Re-route flow to illumina device tables. (#3349)(major)

# Description

Feature branch to re-route the post-processing database flow from the `Flowcell` -> `SampleLaneSequencingMetrics` model paradigm to `IlluminaFlowCell` -> `IlluminaSequencingRun` -> `IlluminaSampleSequencingMetrics`. 
The choice to use a feature branch is to collect all changes and make sure they are tested. Since we need to alter core logic that requires a database migration we cannot do these step by step.

PR in servers: Clinical-Genomics/servers#1394
Data migration script: Clinical-Genomics/add-new-tech#7

## Deploy
```shell
bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b develop-illumina-devices -a
```

## CLI command changes
Commands that need to be updated in servers

- [x] `cg clean flow-cells` -> `cg clean illumina-runs` (requires servers update, PR: <placeholder>)
- [x] `cg backup encrypt-flow-cells` -> `cg backup encrypt-illumina-runs` (requires servers update, PR: <placeholder>)
- [x] `cg backup flow-cells` -> `cg backup illumina-runs` (requires servers update, PR: <placeholder>)
- [x] `cg backup fetch-flow-cell`-> `cg backup fetch-illumina-run` (no update needed)
- [x] `cg demultiplex finish flow-cell` -> `cg demultiplex finish illumina-run` (no update needed in servers
- [x] `cg get flow-cell` -> `cg get sequencing-run` (Does not require a PR in servers)
- [x] `cg set flowcell` -> `cg set sequencing-run` (Does not require a PR in servers)
- [x] `cg store flow-cell`-> `cg store illumina-run` (Does not require a PR in servers)
- [x] `cg store demultiplexed-flow-cell` -> `cg store demultiplexed-run` (Does not require a PR in servers)
- [x] `cg decompress flow-cell` -> `cg decompress illumina-run` (Does not require a PR in servers)

cg/apps/demultiplex/sample_sheet/api.py

@@ -3,10 +3,14 @@
 
 import click
 
-from cg.apps.demultiplex.sample_sheet.read_sample_sheet import get_flow_cell_samples_from_content
-from cg.apps.demultiplex.sample_sheet.sample_models import FlowCellSample
+from cg.apps.demultiplex.sample_sheet.read_sample_sheet import get_samples_from_content
+from cg.apps.demultiplex.sample_sheet.sample_models import IlluminaSampleIndexSetting
 from cg.apps.demultiplex.sample_sheet.sample_sheet_creator import SampleSheetCreator
 from cg.apps.demultiplex.sample_sheet.sample_sheet_validator import SampleSheetValidator
+from cg.apps.demultiplex.sample_sheet.utils import (
+    delete_sample_sheet_from_housekeeper,
+    add_and_include_sample_sheet_path_to_housekeeper,
+)
 from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.apps.lims import LimsAPI
 from cg.apps.lims.sample_sheet import get_flow_cell_samples
@@ -22,17 +26,13 @@
     SampleSheetFormatError,
 )
 from cg.io.controller import ReadFile, WriteFile, WriteStream
-from cg.meta.demultiplex.housekeeper_storage_functions import (
-    add_and_include_sample_sheet_path_to_housekeeper,
-    delete_sample_sheet_from_housekeeper,
-)
 from cg.models.run_devices.illumina_run_directory_data import IlluminaRunDirectoryData
 from cg.utils.files import get_directories_in_path, link_or_overwrite_file
 
 LOG = logging.getLogger(__name__)
 
 
-class SampleSheetAPI:
+class IlluminaSampleSheetService:
     """Sample Sheet API class."""
 
     def __init__(self, flow_cell_dir: str, hk_api: HousekeeperAPI, lims_api: LimsAPI) -> None:
@@ -115,19 +115,19 @@ def _replace_sample_header(sample_sheet_content: list[list[str]]) -> list[list[s
 
     def translate_sample_sheet(self, flow_cell_name: str) -> None:
         """Translate a Bcl2Fastq sample sheet to a BCLConvert sample sheet."""
-        flow_cell: IlluminaRunDirectoryData = self._get_flow_cell(flow_cell_name)
-        if not self._are_necessary_files_in_flow_cell(flow_cell):
+        run_directory_data: IlluminaRunDirectoryData = self._get_flow_cell(flow_cell_name)
+        if not self._are_necessary_files_in_flow_cell(run_directory_data):
             raise MissingFilesError("Missing necessary files in run directory for translation")
         original_content: list[list[str]] = ReadFile.get_content_from_file(
-            file_format=FileFormat.CSV, file_path=flow_cell.sample_sheet_path
+            file_format=FileFormat.CSV, file_path=run_directory_data.sample_sheet_path
         )
         content_with_fixed_header: list[list[str]] = self._replace_sample_header(original_content)
 
