Package: onedep-deposition
OneDep Deposition API WrapperThis wrapper comes with a command line interface that can be executed by runningpython cli.py <command>.API KeyGo to the DepUI in the test server, login to ORCID and then on the left, below the map, click onGenerate Key. Either copy the key to a file in~/onedepapi.jwtin your local laptop, or set it as an environment variable withexport ONEDEP_API_KEY=<key>.OptionsImportant!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 creationThe 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 wbueno@ebi.ac.uk -u 0000-0001-6872-1814,0000-0003-0599-3569 -c "United Kingdom"Allowed experiment types arexray,fiber,neutron,em,ec,nmr,ssnmr.If you are creating an EM deposition, you also MUST specify the subtype using the-soption. Allowed subtypes arehelical,single,subtomogram,tomography. Example:python cli.py -h http://local.wwpdb.org:12000/deposition --no_ssl_verify deposition create -t em -s helical -e wbueno@ebi.ac.uk -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-Eoption.For NMR depositions, you may specify a related BMRB code using the-Boption.Deposition detailsUse the commandpython cli.py deposition get <dep_id>to get details of a deposition.UsersThe 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>FilesAs 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 datafsc-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 displayadd-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 displayadd-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: MTZco-cif: Coordinates (mmCIF format)xs-cif: mmCIF (structure factors)xs-mtz: MTZxa-par: Parameter filexa-top: Topology filexa-mat: Virus matrixco-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)ProcessAfter uploading files, we can start the processing step with thedeposition processcommand. To get the status of the processing step, run thedeposition statuscommand.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>