Formatting pass

# Conflicts: # models/models/analysis.py
populationgenomics · Jun 26, 2023 · 8754c40 · 8754c40
1 parent 86fc7ad
commit 8754c40
Show file tree

Hide file tree

Showing 6 changed files with 49 additions and 41 deletions.
diff --git a/db/project.xml b/db/project.xml
@@ -697,40 +697,45 @@
 	</changeSet>
 	<changeSet author="michael.franklin" id="2022-10-18_first-class-files">
 		<sql>SET @@system_versioning_alter_history = 1;</sql>
-			<createTable tableName="file">
+		<createTable tableName="file">
 <!--				Maybe should consider "in-progress" flag to shos that it's expecting an output to exist -->
-				<column name="id" type="INT" autoIncrement="true">
-					<constraints primaryKey="true" nullable="false" />
-				</column>
-				<column name="type" type="ENUM('file', 'directory')" />
-				<column name="path" type="TEXT">
-					<constraints unique="true" nullable="false" />
-				</column>
-				<column name="size" type="INT" />
-				<column name="checksum" type="TEXT" />
-
-			</createTable>
+			<column name="id" type="INT" autoIncrement="true">
+				<constraints primaryKey="true" nullable="false" />
+			</column>
+			<column name="type" type="ENUM('file', 'directory')" />
+			<column name="path" type="TEXT">
+				<constraints unique="true" nullable="false" />
+			</column>
+			<column name="size" type="INT" />
+			<column name="checksum" type="TEXT" />
+			<column name="exists" type="BIT" />
+
+		</createTable>
 
 <!--			attach files to analysis-->
-			<createTable tableName="analysis_files">
-				<column name="analysis_id" type="INT">
-					<constraints nullable="false" foreignKeyName="fk_analysis_files_analysis" references="analysis(id)" />
-				</column>
-				<column name="file_id" type="INT">
-					<constraints nullable="false" foreignKeyName="fk_analysis_files_file" references="file(id)" />
-				</column>
-				<column name="pattern" type="TEXT"/>
-			</createTable>
-
-		<!--			attach files to analysis-->
-			<createTable tableName="sequence_files">
-				<column name="sequence_id" type="INT">
-					<constraints nullable="false" foreignKeyName="fk_analysis_files_analysis" references="sample_sequencing(id)" />
-				</column>
-				<column name="file_id" type="INT">
-					<constraints nullable="false" foreignKeyName="fk_analysis_files_file" references="file(id)" />
-				</column>
-				<column name="pattern" type="TEXT"/>
-			</createTable>
+		<createTable tableName="analysis_outputs">
+			<column name="analysis_id" type="INT">
+				<constraints nullable="false" foreignKeyName="fk_analysis_outputs_analysis" references="analysis(id)" />
+			</column>
+			<column name="value" type="TEXT">
+				<constraints nullable="true" />
+			</column>
+			<column name="file_id" type="INT">
+				<constraints nullable="true" foreignKeyName="fk_analysis_outputs_file" references="file(id)" />
+			</column>
+			<column name="pattern" type="TEXT"/>
+
+		</createTable>
+
+	<!--			attach files to analysis-->
+		<createTable tableName="sequence_files">
+			<column name="sequence_id" type="INT">
+				<constraints nullable="false" foreignKeyName="fk_sequence_files_sequence" references="sample_sequencing(id)" />
+			</column>
+			<column name="file_id" type="INT">
+				<constraints nullable="false" foreignKeyName="fk_sequence_files_file" references="file(id)" />
+			</column>
+			<column name="pattern" type="TEXT"/>
+		</createTable>
 	</changeSet>
 </databaseChangeLog>
diff --git a/db/python/tables/analysis.py b/db/python/tables/analysis.py
@@ -28,6 +28,7 @@ class AnalysisFilter(GenericFilterModel):
     status: GenericFilter[AnalysisStatus] = None
     meta: GenericMetaFilter = None
     output: GenericFilter[str] = None
+    outputs: GenericMetaFilter = None
     active: GenericFilter[bool] = None
 
     def __hash__(self):  # pylint: disable=useless-parent-delegation
@@ -58,6 +59,7 @@ async def create_analysis(
         sequencing_group_ids: List[int],
         meta: Optional[Dict[str, Any]] = None,
         output: str = None,
+        outputs: dict[str, Any] = None,
         active: bool = True,
         author: str = None,
         project: ProjectId = None,

diff --git a/db/python/tables/file.py b/db/python/tables/file.py
@@ -35,4 +35,4 @@ async def create_files(self, files: list[File]):
         """
         pass
 
-    # endregion CREATE
+    # endregion CREATE
diff --git a/models/models/analysis.py b/models/models/analysis.py
@@ -19,6 +19,7 @@ class AnalysisInternal(SMBase):
     type: str
     status: AnalysisStatus
     output: str = None
+    outputs: dict[str, Any] = None
     sequencing_group_ids: list[int] = []
     timestamp_completed: str | None = None
     project: int | None = None

diff --git a/models/models/file.py b/models/models/file.py
@@ -1,9 +1,10 @@
 from enum import Enum
-from typing import Optional
 
 from pydantic import BaseModel
 
+
 class FileType(Enum):
+    """Type of File that we record"""
     FILE = 'file'
     DIRECTORY = 'directory'
 
@@ -17,3 +18,4 @@ class File(BaseModel):
     # in bytes
     size: int
     checksum: str | None
+    exists: bool
diff --git a/scripts/migrate_files.py b/scripts/migrate_files.py
@@ -26,11 +26,9 @@ async def migrate_analysis():
     rows = await connection.fetch_all(get_query)
     mapped_files = defaultdict(list)
     for r in rows:
-        \mapped_files[r['output']].append(r['id'])
-
-    inserted_files = insert_files(list(mapped_files.keys()))
-
-    for f in inserted_files:
-        File(path=)
-
+        mapped_files[r['output']].append(r['id'])
 
+    # inserted_files = insert_files(list(mapped_files.keys()))
+    #
+    # for f in inserted_files:
+    #     File(path=)