-        flow_cell_samples: list[FlowCellSample] = get_flow_cell_samples_from_content(
+        samples: list[IlluminaSampleIndexSetting] = get_samples_from_content(
             sample_sheet_content=content_with_fixed_header
         )
         bcl_convert_creator = SampleSheetCreator(
-            flow_cell=flow_cell, lims_samples=flow_cell_samples
+            run_directory_data=run_directory_data, samples=samples
         )
         new_content = bcl_convert_creator.construct_sample_sheet()
         self.validator.validate_sample_sheet_from_content(new_content)
@@ -141,15 +141,17 @@ def translate_sample_sheet(self, flow_cell_name: str) -> None:
         WriteFile.write_file_from_content(
             content=new_content,
             file_format=FileFormat.CSV,
-            file_path=flow_cell.sample_sheet_path,
+            file_path=run_directory_data.sample_sheet_path,
         )
 
-    def _use_sample_sheet_from_housekeeper(self, flow_cell: IlluminaRunDirectoryData) -> None:
+    def _use_sample_sheet_from_housekeeper(
+        self, run_directory_data: IlluminaRunDirectoryData
+    ) -> None:
         """
         Copy the sample sheet from Housekeeper to the flow cell directory if it exists and is valid.
         """
-        sample_sheet_path: Path = self.hk_api.get_sample_sheet_path(flow_cell.id)
-        flow_cell.set_sample_sheet_path_hk(sample_sheet_path)
+        sample_sheet_path: Path = self.hk_api.get_sample_sheet_path(run_directory_data.id)
+        run_directory_data.set_sample_sheet_path_hk(sample_sheet_path)
         self.validate_sample_sheet(sample_sheet_path)
 
         if self.dry_run:
@@ -159,7 +161,7 @@ def _use_sample_sheet_from_housekeeper(self, flow_cell: IlluminaRunDirectoryData
             )
             return
         LOG.info("Sample sheet from Housekeeper is valid. Copying it to sequencing run directory")
-        link_or_overwrite_file(src=sample_sheet_path, dst=flow_cell.sample_sheet_path)
+        link_or_overwrite_file(src=sample_sheet_path, dst=run_directory_data.sample_sheet_path)
 
     def _use_flow_cell_sample_sheet(self, flow_cell: IlluminaRunDirectoryData) -> None:
         """Use the sample sheet from the flow cell directory if it is valid."""
@@ -186,7 +188,7 @@ def _get_sample_sheet_content(self, flow_cell: IlluminaRunDirectoryData) -> list
         Raises:
              LimsDataError: If no samples are found in LIMS for the flow cell.
         """
-        lims_samples: list[FlowCellSample] = list(
+        lims_samples: list[IlluminaSampleIndexSetting] = list(
             get_flow_cell_samples(
                 lims=self.lims_api,
                 flow_cell_id=flow_cell.id,
@@ -196,7 +198,7 @@ def _get_sample_sheet_content(self, flow_cell: IlluminaRunDirectoryData) -> list
             message: str = f"Could not find any samples in LIMS for {flow_cell.id}"
             LOG.warning(message)
             raise LimsDataError(message)
-        creator = SampleSheetCreator(flow_cell=flow_cell, lims_samples=lims_samples)
+        creator = SampleSheetCreator(run_directory_data=flow_cell, samples=lims_samples)
         LOG.info(
             f"Constructing sample sheet for the {flow_cell.sequencer_type} flow cell {flow_cell.id}"
         )

cg/apps/demultiplex/sample_sheet/read_sample_sheet.py

@@ -2,14 +2,14 @@
 
 from pydantic import TypeAdapter
 
-from cg.apps.demultiplex.sample_sheet.sample_models import FlowCellSample
+from cg.apps.demultiplex.sample_sheet.sample_models import IlluminaSampleIndexSetting
 from cg.constants.demultiplexing import SampleSheetBcl2FastqSections, SampleSheetBCLConvertSections
 from cg.exc import SampleSheetContentError, SampleSheetFormatError
 
