Adding a new attribute for experiment: nucleic_acid_type

project_tracking/db_action.py

@@ -53,13 +53,22 @@ def to_dict(self):
         return rv
 
 class DidNotFindError(Error):
-    """DidNotFind"""
+    """DidNotFindError"""
     def __init__(self, message=None, table=None, attribute=None, query=None):
         super().__init__(message)
         if message:
             self.message = message
         else:
-            self.message = f"{table} with {attribute} {query} doesn't exist on database"
+            self.message = f"'{table}' with '{attribute}' '{query}' doesn't exist on database"
+
+class RequestError(Error):
+    """RequestError"""
+    def __init__(self, message=None, argument=None):
+        super().__init__(message)
+        if message:
+            self.message = message
+        else:
+            self.message = f"For current request '{argument}' is required"
 
 def name_to_id(model_class, name, session=None):
     """
@@ -590,6 +599,7 @@ def ingest_run_processing(project_id: str, ingest_data, session=None):
                 experiment = Experiment.from_attributes(
                     sequencing_technology=readset_json[vb.EXPERIMENT_SEQUENCING_TECHNOLOGY],
                     type=readset_json[vb.EXPERIMENT_TYPE],
+                    nucleic_acid_type=readset_json[vb.EXPERIMENT_NUCLEIC_ACID_TYPE],
                     library_kit=readset_json[vb.EXPERIMENT_LIBRARY_KIT],
                     kit_expiration_date=kit_expiration_date,
                     session=session
@@ -752,6 +762,7 @@ def digest_readset_file(project_id: str, digest_data, session=None):
     if not session:
         session = database.get_session()
 
+    patients = []
     samples = []
     readsets = []
     output = []
@@ -760,21 +771,73 @@ def digest_readset_file(project_id: str, digest_data, session=None):
         }
 
     location_endpoint = None
-
     if vb.LOCATION_ENDPOINT in digest_data.keys():
         location_endpoint = digest_data[vb.LOCATION_ENDPOINT]
 
+    if vb.EXPERIMENT_NUCLEIC_ACID_TYPE in digest_data.keys():
+        nucleic_acid_type = digest_data[vb.EXPERIMENT_NUCLEIC_ACID_TYPE]
+    else:
+        raise RequestError(argument="experiment_nucleic_acid_type")
+
+    if vb.PATIENT_NAME in digest_data.keys():
+        for patient_name in digest_data[vb.PATIENT_NAME]:
+            patient = session.scalars(
+                select(Patient)
+                .where(Patient.name == patient_name)
+                .join(Patient.samples)
+                .join(Sample.readsets)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
+            if patient:
+                patients.append(patient)
+            else:
+                raise DidNotFindError(table="Patient", attribute="name", query=patient_name)
+    if vb.PATIENT_ID in digest_data.keys():
+        for patient_id in digest_data[vb.PATIENT_ID]:
+            # logger.debug(f"\n\n{patient_id}\n\n")
+            patient = session.scalars(
+                select(Patient)
+                .where(Patient.id == patient_id)
+                .join(Patient.samples)
+                .join(Sample.readsets)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
+            if patient:
+                patients.append(patient)
+            else:
+                raise DidNotFindError(table="Patient", attribute="id", query=patient_id)
+    if patients:
+        set(patients)
+        for patient in patients:
+            for sample in patient.samples:
+                for readset in sample.readsets:
+                    readsets.append(readset)
+
     if vb.SAMPLE_NAME in digest_data.keys():
         for sample_name in digest_data[vb.SAMPLE_NAME]:
-            sample = session.scalars(select(Sample).where(Sample.name == sample_name)).unique().first()
+            sample = session.scalars(
+                select(Sample)
+                .where(Sample.name == sample_name)
+                .join(Sample.readsets)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
             if sample:
                 samples.append(sample)
             else:
                 raise DidNotFindError(table="Sample", attribute="name", query=sample_name)
     if vb.SAMPLE_ID in digest_data.keys():
         for sample_id in digest_data[vb.SAMPLE_ID]:
             # logger.debug(f"\n\n{sample_id}\n\n")
-            sample = session.scalars(select(Sample).where(Sample.id == sample_id)).unique().first()
+            sample = session.scalars(
+                select(Sample)
+                .where(Sample.id == sample_id)
+                .join(Sample.readsets)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
             if sample:
                 samples.append(sample)
             else:
@@ -784,16 +847,27 @@ def digest_readset_file(project_id: str, digest_data, session=None):
         for sample in samples:
             for readset in sample.readsets:
                 readsets.append(readset)
+
     if vb.READSET_NAME in digest_data.keys():
         for readset_name in digest_data[vb.READSET_NAME]:
-            readset = session.scalars(select(Readset).where(Readset.name == readset_name)).unique().first()
+            readset = session.scalars(
+                select(Readset)
+                .where(Readset.name == readset_name)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
             if readset:
                 readsets.append(readset)
             else:
                 raise DidNotFindError(table="Readset", attribute="name", query=readset_name)
     if vb.READSET_ID in digest_data.keys():
         for readset_id in digest_data[vb.READSET_ID]:
-            readset = session.scalars(select(Readset).where(Readset.id == readset_id)).unique().first()
+            readset = session.scalars(
+                select(Readset)
+                .where(Readset.id == readset_id)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
             if readset:
                 readsets.append(readset)
             else:
@@ -802,7 +876,6 @@ def digest_readset_file(project_id: str, digest_data, session=None):
         set(readsets)
         for readset in readsets:
             readset_files = []
-            logger.debug(f"\n\n{readset}\n\n")
             bed = None
             fastq1 = None
             fastq2 = None
@@ -869,35 +942,93 @@ def digest_pair_file(project_id: str, digest_data, session=None):
     # readsets = []
     output = []
 
