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Merge pull request #455 from tcezard/EVA3586_split_release_in_steps
EVA-3586 - Split release job in single steps and chains them up in nextflow
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eva-accession-release-automation/publish_release_to_ftp/README_release_changelog.txt
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eva-accession-release-automation/publish_release_to_ftp/README_release_general_info.txt
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EVA RefSNP release 5 | ||
EVA RefSNP release 6 | ||
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Feedback | ||
================================== | ||
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eva-accession-release-automation/run_release_in_embassy/run_release_active_for_assembly.py
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# Copyright 2020 EMBL - European Bioinformatics Institute | ||
# | ||
# Licensed under the Apache License, Version 2.0 (the "License"); | ||
# you may not use this file except in compliance with the License. | ||
# You may obtain a copy of the License at | ||
# | ||
# http://www.apache.org/licenses/LICENSE-2.0 | ||
# | ||
# Unless required by applicable law or agreed to in writing, software | ||
# distributed under the License is distributed on an "AS IS" BASIS, | ||
# 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. | ||
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import click | ||
import sys | ||
import traceback | ||
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from ebi_eva_common_pyutils.logger import logging_config | ||
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from run_release_in_embassy.create_release_properties_file import create_release_properties_file_for_assembly | ||
from run_release_in_embassy.release_common_utils import open_mongo_port_to_tempmongo, close_mongo_port_to_tempmongo | ||
from ebi_eva_common_pyutils.command_utils import run_command_with_output | ||
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logger = logging_config.get_logger(__name__) | ||
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def run_release_for_assembly(private_config_xml_file, profile, taxonomy_id, assembly_accession, | ||
release_species_inventory_table, release_version, assembly_release_folder, release_jar_path, | ||
memory): | ||
exit_code = -1 | ||
try: | ||
port_forwarding_process_id, mongo_port = open_mongo_port_to_tempmongo(private_config_xml_file, profile, | ||
taxonomy_id, assembly_accession, | ||
release_species_inventory_table, | ||
release_version) | ||
release_properties_file = create_release_properties_file_for_assembly(private_config_xml_file, profile, | ||
taxonomy_id, assembly_accession, | ||
release_species_inventory_table, | ||
release_version, assembly_release_folder, | ||
job_name='ACTIVE_ACCESSION_RELEASE_JOB', | ||
file_name='active_release') | ||
release_command = 'java -Xmx{0}g -jar {1} --spring.config.location=file:{2} --spring.data.mongodb.port={3}'\ | ||
.format(memory, release_jar_path, release_properties_file, mongo_port) | ||
run_command_with_output("Running release pipeline for assembly: " + assembly_accession, release_command) | ||
exit_code = 0 | ||
except Exception as ex: | ||
logger.error("Encountered an error while running release for assembly: " + assembly_accession + "\n" | ||
+ traceback.format_exc()) | ||
exit_code = -1 | ||
finally: | ||
close_mongo_port_to_tempmongo(port_forwarding_process_id) | ||
logger.info("Java release pipeline run completed with exit_code: " + str(exit_code)) | ||
sys.exit(exit_code) | ||
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@click.option("--private-config-xml-file", help="ex: /path/to/eva-maven-settings.xml", required=True) | ||
@click.option("--profile", help="Maven profile to use, ex: internal", required=True) | ||
@click.option("--taxonomy-id", help="ex: 9913", required=True) | ||
@click.option("--assembly-accession", help="ex: GCA_000003055.6", required=True) | ||
@click.option("--release-species-inventory-table", default="eva_progress_tracker.clustering_release_tracker", | ||
required=False) | ||
@click.option("--release-version", help="ex: 2", type=int, required=True) | ||
@click.option("--assembly-release-folder", required=True) | ||
@click.option("--release-jar-path", required=True) | ||
@click.option("--memory", help="Memory in GB. ex: 8", default=8, type=int, required=False) | ||
@click.command() | ||
def main(private_config_xml_file, profile, taxonomy_id, assembly_accession, release_species_inventory_table, | ||
release_version, assembly_release_folder, release_jar_path, memory): | ||
logging_config.add_stdout_handler() | ||