 LOG = logging.getLogger(__name__)
 
 
-def validate_samples_are_unique(samples: list[FlowCellSample]) -> None:
+def validate_samples_are_unique(samples: list[IlluminaSampleIndexSetting]) -> None:
     """Validate that each sample only exists once."""
     sample_ids: set = set()
     for sample in samples:
@@ -21,9 +21,9 @@ def validate_samples_are_unique(samples: list[FlowCellSample]) -> None:
         sample_ids.add(sample_id)
 
 
-def validate_samples_unique_per_lane(samples: list[FlowCellSample]) -> None:
+def validate_samples_unique_per_lane(samples: list[IlluminaSampleIndexSetting]) -> None:
     """Validate that each sample only exists once per lane in a sample sheet."""
-    sample_by_lane: dict[int, list[FlowCellSample]] = get_samples_by_lane(samples)
+    sample_by_lane: dict[int, list[IlluminaSampleIndexSetting]] = get_samples_by_lane(samples)
     for lane, lane_samples in sample_by_lane.items():
         LOG.debug(f"Validate that samples are unique in lane: {lane}")
         validate_samples_are_unique(samples=lane_samples)
@@ -59,28 +59,28 @@ def get_raw_samples_from_content(sample_sheet_content: list[list[str]]) -> list[
 
 
 def get_samples_by_lane(
-    samples: list[FlowCellSample],
-) -> dict[int, list[FlowCellSample]]:
+    samples: list[IlluminaSampleIndexSetting],
+) -> dict[int, list[IlluminaSampleIndexSetting]]:
     """Group and return samples by lane."""
     LOG.debug("Order samples by lane")
-    sample_by_lane: dict[int, list[FlowCellSample]] = {}
+    sample_by_lane: dict[int, list[IlluminaSampleIndexSetting]] = {}
     for sample in samples:
         if sample.lane not in sample_by_lane:
             sample_by_lane[sample.lane] = []
         sample_by_lane[sample.lane].append(sample)
     return sample_by_lane
 
 
-def get_flow_cell_samples_from_content(
+def get_samples_from_content(
     sample_sheet_content: list[list[str]],
-) -> list[FlowCellSample]:
+) -> list[IlluminaSampleIndexSetting]:
     """
-    Return the samples in a sample sheet as a list of FlowCellSample objects.
+    Return the samples in a sample sheet as a list of IlluminaIndexSettings objects.
     Raises:
         ValidationError: if the samples do not have the correct attributes based on their model.
     """
     raw_samples: list[dict[str, str]] = get_raw_samples_from_content(
         sample_sheet_content=sample_sheet_content
     )
-    adapter = TypeAdapter(list[FlowCellSample])
+    adapter = TypeAdapter(list[IlluminaSampleIndexSetting])
     return adapter.validate_python(raw_samples)

cg/apps/demultiplex/sample_sheet/sample_models.py

@@ -17,8 +17,8 @@
 LOG = logging.getLogger(__name__)
 
 
-class FlowCellSample(BaseModel):
-    """Class that represents a flow cell sample."""
+class IlluminaSampleIndexSetting(BaseModel):
+    """Class that represents index settings for a sample on an Illumina run."""
 
     lane: int = Field(..., alias=SampleSheetBCLConvertSections.Data.LANE)
     sample_id: SampleId = Field(..., alias=SampleSheetBCLConvertSections.Data.SAMPLE_INTERNAL_ID)
@@ -80,7 +80,9 @@ def update_override_cycles(self, run_parameters: RunParameters) -> None:
         )
         self.override_cycles = read1_cycles + index1_cycles + index2_cycles + read2_cycles
 
