emen2client.py

emen2client.py serves two functions.

1. 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 and EMEN2/API/emen2client.py for details.

2. Provides a simple command-line interface for bulk upload and download from the database.

This page documents how to use emen2client.py for upload and download.

Download

* emen2client.py

Usage

./emen2client.py <action>
Actions available: upload, download
For detailed help: ./emen2client.py <action> --help

Download Usage

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.

Example:

[irees@mbp ~/data]$ emen2client.py download 123456

Username: ianrees
Password: 

1 of 1: 404229
        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 ....

Upload Usage

emen2client.py upload --help

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

Example:

[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) 60000.0
                8) 30.0
                9) 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