onedep-deposition 0.1.dev5

Package for wrapping the OneDep deposition API services

OneDep Deposition API Wrapper

This wrapper comes with a command line interface that can be executed by running python cli.py <command>.

API Key

Go to the DepUI in the test server, login to ORCID and then on the left, below the map, click on Generate Key. Either copy the key to a file in ~/onedepapi.jwt in your local laptop, or set it as an environment variable with export ONEDEP_API_KEY=<key>.

Options

Important!

Be mindful of the options we use in the commands here. If you are running in a test server, you will have to explicitly set the hostname and SSL verification flag for every command. The options are --hostname <host> and --no_ssl_verify.

Deposition creation

The command deposition create to start a new deposition:

python cli.py deposition create -t <exp type> -e <email> -u <users comma separated> -c <country>

For example, to create an x-ray deposition:

python cli.py -h http://local.wwpdb.org:12000/deposition --no_ssl_verify deposition create -t xray -e [e-mail] -u 0000-0001-6872-1814,0000-0003-0599-3569 -c "United Kingdom"

Allowed experiment types are xray, fiber, neutron, em, ec, nmr, ssnmr.

If you are creating an EM deposition, you also MUST specify the subtype using the -s option. Allowed subtypes are helical, single, subtomogram, tomography. Example:

python cli.py -h http://local.wwpdb.org:12000/deposition --no_ssl_verify deposition create -t em -s helical -e [e-mail] -u 0000-0001-6872-1814,0000-0003-0599-3569 -c "United Kingdom"

Also, for EM and EC depositions, you may specify a related EMDB code using the -E option.

For NMR depositions, you may specify a related BMRB code using the -B option.

Deposition details

Use the command python cli.py deposition get <dep_id> to get details of a deposition.

Users

The commands below can be used to manage users access for a deposition (add, remove, get):

python cli.py users get <dep_id>
python cli.py users add <dep_id> <user_orcid>
python cli.py users remove <dep_id> <user_orcid>

Files

As it is with users, files have their own command group. To upload a file, you need to run:

python cli.py files upload <dep_id> <file_path> <file_type>

Allowed file types are:

• layer-lines: Layer line data
• fsc-xml: FSC file (XML format)
• co-pdb: Coordinates (PDB format)
• co-cif: Coordinates (mmCIF format)
• vo-map: EM map (MRC/CCP4 format)
• img-emdb: Entry image for public display
• add-map: Additional EM map (MRC/CCP4 format)
• mask-map: EM mask (MRC/CCP4 format)
• half-map: EM half map (MRC/CCP4 format)
• co-cif: Coordinates (mmCIF format)
• vo-map: EM map (MRC/CCP4 format)
• img-emdb: Entry image for public display
• add-map: Additional EM map (MRC/CCP4 format)
• mask-map: EM mask (MRC/CCP4 format)
• half-map: EM half map (MRC/CCP4 format)
• xs-cif: mmCIF (structure factors)
• xs-mtz: MTZ
• co-cif: Coordinates (mmCIF format)
• xs-cif: mmCIF (structure factors)
• xs-mtz: MTZ
• xa-par: Parameter file
• xa-top: Topology file
• xa-mat: Virus matrix
• co-pdb: Coordinates (PDB format)
• co-cif: Coordinates (mmCIF format)
• nm-shi: Assigned chemical shift file (NMR-STAR V3.1 format)
• nm-res-amb: Restraint file (AMBER format)
• nm-aux-amb: Topology file (AMBER format)
• nm-res-bio: Restraint file (BIOSYM format)
• nm-res-cha: Restraint file (CHARMM format)
• nm-res-cns: Restraint file (CNS format)
• nm-res-cya: Restraint file (CYANA format)
• nm-res-dyn: Restraint file (DYNAMO/PALES/TALOS format)
• nm-res-gro: Restraint file (GROMACS format)
• nm-aux-gro: Topology file (GROMACS format)
• nm-res-isd: Restraint file (ISD format)
• nm-res-ros: Restraint file (ROSETTA format)
• nm-res-syb: Restraint file (SYBYL format)
• nm-res-xpl: Restraint file (XPLOR-NIH format)
• nm-res-oth: Restraint file (other format)
• nm-pea-any: Spectral peak list file (any format)
• nm-uni-nef: NMR Unified Data (NEF, NMR Exchange Format)
• nm-uni-str: NMR Unified Data (NMR-STAR V3.2 format)

Process

After uploading files, we can start the processing step with the deposition process command. To get the status of the processing step, run the deposition status command.

python cli.py deposition process <dep_id> python cli.py deposition status <dep_id>

To process EM data, you will need to provide a JSON file informing the pixel spacing and contour level for each uploaded map. This file must be in the following format: [{"file_id": X, "spacing": Y, "contour": Z}, ...]

python cli.py deposition process <dep_id> -V <path_to_json_file>