Merge pull request #41 from tcezard/package_data

Move the Nextflow and etc folders to eva_submission

eva_submission/__init__.py

@@ -1,4 +1,8 @@
 import os
+import eva_submission
+
 
 ROOT_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))  # This is your Project Root
-MODULE_DIR = os.path.dirname(os.path.abspath(__file__))  # This is the module Root
+
+NEXTFLOW_DIR = os.path.join(os.path.dirname(os.path.abspath(eva_submission.__file__)), 'nextflow')
+ETC_DIR = os.path.join(os.path.dirname(os.path.abspath(eva_submission.__file__)), 'etc')

eva_submission/eload_brokering.py

@@ -6,7 +6,7 @@
 from ebi_eva_common_pyutils import command_utils
 from ebi_eva_common_pyutils.config import cfg
 
-from eva_submission import ROOT_DIR
+from eva_submission import ROOT_DIR, NEXTFLOW_DIR
 from eva_submission.ENA_submission.upload_to_ENA import ENAUploader
 from eva_submission.biosamples_submission import SampleMetadataSubmitter
 from eva_submission.eload_submission import Eload
@@ -94,7 +94,7 @@ def _run_brokering_prep_workflow(self):
         brokering_config_file = os.path.join(self.eload_dir, 'brokering_config_file.yaml')
         with open(brokering_config_file, 'w') as open_file:
             yaml.safe_dump(brokering_config, open_file)
-        validation_script = os.path.join(ROOT_DIR, 'nextflow', 'prepare_brokering.nf')
+        validation_script = os.path.join(NEXTFLOW_DIR, 'prepare_brokering.nf')
         try:
             command_utils.run_command_with_output(
                 'Nextflow brokering preparation process',

eva_submission/eload_ingestion.py

@@ -12,7 +12,7 @@
 from ebi_eva_common_pyutils.pg_utils import get_all_results_for_query, execute_query
 import pymongo
 
-from eva_submission import ROOT_DIR
+from eva_submission import NEXTFLOW_DIR
 from eva_submission.assembly_taxonomy_insertion import insert_new_assembly_and_taxonomy
 from eva_submission.eload_submission import Eload
 from eva_submission.eload_utils import get_metadata_conn, get_mongo_creds, get_accession_pg_creds
@@ -246,7 +246,7 @@ def run_accession_workflow(self):
         accession_config_file = os.path.join(self.project_dir, 'accession_config_file.yaml')
         with open(accession_config_file, 'w') as open_file:
             yaml.safe_dump(accession_config, open_file)
-        accession_script = os.path.join(ROOT_DIR, 'nextflow', 'accession.nf')
+        accession_script = os.path.join(NEXTFLOW_DIR, 'accession.nf')
         try:
             command_utils.run_command_with_output(
                 'Nextflow Accessioning process',
@@ -296,7 +296,7 @@ def run_variant_load_workflow(self):
         load_config_file = os.path.join(self.project_dir, 'load_config_file.yaml')
         with open(load_config_file, 'w') as open_file:
             yaml.safe_dump(load_config, open_file)
-        variant_load_script = os.path.join(ROOT_DIR, 'nextflow', 'variant_load.nf')
+        variant_load_script = os.path.join(NEXTFLOW_DIR, 'variant_load.nf')
         try:
             command_utils.run_command_with_output(
                 'Nextflow Variant Load process',

eva_submission/eload_validation.py

@@ -7,7 +7,7 @@
 from ebi_eva_common_pyutils import command_utils
 from ebi_eva_common_pyutils.config import cfg
 
