From 249847d3cee38c129193b1f5565adfccf6e6cf38 Mon Sep 17 00:00:00 2001 From: April Shen Date: Tue, 26 Mar 2024 13:51:43 +0000 Subject: [PATCH] fix on test --- .../create_release_tracking_table.py | 2 ++ 1 file changed, 2 insertions(+) rename eva-accession-release-automation/{ => run_release_in_embassy}/create_release_tracking_table.py (99%) diff --git a/eva-accession-release-automation/create_release_tracking_table.py b/eva-accession-release-automation/run_release_in_embassy/create_release_tracking_table.py similarity index 99% rename from eva-accession-release-automation/create_release_tracking_table.py rename to eva-accession-release-automation/run_release_in_embassy/create_release_tracking_table.py index d5aa6b70a..e02fbdb06 100644 --- a/eva-accession-release-automation/create_release_tracking_table.py +++ b/eva-accession-release-automation/run_release_in_embassy/create_release_tracking_table.py @@ -13,6 +13,7 @@ # See the License for the specific language governing permissions and # limitations under the License. import argparse +import re from collections import defaultdict from functools import cached_property from itertools import cycle @@ -111,6 +112,7 @@ def _fill_from_supported_assembly_tracker(self): def _insert_entry_for_taxonomy_and_assembly(self, tax, asm_acc, sources, sc_name=None, fasta_path=None, report_path=None, release_folder_name=None): sc_name = sc_name if sc_name else get_scientific_name_from_ensembl(tax) + sc_name = re.sub("'", "\\'", sc_name) # a special fix to insert Ambystoma 'unisexual hybrid' verbatim if asm_acc != 'Unmapped': ncbi_assembly = NCBIAssembly(asm_acc, sc_name, self.ref_dir) fasta_path = fasta_path if fasta_path else ncbi_assembly.assembly_fasta_path