validation function

Rappsilber-Laboratory · Sep 23, 2024 · bb37025 · bb37025
1 parent be492b5
commit bb37025
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Showing 7 changed files with 3,990 additions and 139 deletions.
diff --git a/models/match.py b/models/match.py
@@ -9,7 +9,6 @@ class Match(Base):
     id: Mapped[str] = mapped_column(Text, primary_key=True, nullable=False)
     upload_id: Mapped[int] = mapped_column(Integer, ForeignKey("upload.id"), index=True, primary_key=True,
                                            nullable=False)
-    id: Mapped[str] = mapped_column(Text, primary_key=True, nullable=False)
     spectrum_id: Mapped[str] = mapped_column(Text, nullable=True)
     spectra_data_id: Mapped[int] = mapped_column(Integer, nullable=True)  # nullable for csv data
     multiple_spectra_identification_id: Mapped[str] = mapped_column(Integer, nullable=True)

diff --git a/parser/MzIdParser.py b/parser/MzIdParser.py
@@ -1007,6 +1007,12 @@ def iterfind_when(source, target_name, condition_name, stack_predicate, **kwargs
                 tag.clear()
 
 
+class SqliteMzIdParser(MzIdParser):
+
+    def write_new_upload(self):
+        """Overrides base class function - not needed for xiSPEC."""
+        self.writer.upload_id = 1
+
 class XiSpecMzIdParser(MzIdParser):
 
     def write_new_upload(self):

diff --git a/parser/database/create_db_schema.py b/parser/database/create_db_schema.py
@@ -22,7 +22,7 @@ def drop_db(connection_str):
 def create_schema(connection_str):
     engine = create_engine(connection_str)  # , echo=True)
     Base.metadata.create_all(engine)
-    logging.info(Base.metadata.tables)
+    # logging.info(Base.metadata.tables)
     engine.dispose()