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Merge pull request #8490 from jmchilton/fix_data_dir

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Fix some data_dir stuff in galaxy.config.
This commit is contained in:
Björn Grüning
2019-08-23 08:30:06 +02:00
committed by GitHub
parent 4b93b9fc0a 08b39a2b7d
commit 1db199763f
1 changed files with 4 additions and 5 deletions
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lib/galaxy/config/__init__.py
+4 -5
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@@ -359,8 +359,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
self.template_path = resolve_path(kwargs.get("template_path", "templates"), self.root)
self.template_cache = resolve_path(kwargs.get("template_cache_path", "compiled_templates"), self.data_dir)
self.job_queue_cleanup_interval = int(kwargs.get("job_queue_cleanup_interval", "5"))
self.cluster_files_directory = os.path.abspath(kwargs.get("cluster_files_directory", "database/pbs"))
self.cluster_files_directory = os.path.abspath(resolve_path(kwargs.get("cluster_files_directory", "pbs"), self.data_dir))
self.cluster_files_directory = self.resolve_path(kwargs.get("cluster_files_directory", os.path.join(self.data_dir, "pbs")))
# Fall back to legacy job_working_directory config variable if set.
default_jobs_directory = kwargs.get("job_working_directory", "jobs_directory")
@@ -376,7 +375,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
# should probably drop the backward compatiblity to save the path check.
self.container_image_cache_path = resolve_path(kwargs.get("container_image_cache_path", "container_images"), self.data_dir)
if not os.path.exists(self.container_image_cache_path):
self.container_image_cache_path = self.resolve_path(kwargs.get("container_image_cache_path", "database/container_cache"))
self.container_image_cache_path = self.resolve_path(kwargs.get("container_image_cache_path", os.path.join(self.data_dir, "container_cache")))
self.outputs_to_working_directory = string_as_bool(kwargs.get('outputs_to_working_directory', False))
self.output_size_limit = int(kwargs.get('output_size_limit', 0))
self.retry_job_output_collection = int(kwargs.get('retry_job_output_collection', 0))
@@ -580,7 +579,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
self.nginx_upload_store = os.path.abspath(self.nginx_upload_store)
self.object_store = kwargs.get('object_store', 'disk')
self.object_store_check_old_style = string_as_bool(kwargs.get('object_store_check_old_style', False))
self.object_store_cache_path = resolve_path(kwargs.get("object_store_cache_path", "database/object_store_cache"), self.data_dir)
self.object_store_cache_path = self.resolve_path(kwargs.get("object_store_cache_path", os.path.join(self.data_dir, "object_store_cache")))
self.object_store_store_by = kwargs.get("object_store_store_by", "id")
# Handle AWS-specific config options for backward compatibility
@@ -729,7 +728,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
self.dynamic_proxy_golang_api_key = kwargs.get("dynamic_proxy_golang_api_key", None)
# InteractiveTools propagator mapping file
self.realtime_map = self.resolve_path(kwargs.get("interactivetools_map", "database/interactivetools_map.sqlite"))
self.realtime_map = self.resolve_path(kwargs.get("interactivetools_map", os.path.join(self.data_dir, "interactivetools_map.sqlite")))
self.realtime_prefix = kwargs.get("interactivetools_prefix", "interactivetool")
self.interactivetools_enable = string_as_bool(kwargs.get('interactivetools_enable', False))