-    def _update_barcode_mismatches_1(self, samples_to_compare: list["FlowCellSample"]) -> None:
+    def _update_barcode_mismatches_1(
+        self, samples_to_compare: list["IlluminaSampleIndexSetting"]
+    ) -> None:
         """Assign zero to barcode_mismatches_1 if the hamming distance between self.index
         and the index1 of any sample in the lane is below the minimum threshold."""
         for sample in samples_to_compare:
@@ -96,7 +98,7 @@ def _update_barcode_mismatches_1(self, samples_to_compare: list["FlowCellSample"
 
     def _update_barcode_mismatches_2(
         self,
-        samples_to_compare: list["FlowCellSample"],
+        samples_to_compare: list["IlluminaSampleIndexSetting"],
         is_reverse_complement: bool,
     ) -> None:
         """Assign zero to barcode_mismatches_2 if the hamming distance between self.index2
@@ -130,7 +132,7 @@ def process_indexes(self, run_parameters: RunParameters):
 
     def update_barcode_mismatches(
         self,
-        samples_to_compare: list["FlowCellSample"],
+        samples_to_compare: list["IlluminaSampleIndexSetting"],
         is_run_single_index: bool,
         is_reverse_complement: bool,
     ) -> None:

cg/apps/demultiplex/sample_sheet/sample_sheet_creator.py

@@ -3,7 +3,7 @@
 import logging
 
 from cg.apps.demultiplex.sample_sheet.read_sample_sheet import get_samples_by_lane
-from cg.apps.demultiplex.sample_sheet.sample_models import FlowCellSample
+from cg.apps.demultiplex.sample_sheet.sample_models import IlluminaSampleIndexSetting
 from cg.constants.demultiplexing import IndexSettings, SampleSheetBCLConvertSections
 from cg.models.demultiplex.run_parameters import RunParameters
 from cg.models.run_devices.illumina_run_directory_data import IlluminaRunDirectoryData
@@ -12,22 +12,22 @@
 
 
 class SampleSheetCreator:
-    """Base class for sample sheet creation."""
+    """Base class for sample sheet creation for an Illumina run."""
 
     def __init__(
         self,
-        flow_cell: IlluminaRunDirectoryData,
-        lims_samples: list[FlowCellSample],
+        run_directory_data: IlluminaRunDirectoryData,
+        samples: list[IlluminaSampleIndexSetting],
     ):
-        self.flow_cell: IlluminaRunDirectoryData = flow_cell
-        self.flow_cell_id: str = flow_cell.id
-        self.lims_samples: list[FlowCellSample] = lims_samples
-        self.run_parameters: RunParameters = flow_cell.run_parameters
+        self.run_directory_data: IlluminaRunDirectoryData = run_directory_data
+        self.flow_cell_id: str = run_directory_data.id
+        self.samples: list[IlluminaSampleIndexSetting] = samples
+        self.run_parameters: RunParameters = run_directory_data.run_parameters
         self.index_settings: IndexSettings = self.run_parameters.index_settings
 
     def convert_sample_to_header_dict(
         self,
-        sample: FlowCellSample,
+        sample: IlluminaSampleIndexSetting,
         data_column_names: list[str],
     ) -> list[str]:
         """Convert a lims sample object to a list that corresponds to the sample sheet headers."""
@@ -49,7 +49,7 @@ def get_additional_sections_sample_sheet(self) -> list[list[str]]:
             [
                 SampleSheetBCLConvertSections.Header.INSTRUMENT_PLATFORM_TITLE.value,
                 SampleSheetBCLConvertSections.Header.instrument_platform_sequencer().get(
-                    self.flow_cell.sequencer_type
+                    self.run_directory_data.sequencer_type
                 ),
             ],
             SampleSheetBCLConvertSections.Header.index_orientation_forward(),
@@ -102,7 +102,7 @@ def create_sample_sheet_content(self) -> list[list[str]]:
         sample_sheet_content: list[list[str]] = (
             self.get_additional_sections_sample_sheet() + complete_data_section
         )
-        for sample in self.lims_samples:
+        for sample in self.samples:
             sample_sheet_content.append(
                 self.convert_sample_to_header_dict(
                     sample=sample,
@@ -113,15 +113,15 @@ def create_sample_sheet_content(self) -> list[list[str]]:
 
