diff --git a/constants.py b/constants.py index 0eada7f4ed16aa559fa65dc50093ee84de4318ff..ca78c4a78cf72d584544124fa2b17aa5ee4f2733 100644 --- a/constants.py +++ b/constants.py @@ -20,7 +20,6 @@ ORG_PARAM_DATA_BLASTP_PATH = "blastp_path" ORG_PARAM_DATA_BLASTX_PATH = "blastx_path" ORG_PARAM_DATA_GENOME_VERSION = "genome_version" ORG_PARAM_DATA_OGS_VERSION = "ogs_version" -ORG_PARAM_DATA_PERFORMED_BY = "performed_by" ORG_PARAM_SERVICES = "services" ORG_PARAM_SERVICES_BLAST = "blast" ORG_PARAM_SERVICES_GO = "go" diff --git a/examples/citrus_sinensis.yml b/examples/citrus_sinensis.yml index 38087bbe0cfe9b87dbd6519ddebd32730aab1dc7..7229c3b365f667b5814875cc66de6353973bf0de 100644 --- a/examples/citrus_sinensis.yml +++ b/examples/citrus_sinensis.yml @@ -31,7 +31,6 @@ genome_version: 1.0 # Same as genome version, but for the OGS analysis ogs_version: 1.0 - performed_by: services: # List the optional services/resources to add blast: 0 # "1" to add links to blast form, "some/url" to specify, multiple urls as "Name1=url1&Name2=url2", "0" to disable it. Default: "0" diff --git a/speciesData.py b/speciesData.py index 2c16840b475c6570906ab359fd07efe3ec3cb7b0..c012a46856e2c57d2cb3df83dfe6a2968b3c40b0 100755 --- a/speciesData.py +++ b/speciesData.py @@ -66,11 +66,10 @@ class SpeciesData: self.genus = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_GENUS]) self.strain = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_STRAIN]) self.sex = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_SEX]) - self.common = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_COMMON_NAME]) + self.common_name = self.clean_string(parameters_dictionary_description[constants.ORG_PARAM_DESC_COMMON_NAME]) self.date = datetime.today().strftime("%Y-%m-%d") self.origin = parameters_dictionary_description[constants.ORG_PARAM_DESC_ORIGIN] - self.performed = parameters_dictionary_data[constants.ORG_PARAM_DATA_PERFORMED_BY] if parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_VERSION] == "": self.genome_version = "1.0" @@ -100,10 +99,8 @@ class SpeciesData: self.genus_uppercase = self.genus[0].upper() + self.genus_lowercase[1:] self.genus_species = "{0}_{1}".format(self.genus_lowercase, self.species_lowercase) - self.chado_species_name = "{0} {1}".format(self.species, self.sex) self.full_name = ' '.join(utilities.filter_empty_not_empty_items([self.genus_uppercase, self.species, self.strain, self.sex])["not_empty"]) self.full_name_lowercase = self.full_name.lower() - self.abbreviation = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase[0], self.species, self.strain, self.sex])["not_empty"]) self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items( [self.genus_lowercase, self.species_lowercase, self.strain.lower(), diff --git a/templates/organisms.yml.j2 b/templates/organisms.yml.j2 index 019fce089740ba1634b15f2756f8d04e5fa2e5f3..2a127adb360d4d5a1579cdcd8a3d1f99d196f5be 100644 --- a/templates/organisms.yml.j2 +++ b/templates/organisms.yml.j2 @@ -21,7 +21,6 @@ {{ org_param_data_blastx_path }}: {{ org_param_data_blastx_path_value }} {{ org_param_data_genome_version }}: {{ org_param_data_genome_version_value }} {{ org_param_data_ogs_version }}: {{ org_param_data_ogs_version_value }} - {{ org_param_data_performed_by }}: {{ org_param_data_performed_by_value }} {{ org_param_services }}: {{ org_param_services_blast }}: {{ org_param_services_blast_value }} {{ org_param_services_go }}: {{ org_param_services_go_value }} \ No newline at end of file