Python parsing scripts

The Experiment Object, Platform Object and Sample Object are Python objects used as proxy to import a new experiment in the database

The file name of the experiment, platform or sample is stored in the variable named INPUT_FILE The name of the entity (experiment, platform or sample name) is stored in the variable named ENTITY_NAME To access parameters passed to each script use the list PARAMETERS Within each entity (experiment, platform or sample) you can choose the execution order of the script using the Order column.

To access Experiment Object use the EXPERIMENT_OBJECT variable in the Python script used with experiment files.


EXPERIMENT_OBJECT.experiment_access_id: (string) the experiment access id EXPERIMENT_OBJECT.experiment_name: (string) the experiment name EXPERIMENT_OBJECT.scientific_paper_ref: (string) pubblication associated to the experiment EXPERIMENT_OBJECT.description: (string) the experiment description

To access Platform Object use the PLATFORM_OBJECT variable in the Python script used with platform files.


PLATFORM_OBJECT.platform_access_id (string) the platform access id PLATFORM_OBJECT.platform_name (string) the platform name PLATFORM_OBJECT.platform_type (string) ‘microarray or rna-seq’ PLATFORM_OBJECT.description (string) the platform description PLATFORM_OBJECT.add_bio_feature_reporter_data(name, description, **kwargs): add a reporter to the platform

**kwargs are platform_type dependent. i.e. for ‘microarray’ they are probe_access_id, probe_set_name, probe_type and sequence

To access Sample Object use the SAMPLE_OBJECT variable in the Python script used with sample files.

SAMPLE_OBJECT variables and methods

SAMPLE_OBJECT.sample_name (string) the sample name SAMPLE_OBJECT.description (string) the sample description SAMPLE_OBJECT.add_raw_data(bio_feature_reporter_name, value): add raw data of this sample