FIX config, start #116, refactor FileService

server/migrations/env.py

@@ -7,7 +7,7 @@
 
 from scimodom.database.database import Base
 import scimodom.database.models  # noqa
-from scimodom.config import get_config
+from scimodom.config import set_config_from_environment, get_config
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -33,6 +33,7 @@
 
 
 def get_database_url() -> str:
+    set_config_from_environment()
     return get_config().DATABASE_URI
 
 

server/src/scimodom/config.py

@@ -109,10 +109,10 @@ class _Config(Config):
         NOTIFICATION_ADDRESS = get_required_parameter("NOTIFICATION_ADDRESS")
         HTTP_PUBLIC_URL = get_required_parameter("HTTP_PUBLIC_URL")
 
-        FLASK_DEBUG = eval(os.getenv("FLASK_DEBUG", Config.FLASK_DEBUG))
+        FLASK_DEBUG = eval(os.getenv("FLASK_DEBUG", str(Config.FLASK_DEBUG)))
         SESSION_COOKIE_SAMESITE = os.getenv("SESSION_COOKIE_SAMESITE")
         SESSION_COOKIE_SECURE = eval(
-            os.getenv("SESSION_COOKIE_SECURE", Config.SESSION_COOKIE_SECURE)
+            os.getenv("SESSION_COOKIE_SECURE", str(Config.SESSION_COOKIE_SECURE))
         )
 
         JWT_SECRET_KEY = SECRET_KEY

server/src/scimodom/services/annotation/generic.py

@@ -141,7 +141,7 @@ def get_release_path(self, annotation: Annotation) -> Path:
         ).scalar_one()
         organism_name = "_".join(organism_name.lower().split()).capitalize()
         assembly_name = self._assembly_service.get_name_for_version(annotation.taxa_id)
-        path = self._file_service.get_annotation_dir()
+        path = self._file_service.get_annotation_parent_dir()
         return Path(path, organism_name, assembly_name, str(annotation.release))
 
     def _release_exists(self, annotation_id) -> bool:

server/src/scimodom/services/annotation/gtrnadb.py

@@ -151,7 +151,7 @@ def _patch_annotation(self, annotation_file: Path, seqids: list[str]):
 
     # TODO
     def _update_annotation(self, domain, fasta_file):
-        annotation_path = self._file_service.get_annotation_dir()
+        annotation_path = self._file_service.get_annotation_parent_dir()
         model_file = Path(annotation_path, domain).with_suffix(".cm").as_posix()
         sprinzl_file = Path(annotation_path, domain).with_suffix(".txt").as_posix()
         self._external_service.get_sprinzl_mapping(model_file, fasta_file, sprinzl_file)

server/src/scimodom/services/file.py

@@ -53,11 +53,16 @@ def __init__(
         self._import_path = import_path
 
         for path in [
+            data_path,
             temp_path,
             upload_path,
-            self._get_gene_cache_dir(),
-            self.get_annotation_dir(),
+            import_path,
             self.get_project_metadata_dir(),
+            self._get_project_request_dir(),
+            self.get_annotation_parent_dir(),
+            self.get_assembly_parent_dir(),
+            self._get_gene_cache_dir(),
+            self.get_bam_files_parent_dir(),
         ]:
             makedirs(path, exist_ok=True)
 
@@ -83,7 +88,7 @@ def open_import_file(self, name: str):
 
     # annotation
 
-    def get_annotation_dir(self) -> Path:
+    def get_annotation_parent_dir(self) -> Path:
         """Construct parent path to annotation files.
 
         :returns: Path to annotation
@@ -190,6 +195,14 @@ def _get_project_request_dir(self):
 
     # Assembly
 
+    def get_assembly_parent_dir(self) -> Path:
+        """Construct parent path to assembly files.
+
+        :returns: Path to assembly
+        :rtype: Path
+        """
+        return Path(self._data_path, "assembly")
+
     def get_assembly_file_path(
         self,
         taxa_id: int,
@@ -301,8 +314,7 @@ def _get_dir_name_from_organism(organism) -> str:
     def _get_assembly_dir(self, taxa_id: int, assembly_name: str) -> Path:
         organism = self._get_organism_from_taxa_id(taxa_id)
         return Path(
-            self._data_path,
-            "assembly",
+            self.get_assembly_parent_dir(),
             self._get_dir_name_from_organism(organism),
             assembly_name,
         )
@@ -378,6 +390,14 @@ def get_temp_path(self) -> str:
 
     # BAM file
 
+    def get_bam_files_parent_dir(self):
+        """Construct parent path to BAM files.
+
+        :returns: Path to BAM files
+        :rtype: Path
+        """
+        return Path(self._data_path, "bam_files")
+
     def create_or_update_bam_file(
         self,
         dataset: Dataset,
@@ -419,11 +439,14 @@ def _update_bam_file(self, bam_file, data_stream, max_size):
 
     def _get_bam_file_tmp_path(self, bam_file):
         return join(
-            join(self._data_path, "bam_files"), f"tmp.{bam_file.storage_file_name}"
+            self.get_bam_files_parent_dir().as_posix(),
+            f"tmp.{bam_file.storage_file_name}",
         )
 
     def _get_bam_file_path(self, bam_file):
-        return join(join(self._data_path, "bam_files"), bam_file.storage_file_name)
+        return join(
+            self.get_bam_files_parent_dir().as_posix(), bam_file.storage_file_name
+        )
 
     @staticmethod
     def _handle_upload_error(exception, path):

server/tests/integration/services/test_file_service.py

@@ -68,7 +68,7 @@ def test_count_lines(Session, tmp_path):
 
 def test_get_annotation_path(Session, tmp_path):
     service = _get_file_service(Session, tmp_path)
-    assert service.get_annotation_dir() == Path(tmp_path, "t_data", "annotation")
+    assert service.get_annotation_parent_dir() == Path(tmp_path, "t_data", "annotation")
 
 
 def test_update_gene_cache(Session, tmp_path):

server/tests/unit/services/test_ensembl_annotation.py

@@ -79,7 +79,7 @@ def get_assembly_file_path(
             return Path(f"/data/assembly/{taxa_id}/{file_type.value}")
 
     @staticmethod
-    def get_annotation_dir():
+    def get_annotation_parent_dir():
         return "/data/annotation"