Use Scout38 for raredisease upload

cg/cli/upload/utils.py

@@ -26,7 +26,11 @@ def suggest_cases_to_upload(status_db: Store, workflow: Workflow | None = None)
 
 def get_scout_api_by_case(cg_config: CGConfig, case_id: str) -> ScoutAPI:
     workflow = cg_config.status_db.get_case_by_internal_id(case_id).data_analysis
-    return cg_config.scout_api_38 if workflow == Workflow.NALLO else cg_config.scout_api_37
+    return (
+        cg_config.scout_api_38
+        if workflow in [Workflow.NALLO, Workflow.RAREDISEASE]
+        else cg_config.scout_api_37
+    )
 
 
 def get_scout_api_by_genome_build(cg_config: CGConfig, genome_build: str) -> ScoutAPI:

cg/meta/delivery_report/templates/macros/uploaded_files/uploaded_files.html

@@ -6,115 +6,115 @@
 
 {% macro uploaded_files(case, customer) %}
 {% set data_delivery = case.data_analysis.data_delivery %}
-  {% if "fastq" in data_delivery or "analysis" in data_delivery or "scout" in data_delivery %}
-    <div class="container mb-5">
-      <h3 class="mb-4">Uppladdade filer</h3>
-      <div class="alert alert-info" role="alert">
-        Ytterligare information om de specifika levererade filerna finns på:
-        <a href="https://clinical.scilifelab.se/data-delivery" class="alert-link">
-          https://clinical.scilifelab.se/data-delivery</a>.
-      </div>
-      <!-- Scout files -->
-      {{ scout_files(case=case, customer_id=customer.id, scout_access=customer.scout_access) }}
-      <!-- Caesar files -->
-      {{ caesar_files(case=case, customer_id=customer.id) }}
-    </div>
-  {% endif %}
+{% if "fastq" in data_delivery or "analysis" in data_delivery or "scout" in data_delivery %}
+<div class="container mb-5">
+  <h3 class="mb-4">Uppladdade filer</h3>
+  <div class="alert alert-info" role="alert">
+    Ytterligare information om de specifika levererade filerna finns på:
+    <a href="https://clinical.scilifelab.se/data-delivery" class="alert-link">
+      https://clinical.scilifelab.se/data-delivery</a>.
+  </div>
+  <!-- Scout files -->
+  {{ scout_files(case=case, customer_id=customer.id, scout_access=customer.scout_access) }}
+  <!-- Caesar files -->
+  {{ caesar_files(case=case, customer_id=customer.id) }}
+</div>
+{% endif %}
 {% endmacro %}
 
 {% macro scout_files(case, customer_id, scout_access) %}
 {% set workflow = case.data_analysis.workflow %}
-  {% if scout_access and "scout" in case.data_analysis.data_delivery %}
-    <h4 class="mt-4 mb-3">Scout</h4>
-    <div class="alert alert-info" role="alert">
-      Varianter finns uppladdade i Scout:
-      {% if "nallo" in workflow %}
-        <a href="https://scout38.sys.scilifelab.se/{{ customer_id }}/{{ case.name }}" class="alert-link">
-          https://scout38.sys.scilifelab.se/{{ customer_id }}/{{ case.name }}</a>.
-      {% else %}
-        <a href="https://scout.scilifelab.se/{{ customer_id }}/{{ case.name }}" class="alert-link">
-          https://scout.scilifelab.se/{{ customer_id }}/{{ case.name }}</a>.
-      {% endif %}
-    </div>
-    {% if "balsamic" in workflow %}
-      <!-- BALSAMIC Scout files -->
-      {{ balsamic_scout_files(scout_files=case.data_analysis.scout_files, case_id=case.id, case_name=case.name) }}
-    {% elif workflow == "mip-dna" %}
-      <!-- MIP-DNA Scout files -->
-      {{ mip_dna_scout_files(scout_files=case.data_analysis.scout_files, case_id=case.id, case_name=case.name) }}
-    {% elif workflow == "nallo" %}
-      <!-- Nallo Scout files -->
-      {{ nallo_scout_files(scout_files=case.data_analysis.scout_files, case_id=case.id, case_name=case.name) }}
-    {% elif workflow == "raredisease" %}
-      <!-- Raredisease Scout files -->
-      {{ raredisease_scout_files(scout_files=case.data_analysis.scout_files, case_id=case.id, case_name=case.name) }}
-    {% elif workflow == "rnafusion" %}
-      <!-- Rnafusion Scout files -->
-      {{ rnafusion_scout_files(scout_files=case.data_analysis.scout_files, case_id=case.id, case_name=case.name) }}
-    {% endif %}
+{% if scout_access and "scout" in case.data_analysis.data_delivery %}
+<h4 class="mt-4 mb-3">Scout</h4>
+<div class="alert alert-info" role="alert">
+  Varianter finns uppladdade i Scout:
+  {% if workflow in ["nallo", "raredisease"] %}
+  <a href="https://scout38.sys.scilifelab.se/{{ customer_id }}/{{ case.name }}" class="alert-link">
+    https://scout38.sys.scilifelab.se/{{ customer_id }}/{{ case.name }}</a>.
+  {% else %}
+  <a href="https://scout.scilifelab.se/{{ customer_id }}/{{ case.name }}" class="alert-link">
+    https://scout.scilifelab.se/{{ customer_id }}/{{ case.name }}</a>.
   {% endif %}
+</div>
+{% if "balsamic" in workflow %}
+<!-- BALSAMIC Scout files -->
+{{ balsamic_scout_files(scout_files=case.data_analysis.scout_files, case_id=case.id, case_name=case.name) }}
+{% elif workflow == "mip-dna" %}
+<!-- MIP-DNA Scout files -->
+{{ mip_dna_scout_files(scout_files=case.data_analysis.scout_files, case_id=case.id, case_name=case.name) }}
+{% elif workflow == "nallo" %}
+<!-- Nallo Scout files -->
+{{ nallo_scout_files(scout_files=case.data_analysis.scout_files, case_id=case.id, case_name=case.name) }}
+{% elif workflow == "raredisease" %}
+<!-- Raredisease Scout files -->
+{{ raredisease_scout_files(scout_files=case.data_analysis.scout_files, case_id=case.id, case_name=case.name) }}
+{% elif workflow == "rnafusion" %}
+<!-- Rnafusion Scout files -->
+{{ rnafusion_scout_files(scout_files=case.data_analysis.scout_files, case_id=case.id, case_name=case.name) }}
+{% endif %}
+{% endif %}
 {% endmacro %}
 
