Merge pull request #449 from tcezard/EVA3580

EVA-3580 - New function to get the release to run

eva-accession-release-automation/run_release_in_embassy/release_metadata.py

@@ -90,3 +90,33 @@ def get_release_inventory_info_for_assembly(taxonomy_id, assembly_accession, rel
         raise Exception("Could not find release inventory pertaining to taxonomy ID: {0} and assembly: {1} "
                         .format(taxonomy_id, assembly_accession))
     return results[0][0]
+
+
+def get_release_for_status_and_version(release_species_inventory_table, metadata_connection_handle, status=None,
+                                       release_version=None, taxonomy_id=None, assembly_accessions=None):
+    def format_list(list_to_format):
+        return f"({str(list_to_format).strip('[]')})"
+
+    if status:
+        if 'Pending' in status:
+            status.remove('Pending')
+            if status:
+                status_statement = f"and (release_status in {format_list(status)} or release_status is null) "
+            else:
+                status_statement = f"and release_status is null "
+        else:
+            status_statement = f"and release_status in {format_list(status)} "
+    else:
+        status_statement = None
+
+    query = ''.join((
+        f"select taxonomy, assembly_accession, release_version, release_status from {release_species_inventory_table} ",
+        f"where should_be_released ",
+        f"and num_rs_to_release > 0 ",
+        f"{status_statement}" if status_statement else '',
+        f"and release_version={release_version} " if release_version else '',
+        f"and taxonomy={taxonomy_id} " if taxonomy_id else '',
+        f"and assembly_accessions in {format_list(assembly_accessions)} " if assembly_accessions else '',
+        "ORDER BY release_version, taxonomy, assembly_accession"
+    ))
+    return get_all_results_for_query(metadata_connection_handle, query)

eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py

@@ -11,17 +11,19 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+import sys
 from argparse import ArgumentParser
 
 import os
 from functools import lru_cache
 
 import yaml
 from ebi_eva_common_pyutils.command_utils import run_command_with_output
+from ebi_eva_common_pyutils.common_utils import pretty_print
 from ebi_eva_common_pyutils.logger import logging_config
 from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
 from ebi_eva_common_pyutils.config import cfg
-from run_release_in_embassy.release_metadata import get_release_assemblies_for_taxonomy
+from run_release_in_embassy.release_metadata import get_release_assemblies_for_taxonomy, get_release_for_status_and_version
 from run_release_in_embassy.release_common_utils import get_release_folder_name
 
 
@@ -105,6 +107,23 @@ def run_release_for_species(taxonomy_id, release_assemblies, release_version, re
             run_command_with_output(f"Running workflow file {workflow_file_path}", workflow_command)
 
 
+def list_release_per_status(status, release_version, taxonomy_id, assembly_accessions):
+    private_config_xml_file = cfg.query("maven", "settings_file")
+    profile = cfg.query("maven", "environment")
+    release_species_inventory_table = cfg.query('release', 'inventory_table')
+    with get_metadata_connection_handle(profile, private_config_xml_file) as metadata_connection_handle:
+        header = ['taxonomy', 'assembly_accession', 'release_version', 'release_status']
+        table = []
+        for taxonomy, assembly_accession, release_version, release_status in get_release_for_status_and_version(
+                release_species_inventory_table, metadata_connection_handle, status, release_version=release_version,
+                taxonomy_id=taxonomy_id, assembly_accessions=assembly_accessions
+        ):
+            if release_status is None:
+                release_status = 'Pending'
+            table.append((taxonomy, assembly_accession, release_version, release_status))
+        pretty_print(header, table)
+
+
 def load_config(*args):
     cfg.load_config_file(
         *args,
@@ -115,16 +134,27 @@ def load_config(*args):
 
 def main():
     argparse = ArgumentParser()
-    argparse.add_argument("--taxonomy_id", help="ex: 9913", required=True)
+    argparse.add_argument("--list_status", nargs='+',
+                          help="Generate the list of species and assembly that needs to be released",
+                          choices=['Pending', 'Started', 'Completed'])
+    argparse.add_argument("--taxonomy_id", help="ex: 9913")
     argparse.add_argument("--assembly_accessions", nargs='+', help="ex: GCA_000003055.3")
-    argparse.add_argument("--release_version", required=True)
-    argparse.add_argument("--resume", default=False, required=False,
+    argparse.add_argument("--release_version")
+    argparse.add_argument("--resume", default=False,
                           help="Resume the nextflow pipeline for the specified taxonomy and assembly")
     args = argparse.parse_args()
     load_config()
     logging_config.add_stdout_handler()
-
-    run_release_for_species(args.taxonomy_id, args.assembly_accessions, args.release_version, args.resume)
+    if args.list_status:
+        list_release_per_status(args.list_status, args.release_version, args.taxonomy_id, args.assembly_accessions)
+    else:
+        if not args.taxonomy_id:
+            logger.error('--taxonomy_id is required when running the release')
+            sys.exit(1)
+        if not args.release_version:
+            logger.error('--release_version is required when running the release')
+            sys.exit(1)
+        run_release_for_species(args.taxonomy_id, args.assembly_accessions, args.release_version, args.resume)
 
 
 if __name__ == "__main__":