70377c624fdc514cd5897985c67c922cba613c1d,foreman/data_refinery_foreman/surveyor/transcriptome_index.py,TranscriptomeIndexSurveyor,discover_species,#TranscriptomeIndexSurveyor#,259

Before Change

            organism_name = None

        // Survey jobs are on a per-organism basis.
        for species in specieses:
            if species["name"] == organism_name:
                specieses = [species]
                logger.info("Found species " + organism_name + " on Ensembl.",
                            survey_job=self.survey_job.id)
                break

        species_surveyed = 0
        all_new_species = []
        for species in specieses:
            if number_of_organisms != -1 and species_surveyed >= number_of_organisms:
                break

            all_new_species.append(self._generate_files(species))
            species_surveyed += 1

        return all_new_species

After Change

            for species in specieses:
                all_new_species.append(self._generate_files(species))

        if len(all_new_species) == 0:
            logger.error("Unable to find any species!",
                         ensembl_division=ensembl_division,
                         organism_name=organism_name)

        return all_new_species

Instances