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| 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. |
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emen2client.py --help |
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| emen2client.py download --help | == Download Usage == |
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| 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 == |
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| 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 |
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 |
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| Other values, e.g. "volume", will create child records of that type, with 1 file per child record. | Other values, e.g. "volume", will create child records of that type, with 1 file per child record. |
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| Alternatively, you can use "none" for record type and the files will be attached directly to the specified record ID. |
Alternatively, you can use "none" for record type and the files will be attached directly to the specified record ID. |
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| [irees@mbp ~/data]$ emen2client.py upload ccd 410082 *.dm3 | [irees@mbp ~/data]$ emen2client.py upload ccd 123456 *.dm3 |
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
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 filesExample:
[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