     def process_samples_for_sample_sheet(self) -> None:
         """Remove unwanted samples and adapt remaining samples."""
-        for lims_sample in self.lims_samples:
-            lims_sample.process_indexes(run_parameters=self.run_parameters)
+        for sample in self.samples:
+            sample.process_indexes(run_parameters=self.run_parameters)
         is_reverse_complement: bool = (
             self.index_settings.are_i5_override_cycles_reverse_complemented
         )
-        for lane, samples_in_lane in get_samples_by_lane(self.lims_samples).items():
+        for lane, samples_in_lane in get_samples_by_lane(self.samples).items():
             LOG.info(f"Updating barcode mismatch values for samples in lane {lane}")
-            for lims_sample in samples_in_lane:
-                lims_sample.update_barcode_mismatches(
+            for sample in samples_in_lane:
+                sample.update_barcode_mismatches(
                     samples_to_compare=samples_in_lane,
                     is_run_single_index=self.run_parameters.is_single_index,
                     is_reverse_complement=is_reverse_complement,

cg/apps/demultiplex/sample_sheet/sample_sheet_models.py

@@ -3,25 +3,25 @@
 
 from pydantic import BaseModel
 
-from cg.apps.demultiplex.sample_sheet.sample_models import FlowCellSample
+from cg.apps.demultiplex.sample_sheet.sample_models import IlluminaSampleIndexSetting
 
 LOG = logging.getLogger(__name__)
 
 
 class SampleSheet(BaseModel):
-    samples: list[FlowCellSample]
+    samples: list[IlluminaSampleIndexSetting]
 
     def get_non_pooled_lanes_and_samples(self) -> list[tuple[int, str]]:
         """Return tuples of non-pooled lane and sample ids."""
         non_pooled_lane_sample_id_pairs: list[tuple[int, str]] = []
-        non_pooled_samples: list[FlowCellSample] = self.get_non_pooled_samples()
+        non_pooled_samples: list[IlluminaSampleIndexSetting] = self.get_non_pooled_samples()
         for sample in non_pooled_samples:
             non_pooled_lane_sample_id_pairs.append((sample.lane, sample.sample_id))
         return non_pooled_lane_sample_id_pairs
 
-    def get_non_pooled_samples(self) -> list[FlowCellSample]:
+    def get_non_pooled_samples(self) -> list[IlluminaSampleIndexSetting]:
         """Return samples that are sequenced solo in their lane."""
-        lane_samples: dict[int, list[FlowCellSample]] = defaultdict(list)
+        lane_samples: dict[int, list[IlluminaSampleIndexSetting]] = defaultdict(list)
         for sample in self.samples:
             lane_samples[sample.lane].append(sample)
         return [samples[0] for samples in lane_samples.values() if len(samples) == 1]

cg/apps/demultiplex/sample_sheet/sample_sheet_validator.py

@@ -7,11 +7,11 @@
 
 from cg.apps.demultiplex.sample_sheet.override_cycles_validator import OverrideCyclesValidator
 from cg.apps.demultiplex.sample_sheet.read_sample_sheet import (
-    get_flow_cell_samples_from_content,
+    get_samples_from_content,
     get_raw_samples_from_content,
     validate_samples_unique_per_lane,
 )
-from cg.apps.demultiplex.sample_sheet.sample_models import FlowCellSample
+from cg.apps.demultiplex.sample_sheet.sample_models import IlluminaSampleIndexSetting
 from cg.apps.demultiplex.sample_sheet.sample_sheet_models import SampleSheet
 from cg.constants.constants import FileFormat
 from cg.constants.demultiplexing import NAME_TO_INDEX_SETTINGS, SampleSheetBCLConvertSections
@@ -115,7 +115,7 @@ def _validate_samples(self) -> None:
         """
         LOG.debug("Validating samples")
         try:
-            validated_samples: list[FlowCellSample] = get_flow_cell_samples_from_content(
+            validated_samples: list[IlluminaSampleIndexSetting] = get_samples_from_content(
                 sample_sheet_content=self.content
             )
         except ValidationError as error:
@@ -181,5 +181,5 @@ def get_sample_sheet_object_from_file(self, file_path: Path) -> SampleSheet:
             SampleSheetError: If the sample sheet is not valid.
         """
         self.validate_sample_sheet_from_file(file_path)
-        samples: list[FlowCellSample] = get_flow_cell_samples_from_content(self.content)
+        samples: list[IlluminaSampleIndexSetting] = get_samples_from_content(self.content)
         return SampleSheet(samples=samples)