API reference

Utility functions that make it easier to write a Resolwe process.

class resolwe_runtime_utils.OutputType

An enumeration.

resolwe_runtime_utils.command(name, data)

Create a command from command name and payload.

resolwe_runtime_utils.send_message(data, header_size=8)

Send data over socket.

resolwe_runtime_utils.collect_entry(entry, references)

Get the size of the entry and its references and upload them.

The entry and its references are uploaded to the chosen storage connector.

NOTE: This process may take considerable amount of time.

Args entry:file or directory that is being collected. Args references:  references belonging to the entry.

resolwe_runtime_utils.save_list(key, *values)

Construct save_list command.

resolwe_runtime_utils.annotate_entity(key, value)

Construct annotate entity command.

resolwe_runtime_utils.save(key, value)

Construct save command.

resolwe_runtime_utils.save_file(key, file_path, *refs)

Construct save file command.

Data is of the form: { key: {“file”: file_path, “size”: file_size, “total_size”: total_size }}

with added references

“refs”: [refs[0], refs[1], … ]

when applicable.

resolwe_runtime_utils.save_file_list(key, *files_refs)

Construct the save files command.

Each parameter is a file-refs specification of the form: <file-path>:<reference1>,<reference2>, …, where the colon ‘:’ and the list of references are optional.

Data object is of the form: { key: {“file”: file_path}}, or { key: {“file”: file_path, “refs”: [refs[0], refs[1], … ]}}

resolwe_runtime_utils.save_dir(key, dir_path, *refs)

Construct save dir command.

Data object is of the form: { key: {“dir”: dir_path}}, or { key: {“dir”: dir_path, “refs”: [refs[0], refs[1], … ]}}

resolwe_runtime_utils.save_dir_list(key, *dirs_refs)

Construct save dirs command.

Each parameter is a dir-refs specification of the form: <dir-path>:<reference1>,<reference2>, …, where the colon ‘:’ and the list of references are optional.

Data object is of the form: { key: {“dir”: dir_path}}, or { key: {“dir”: dir_path, “refs”: [refs[0], refs[1], … ]}}

resolwe_runtime_utils.info(value)

Construct info command.

resolwe_runtime_utils.warning(value)

Construct warning command.

resolwe_runtime_utils.error(value)

Construct error command.

resolwe_runtime_utils.progress(progress)

Construct progress command.

Progress is reported as float between 0 and 1 and sent to listener as int between 0 and 100.

resolwe_runtime_utils.checkrc(rc, *args)

Check if rc (return code) meets requirements.

Check if rc is 0 or is in args list that contains acceptable return codes. Last argument of args can optionally be error message that is printed if rc doesn’t meet requirements.

Output is JSON of the form:

{“proc.rc”: <rc>,

“proc.error”: “<error_msg>”},

where “proc.error” entry is omitted if empty.

resolwe_runtime_utils.export_file(file_path)

Construct export command.

resolwe_runtime_utils.run(process_slug, run)

Run process with the given slug with the given inputs.

The argument run must be a valid JSON string representing the inputs.

class resolwe_runtime_utils.ImportedFormat

Import destination file format.

resolwe_runtime_utils.import_file(src, file_name, imported_format='both', progress_from=0.0, progress_to=None)

Import file to working directory.

Parameters:

• src – Source file path or URL
• file_name – Source file name
• imported_format – Import file format (extracted, compressed or both)
• progress_from – Initial progress value
• progress_to – Final progress value

Returns:

Destination file path (if extracted and compressed, extracted path given)