avidaR 1.1.3

Improvements

More friendly error messages for helping in solving issues caused by service availability, not valid user requests, unauthorized access, and others.

New features

Added timeout parameter in method set_access_options() to limit the amount of time waiting data from the service.

Bug fixes

Removed top-level code which creates triplestore object and set default access options. Read more about how to properly connect to ‘avidaDB’.

avidaR 1.1.2

Improvements

If seed_id is not specified, a randomly-chosen seed_id value is used to speed up the execution of the following functions:
- get_genome_id_from_logic_operation
- get_genome_id_from_phenotype_id
- get_transcriptome_id_from_logic_operation
- get_transcriptome_id_from_phenotype_id
- get_transcriptome_id_from_logic_operation
- get_transcriptome_id_from_phenotype_id
The function get_mutant_at_pos has been expanded:
- The function parameter genome_id has been added, and the previous parameters (inst_replaced , inst_replaced_by, and pos) can be now omitted by the user.
- If genome_id is not specified, a randomly chosen genome_id (between those provided by the function get_genome_id_of_wild_type_organisms) will be used.
- If inst_replaced and/or inst_replaced_by is/are not specified, all mutations at the specified position on the genome are shown.
- If the parameter pos is not specified, all mutations at all positions on the genome are shown (depending on the values of inst_replaced and inst_replaced_by).

New features

Added function get_db_summary that will provide a summary of the database.
Added get_genome_id_of_wild_type_organisms to identify the genomes of the organisms that were used as wild-type organisms.

Bug fixes

Removed a line from the clause WHERE that was slowing down the execution of the function get_transcriptome_id_from_phenotype_id.
The use of exponential notation was prevented because it provided empty results when requesting data by identifiers like genome_10000000.