-from eva_submission import ROOT_DIR
+from eva_submission import NEXTFLOW_DIR
 from eva_submission.eload_submission import Eload
 from eva_submission.eload_utils import resolve_single_file_path
 from eva_submission.samples_checker import compare_spreadsheet_and_vcf
@@ -130,7 +130,7 @@ def _run_validation_workflow(self):
         validation_confg_file = os.path.join(self.eload_dir, 'validation_confg_file.yaml')
         with open(validation_confg_file, 'w') as open_file:
             yaml.safe_dump(validation_config, open_file)
-        validation_script = os.path.join(ROOT_DIR, 'nextflow', 'validation.nf')
+        validation_script = os.path.join(NEXTFLOW_DIR, 'validation.nf')
         try:
             command_utils.run_command_with_output(
                 'Nextflow Validation process',

eva_submission/xlsx/xlsx_parser_eva.py

@@ -18,14 +18,14 @@
 from cached_property import cached_property
 from ebi_eva_common_pyutils.logger import AppLogger
 
-from eva_submission import ROOT_DIR
+from eva_submission import ETC_DIR
 from eva_submission.xlsx.xlsx_parser import XlsxReader, XlsxWriter
 
 
 class EvaXlsxReader(AppLogger):
 
     def __init__(self, metadata_file):
-        conf = os.path.join(ROOT_DIR, 'etc', 'eva_project_conf.yaml')
+        conf = os.path.join(ETC_DIR, 'eva_project_conf.yaml')
         self.reader = XlsxReader(metadata_file, conf)
         self.metadata_file=metadata_file
 
@@ -97,7 +97,7 @@ def files_per_analysis(self):
 class EvaXlsxWriter(AppLogger):
 
     def __init__(self, metadata_source, metadata_dest=None):
-        conf = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(__file__))), 'etc', 'eva_project_conf.yaml')
+        conf = os.path.join(ETC_DIR, 'eva_project_conf.yaml')
         self.writer = XlsxWriter(metadata_source, conf)
         self.metadata_source = metadata_source
         if metadata_dest:

eva_submission/xlsx/xlsx_validation.py

@@ -7,7 +7,7 @@
 from ebi_eva_common_pyutils.variation.assembly_utils import retrieve_genbank_assembly_accessions_from_ncbi
 from requests import HTTPError
 
-from eva_submission import ROOT_DIR
+from eva_submission import ETC_DIR
 from eva_submission.eload_utils import cast_list
 from eva_submission.xlsx.xlsx_parser_eva import EvaXlsxReader
 
@@ -33,7 +33,7 @@ def cerberus_validation(self):
         Leverage cerberus validation to check the format of the metadata.
         This function adds error statements to the errors attribute
         """
-        config_file = os.path.join(ROOT_DIR, 'etc', 'eva_project_validation.yaml')
+        config_file = os.path.join(ETC_DIR, 'eva_project_validation.yaml')
         with open(config_file) as open_file:
             validation_schema = yaml.safe_load(open_file)
         validator = Validator(validation_schema)

setup.py

@@ -9,7 +9,8 @@
 setup(
     name='eva_submission',
     packages=['eva_submission', 'eva_submission.ENA_submission', 'eva_submission.xlsx'],
-    version='0.5.6',
+    package_data={'eva_submission': ['nextflow/*', 'etc/*']},
+    version='0.5.7',
     license='Apache',
     description='EBI EVA - submission processing tools',
     url='https://github.com/EBIVariation/eva-submission',

tests/test_eload_brokering.py

@@ -6,7 +6,7 @@
 
 from ebi_eva_common_pyutils.config import cfg
 
-from eva_submission import ROOT_DIR
+from eva_submission import NEXTFLOW_DIR
 from eva_submission.biosamples_submission import SampleMetadataSubmitter
 from eva_submission.eload_brokering import EloadBrokering
 from eva_submission.eload_submission import Eload
@@ -68,7 +68,7 @@ def test_run_brokering_prep_workflow(self):
             'nextflow': 'path_to_nextflow'
         }
         temp_dir = 'temporary_directory'
-        nf_script = os.path.join(ROOT_DIR, 'nextflow', 'prepare_brokering.nf')
+        nf_script = os.path.join(NEXTFLOW_DIR, 'prepare_brokering.nf')
         config_file = os.path.join(self.eload.eload_dir, 'brokering_config_file.yaml')
 
         with patch('eva_submission.eload_brokering.command_utils.run_command_with_output') as m_execute, \