D4Science Infrastructure

what's the problem?

I do not know. If you try to execute the algo through the DM you will see that it does not work (it returns an error).
The execution of the script seems to stop at its very beginning, ie after the line system("chmod -R 777 ./")

Ok, I have added logs and republished the script

Following the logs, the problem seems to be located in these lines of the R script (i.e. where I set the default values for the parameters):

cat("setting values to parameters\n")
include_IOTC<-TRUE
include_ICCAT<-TRUE
include_IATTC<-TRUE
include_WCPFC<-TRUE
include_CCSBT<-TRUE
datasets_year_release<-"2017"
iccat_include_type_of_school<-TRUE
iattc_raise_flags_to_schooltype<-TRUE
iattc_dimension_to_use_if_no_raising_flags_to_schooltype<-"flag"
mapping_map_code_lists<-TRUE
mapping_csv_mapping_datasets_url<-"http://data.d4science.org/ZWFMa3JJUHBXWk9NTXVPdFZhbU5BUFEyQnhUeWd1d3lHbWJQNStIS0N6Yz0"
mapping_keep_src_code<-FALSE
gear_filter<-"NULL"
unit_conversion_convert<-FALSE
unit_conversion_csv_conversion_factor_url<-"http://data.d4science.org/Z3V2RmhPK3ZKVStNTXVPdFZhbU5BTTVaWnE3VFAzaElHbWJQNStIS0N6Yz0"
unit_conversion_codelist_geoidentifiers_conversion_factors<-"areas_conversion_factors_numtoweigth_ird"
raising_georef_to_nominal<-TRUE
aggregate_on_5deg_data_with_resolution_inferior_to_5deg<-TRUE
disaggregate_on_5deg_data_with_resolution_superior_to_5deg<-"none"
disaggregate_on_1deg_data_with_resolution_superior_to_1deg<-"none"
spatial_curation_data_mislocated<-"remove"
overlapping_zone_iattc_wcpfc_data_to_keep<-"IATTC"
SBF_data_rfmo_to_keep<-"CCSBT"
metadata_title<-"Global monthly catch of tuna, tuna-like and shark species (%year_start%-%year_end%) aggregated by %spatial_resolution%° squares"
metadata_contact_owner<-"ird@ird.fr"
metadata_contact_metadata<-"paul.taconet@ird.fr@@julien.barde@ird.fr@@emmanuel.blondel@fao.org"
metadata_contact_pointofcontact<-"paul.taconet@ird.fr@@julien.barde@ird.fr@@emmanuel.blondel@fao.org"
metadata_contact_principalinvestigator<-"emmanuel.chassot@ird.fr"
metadata_contact_publisher<-"ird@ird.fr"
metadata_contact_processor<-"paul.taconet@ird.fr"
metadata_description<-"This dataset lists global catch of tuna, tuna-like and shark species from %year_start% to %year_end%. Catches are stratified by month, species, gear, vessel flag reporting country, fishing mode (i.e. type of school used), area (mainly 5° square) and unit of catch (weight or number). This dataset was computed using public domain catch-and-effort datasets released by the five tuna Regional Fisheries Management Organizations: the Indian Ocean Tuna Commission (IOTC), the International Commission for the Conservation of Atlantic Tunas (ICCAT), the Inter-American Tropical Tuna Commission (IATTC), The Western and Central Pacific Fisheries Commission (WCPFC), the Commission for the Conservation of Southern Bluefin Tuna (CCSBT)."
metadata_source<-"IRD"
metadata_supplemental_information<-"IRD"

cat("setting values to parameters OK\n")

If i remember well, there is a weird adhoc "workaround" to make Dataminer understand the boolean parameters... https://wiki.gcube-system.org/gcube/Statistical_Algorithms_Importer:_R_Project_FAQ#Managing_Boolean_values Maybe it is what you are looking for...

The line in my R script is:

metadata_and_parameterization<-push_R_script_to_server(metadata_and_parameterization,virtual_repository_with_R_files,gcube_username,gcube_token)

here I need as values for gcube_username and gcube_token the username and the token of the user that is executing the algo through the Data miner in the VRE

Thanks for the documentation.
However, the logs indicate that the object "gcube_username" does not exist (object 'gcube_username' not found) (https://support.d4science.org/attachments/download/2105/RLOGb8345554-8a50-446c-bf59-aec05145675a.txt , while according to the documentation, this object should exist.

Hi Paul, I guarantee the variables are there because they are used extensively by other algorithms (also some we are currently running every day).

However, global variables are deleted if you use cleaning instruction such as rm(list=ls(all=TRUE)) at the beginning of your code. These instructions are not necessary on the DataMiner since when an algorithm runs it is always executed in a completely new environment.

Hi Paul,
I think you just miss to use a "<<-" instead of "<-":

Since they are global variables, I would use directly gcube_username and gcube_token. Thus, I would write

username<<-gcube_username
token<<-gcube_token

before calling the WS functions. Anyway, also in your code (with the vre_* variables) this should work. You should be done with the lines above.

Overall, I'm referring to the instructions in this page: https://wiki.gcube-system.org/gcube/Workspace_Interaction_From_R

Thanks GianPaolo.
I have modified my code as you indicated and it is working now.
Thank you!