useful in building EMEN2 client applications. It is used by other programs, such as EMDash. See EMEN2/API for details.
3. Provides a mechanism for uploading EMAN/EMAN2 processing data, including CTF parameters and box coordinates.
This page documents how to use emen2client.py for upload and download.
Use the link below to download emen2client.py:
./emen2client.py <action> Actions available: upload, download For detailed help: ./emen2client.py <action> --help
When run from the command line, emen2client.py has two actions: upload and download. Select an action by specifying it as the first command line argument.
The "download" action is used to batch download files from the database. A Record ID is required; in most cases, this will be the Record ID of a grid_imaging session containing CCD frames. There are a number of options, detailed below, although in most cases the default options are fine. You can optionally specify a filename or pattern to filter the list of files that will be downloaded.
Usage: emen2client.py download [options] <recid> [filename-pattern] Options: -h, --help show this help message and exit -U USERNAME, --username=USERNAME Username -P PASSWORD, --password=PASSWORD Password (Note: specifying passwords in shell commands is not secure) -H HOST, --host=HOST Host endpoint URI -C CTXID, --ctxid=CTXID Valid Context ID --recurse=RECURSE Recursion level -o, --overwrite Overwrite existing files (default is to skip) -r, --rename If a file already exists, save with format 'duplicate.recid:original_filename.dm3' -s, --sidecar Include sidecar file with EMEN2 metadata in JSON format --gzip Decompress gzip'd files. Requires gzip in path (default) --no-gzip Do not decompress gzip'd files.
[irees@mbp ~/data]$ emen2client.py download 123456 Username: ianrees Password: 1 of 1: 123456 Checking for items to download Found 92 items in 93 records 1 of 92: 2009110400033 Downloading frame1.dm3.gz -> frame1.dm3... 2 of 92: 2009110400032 Downloading frame2.dm3.gz -> frame2.dm3... 3 of 92: 2009110400031 Downloading frame3.dm3.gz -> frame3.dm3... .... snip ....
The "upload" action will upload files into the database. A record type, record ID, and list of files must be specified. If you are uploading CCD frames, use "ccd", if you are uploading SerielEM tomography stacks, use "stack." Other types are also available, e.g. "volume" to upload a number of density maps.
Usage: emen2client.py upload [options] <record type> <recid> <files to upload> Record type can be any valid database protocol. Some record types have special, application-specific handlers, e.g.: ccd CCD Frames scan Scanned micrographs stack Tomograms Other values, e.g. "volume", will create child records of that type, with 1 file per child record. Alternatively, you can use "none" for record type and the files will be attached directly to the specified record ID. Options: -h, --help show this help message and exit -U USERNAME, --username=USERNAME Username -P PASSWORD, --password=PASSWORD Password (Note: specifying passwords in shell commands is not secure) -H HOST, --host=HOST Host endpoint URI -C CTXID, --ctxid=CTXID Valid Context ID -q, --noninteractive Do not prompt for parameter values -s, --sidecar Write sidecar file after upload -f, --force Force re-upload even if a sidecar is found --metafile Attempt to read JAMES/JADAS metadata files (default) --no-metafile Ignore metadata files
[irees@mbp ~/data]$ emen2client.py upload ccd 123456 *.dm3 Username: ianrees Password: 3 Files to upload: 1.dm3 2.dm3 3.dm3 ----- tem_magnification_set ----- Description: Magnification set on microscope Units: K Common values: 0) 60.0 1) 50.0 2) 40.0 3) 20.0 4) 80.0 5) 100.0 6) 15.0 7) 30.0 8) 25.0 10) None or N/A 11) Enter a different not listed above Selection (0-11): 0 ----- ctf_defocus_set ----- Description: Intended defocus while imaging, underfocus positive Units: um Common values: 0) 1.0 1) -2.0 2) 2.0 3) 1.5 4) 3.0 5) 2.5 6) -3.0 7) -1.5 8) -2.5 9) 0.8 10) None or N/A 11) Enter a different not listed above Selection (0-11): 0 ... snip: additional prompts ommitted for clarity ... 1 of 3: 1.dm3 Preparing for upload Checking and committing records 1.dm3 Done. Uploaded 1.dm3 to record 417171 @ 15210.92 kb/sec 2 of 3: 2.dm3 Preparing for upload Checking and committing records 2.dm3 Done. Uploaded 2.dm3 to record 417172 @ 15080.45 kb/sec 3 of 3: 3.dm3 Preparing for upload Checking and committing records 3.dm3 Done. Uploaded 3.dm3 to record 417173 @ 14253.12 kb/sec
emen2client.py provides growing support for uploading processed image data back into the database. See EMAN2 Integration for details.