+    if vb.EXPERIMENT_NUCLEIC_ACID_TYPE in digest_data.keys():
+        nucleic_acid_type = digest_data[vb.EXPERIMENT_NUCLEIC_ACID_TYPE]
+    else:
+        raise RequestError(argument="experiment_nucleic_acid_type")
+
+    if vb.PATIENT_NAME in digest_data.keys():
+        for patient_name in digest_data[vb.PATIENT_NAME]:
+            patient = session.scalars(
+                select(Patient)
+                .where(Patient.name == patient_name)
+                .join(Patient.samples)
+                .join(Sample.readsets)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
+            if patient:
+                patients.append(patient)
+            else:
+                raise DidNotFindError(table="Patient", attribute="name", query=patient_name)
+    if vb.PATIENT_ID in digest_data.keys():
+        for patient_id in digest_data[vb.PATIENT_ID]:
+            patient = session.scalars(
+                select(Patient)
+                .where(Patient.id == patient_id)
+                .join(Patient.samples)
+                .join(Sample.readsets)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
+            if patient:
+                patients.append(patient)
+            else:
+                raise DidNotFindError(table="Patient", attribute="id", query=patient_id)
+    if patients:
+        set(patients)
+        for patient in patients:
+            for sample in patient.samples:
+                samples.append(sample)
+
     if vb.SAMPLE_NAME in digest_data.keys():
         for sample_name in digest_data[vb.SAMPLE_NAME]:
-            sample = session.scalars(select(Sample).where(Sample.name == sample_name)).unique().first()
-            # logger.info(f"\n\n{sample}\n\n")
+            sample = session.scalars(
+                select(Sample)
+                .where(Sample.name == sample_name)
+                .join(Sample.readsets)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
             if sample:
                 samples.append(sample)
             else:
                 raise DidNotFindError(table="Sample", attribute="name", query=sample_name)
     if vb.SAMPLE_ID in digest_data.keys():
         for sample_id in digest_data[vb.SAMPLE_ID]:
-            sample = session.scalars(select(Sample).where(Sample.id == sample_id)).unique().first()
+            sample = session.scalars(
+                select(Sample)
+                .where(Sample.id == sample_id)
+                .join(Sample.readsets)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
             if sample:
                 samples.append(sample)
             else:
                 raise DidNotFindError(table="Sample", attribute="id", query=sample_id)
     if vb.READSET_NAME in digest_data.keys():
         for readset_name in digest_data[vb.READSET_NAME]:
-            readset = session.scalars(select(Readset).where(Readset.name == readset_name)).unique().first()
+            readset = session.scalars(
+                select(Readset)
+                .where(Readset.name == readset_name)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
             if readset:
                 samples.append(readset.sample)
-                # readsets.append(readset)
             else:
                 raise DidNotFindError(table="Readset", attribute="name", query=readset_name)
     if vb.READSET_ID in digest_data.keys():
         for readset_id in digest_data[vb.READSET_ID]:
-            readset = session.scalars(select(Readset).where(Readset.id == readset_id)).unique().first()
+            readset = session.scalars(
+                select(Readset)
+                .where(Readset.id == readset_id)
+                .join(Readset.experiment)
+                .where(Experiment.nucleic_acid_type == nucleic_acid_type)
+                ).unique().first()
             if readset:
                 samples.append(readset.sample)
-                # readsets.append(readset)
             else:
                 raise DidNotFindError(table="Readset", attribute="id", query=readset_id)
     if samples:
@@ -1066,7 +1197,7 @@ def digest_unanalyzed(project_id: str, digest_data, session=None):
     run_name = digest_data["run_name"]
     if run_name:
         run_id = name_to_id("Run", run_name)[0]
-    experiment_sequencing_technology = digest_data["experiment_sequencing_technology"]
+    experiment_nucleic_acid_type = digest_data["experiment_nucleic_acid_type"]
     location_endpoint = digest_data["location_endpoint"]
 
     if sample_name_flag:
@@ -1096,17 +1227,15 @@ def digest_unanalyzed(project_id: str, digest_data, session=None):
             stmt.where(Run.id == run_id)
             .join(Readset.run)
             )
-    if experiment_sequencing_technology:
+    if experiment_nucleic_acid_type:
         stmt = (
-            stmt.where(Experiment.sequencing_technology == experiment_sequencing_technology)
+            stmt.where(Experiment.nucleic_acid_type == experiment_nucleic_acid_type)
             .join(Readset.experiment)
             )
 