run_release_for_assembly(private_config_xml_file, profile, taxonomy_id, assembly_accession, | ||
release_species_inventory_table, release_version, assembly_release_folder, release_jar_path, | ||
memory) | ||
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if __name__ == "__main__": | ||
main() |
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78
...ccession-release-automation/run_release_in_embassy/run_release_deprecated_for_assembly.py
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# Copyright 2020 EMBL - European Bioinformatics Institute | ||
# | ||
# Licensed under the Apache License, Version 2.0 (the "License"); | ||
# you may not use this file except in compliance with the License. | ||
# You may obtain a copy of the License at | ||
# | ||
# http://www.apache.org/licenses/LICENSE-2.0 | ||
# | ||
# Unless required by applicable law or agreed to in writing, software | ||
# distributed under the License is distributed on an "AS IS" BASIS, | ||
# 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. | ||
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import click | ||
import sys | ||
import traceback | ||
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from ebi_eva_common_pyutils.logger import logging_config | ||
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from run_release_in_embassy.create_release_properties_file import create_release_properties_file_for_assembly | ||
from run_release_in_embassy.release_common_utils import open_mongo_port_to_tempmongo, close_mongo_port_to_tempmongo | ||
from ebi_eva_common_pyutils.command_utils import run_command_with_output | ||
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logger = logging_config.get_logger(__name__) | ||
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def run_release_for_assembly(private_config_xml_file, profile, taxonomy_id, assembly_accession, | ||
release_species_inventory_table, release_version, assembly_release_folder, release_jar_path, | ||
memory): | ||
exit_code = -1 | ||
try: | ||
port_forwarding_process_id, mongo_port = open_mongo_port_to_tempmongo(private_config_xml_file, profile, | ||
taxonomy_id, assembly_accession, | ||
release_species_inventory_table, | ||
release_version) | ||
release_properties_file = create_release_properties_file_for_assembly(private_config_xml_file, profile, | ||
taxonomy_id, assembly_accession, | ||
release_species_inventory_table, | ||
release_version, assembly_release_folder, | ||
job_name='DEPRECATED_ACCESSION_RELEASE_JOB', | ||
file_name='deprecated_release') | ||
release_command = 'java -Xmx{0}g -jar {1} --spring.config.location=file:{2} --spring.data.mongodb.port={3}'\ | ||
.format(memory, release_jar_path, release_properties_file, mongo_port) | ||
run_command_with_output("Running release pipeline for assembly: " + assembly_accession, release_command) | ||
exit_code = 0 | ||
except Exception as ex: | ||
logger.error("Encountered an error while running release for assembly: " + assembly_accession + "\n" | ||
+ traceback.format_exc()) | ||
exit_code = -1 | ||
finally: | ||
close_mongo_port_to_tempmongo(port_forwarding_process_id) | ||
logger.info("Java release pipeline run completed with exit_code: " + str(exit_code)) | ||
sys.exit(exit_code) | ||
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@click.option("--private-config-xml-file", help="ex: /path/to/eva-maven-settings.xml", required=True) | ||
@click.option("--profile", help="Maven profile to use, ex: internal", required=True) | ||
@click.option("--taxonomy-id", help="ex: 9913", required=True) | ||
@click.option("--assembly-accession", help="ex: GCA_000003055.6", required=True) | ||
@click.option("--release-species-inventory-table", default="eva_progress_tracker.clustering_release_tracker", | ||
required=False) | ||
@click.option("--release-version", help="ex: 2", type=int, required=True) | ||
@click.option("--assembly-release-folder", required=True) | ||
@click.option("--release-jar-path", required=True) | ||
@click.option("--memory", help="Memory in GB. ex: 8", default=8, type=int, required=False) | ||
@click.command() | ||
def main(private_config_xml_file, profile, taxonomy_id, assembly_accession, release_species_inventory_table, | ||
release_version, assembly_release_folder, release_jar_path, memory): | ||
logging_config.add_stdout_handler() | ||
run_release_for_assembly(private_config_xml_file, profile, taxonomy_id, assembly_accession, | ||
release_species_inventory_table, release_version, assembly_release_folder, release_jar_path, | ||
memory) | ||
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if __name__ == "__main__": | ||
main() |
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