-    # logger.debug(f"\n\n{stmt}\n\n")
     output = {
         "location_endpoint": location_endpoint,
         key: session.scalars(stmt).unique().all()
     }
-    # logger.debug(f"\n\n{session.scalars(stmt).unique().all()}\n\n")
 
     return json.dumps(output)

project_tracking/model.py

@@ -35,6 +35,12 @@
 
 from . import database
 
+class NucleicAcidTypeEnum(enum.Enum):
+    """nucleic_acid_type enum"""
+    DNA = "DNA"
+    RNA = "RNA"
+
+
 class LaneEnum(enum.Enum):
     """
     lane enum
@@ -43,6 +49,10 @@ class LaneEnum(enum.Enum):
     TWO = "2"
     THREE = "3"
     FOUR = "4"
+    FIVE = "5"
+    SIX = "6"
+    SEVEN = "7"
+    EIGHT = "8"
 
 
 class SequencingTypeEnum(enum.Enum):
@@ -90,6 +100,7 @@ class Base(DeclarativeBase):
     # this is needed for the enum to work properly right now
     # see https://github.com/sqlalchemy/sqlalchemy/discussions/8856
     type_annotation_map = {
+        NucleicAcidTypeEnum: Enum(NucleicAcidTypeEnum),
         LaneEnum: Enum(LaneEnum),
         SequencingTypeEnum: Enum(SequencingTypeEnum),
         StatusEnum: Enum(StatusEnum),
@@ -346,6 +357,7 @@ class Experiment(BaseTable):
         id integer [PK]
         sequencing_technology text
         type text
+        nucleic_acid_type nucleic_acid_type
         library_kit text
         kit_expiration_date text
         deprecated boolean
@@ -358,13 +370,22 @@ class Experiment(BaseTable):
 
     sequencing_technology: Mapped[str] = mapped_column(default=None, nullable=True)
     type: Mapped[str] = mapped_column(default=None, nullable=True)
+    nucleic_acid_type: Mapped[NucleicAcidTypeEnum] = mapped_column(default=None, nullable=False)
     library_kit: Mapped[str] = mapped_column(default=None, nullable=True)
     kit_expiration_date: Mapped[datetime] = mapped_column(default=None, nullable=True)
 
     readsets: Mapped[list["Readset"]] = relationship(back_populates="experiment")
 
     @classmethod
-    def from_attributes(cls, sequencing_technology=None, type=None, library_kit=None, kit_expiration_date=None, session=None):
+    def from_attributes(
+        cls,
+        nucleic_acid_type,
+        sequencing_technology=None,
+        type=None,
+        library_kit=None,
+        kit_expiration_date=None,
+        session=None
+        ):
         """
         get experiment if it exist, set it if it does not exist
         """
@@ -374,13 +395,15 @@ def from_attributes(cls, sequencing_technology=None, type=None, library_kit=None
             select(cls)
                 .where(cls.sequencing_technology == sequencing_technology)
                 .where(cls.type == type)
+                .where(cls.nucleic_acid_type == nucleic_acid_type)
                 .where(cls.library_kit == library_kit)
                 .where(cls.kit_expiration_date == kit_expiration_date)
         ).first()
         if not experiment:
             experiment = cls(
                 sequencing_technology=sequencing_technology,
                 type=type,
+                nucleic_acid_type=nucleic_acid_type,
                 library_kit=library_kit,
                 kit_expiration_date=kit_expiration_date
             )

project_tracking/vocabulary.py

@@ -10,6 +10,7 @@
 
 # patient table
 PATIENT = "patient"
+PATIENT_ID = "patient_id"
 PATIENT_FMS_ID = "patient_fms_id"
 PATIENT_NAME = "patient_name"
 PATIENT_COHORT = "patient_cohort"
@@ -25,6 +26,7 @@
 # experiment table
 EXPERIMENT_SEQUENCING_TECHNOLOGY = "experiment_sequencing_technology"
 EXPERIMENT_TYPE = "experiment_type"
+EXPERIMENT_NUCLEIC_ACID_TYPE = "experiment_nucleic_acid_type"
 EXPERIMENT_LIBRARY_KIT = "experiment_library_kit"
 EXPERIMENT_KIT_EXPIRATION_DATE = "experiment_kit_expiration_date"
 EXPERIMENT_TYPE_LIST = ["PCR-FREE", "RNASEQ"]

tests/conftest.py

@@ -28,7 +28,7 @@ def pre_filled_model():
                          project=project)
 
     sequencing_technology = 'Fancy Buzzword'
-    exp = model.Experiment(sequencing_technology=sequencing_technology)
+    exp = model.Experiment(nucleic_acid_type=model.NucleicAcidTypeEnum.DNA)
     pa_name = "P_O"
     pa = model.Patient(name=pa_name, project=project)
     sa_name = 'gros_bobo'