 {% macro caesar_files(case, customer_id) %}
 {% set data_delivery = case.data_analysis.data_delivery %}
-  {% if "fastq" in data_delivery or "analysis" in data_delivery %}
-    <h4 class="mt-4 mb-3">Leveransinkorg (Caesar)</h4>
-    <div class="alert alert-info" role="alert">
-      Filer som ska laddas upp till din inkorg:
-      <a class="alert-link">/home/{{ customer_id }}/inbox/{{ case.samples[0].ticket }}</a>.
-    </div>
-    <!-- Analysis files -->
-    {{ analysis_files(case=case) }}
-    <!-- Fastq files -->
-    {{ fastq_files(case=case) }}
-  {% endif %}
+{% if "fastq" in data_delivery or "analysis" in data_delivery %}
+<h4 class="mt-4 mb-3">Leveransinkorg (Caesar)</h4>
+<div class="alert alert-info" role="alert">
+  Filer som ska laddas upp till din inkorg:
+  <a class="alert-link">/home/{{ customer_id }}/inbox/{{ case.samples[0].ticket }}</a>.
+</div>
+<!-- Analysis files -->
+{{ analysis_files(case=case) }}
+<!-- Fastq files -->
+{{ fastq_files(case=case) }}
+{% endif %}
 {% endmacro %}
 
 {% macro analysis_files(case) %}
-  {% if "analysis" in case.data_analysis.data_delivery %}
-    <table class="table w-auto align-middle" aria-describedby="uploaded-analysis-files-table">
-      <thead class="table-secondary">
-        <tr>
-          <th scope="col" colspan="2">Analysfiler</th>
-        </tr>
-      </thead>
-      <tbody>
-        {{ delivered_files(row_title=case.name, files=case.data_analysis.delivered_files) }}
-        {% for sample in case.samples %}
-          {{ delivered_files(row_title=sample.name, files=sample.delivered_files) }}
-        {% endfor %}
-      </tbody>
-    </table>
-  {% endif %}
+{% if "analysis" in case.data_analysis.data_delivery %}
+<table class="table w-auto align-middle" aria-describedby="uploaded-analysis-files-table">
+  <thead class="table-secondary">
+    <tr>
+      <th scope="col" colspan="2">Analysfiler</th>
+    </tr>
+  </thead>
+  <tbody>
+    {{ delivered_files(row_title=case.name, files=case.data_analysis.delivered_files) }}
+    {% for sample in case.samples %}
+    {{ delivered_files(row_title=sample.name, files=sample.delivered_files) }}
+    {% endfor %}
+  </tbody>
+</table>
+{% endif %}
 {% endmacro %}
 
 {% macro fastq_files(case) %}
-  {% if "fastq" in case.data_analysis.data_delivery %}
-    <table class="table w-auto align-middle" aria-describedby="uploaded-fastq-files-table">
-      <thead class="table-secondary">
-        <tr>
-          <th scope="col" colspan="2">Fastq-filer</th>
-        </tr>
-      </thead>
-      <tbody>
-        {% for sample in case.samples %}
-          <!-- Delivered files -->
-          {{ delivered_files(row_title=sample.name, files=sample.delivered_fastq_files) }}
-        {% endfor %}
-      </tbody>
-    </table>
-  {% endif %}
-{% endmacro %}
-
-{% macro delivered_files(row_title, files) %}
-  {% if files != "N/A" %}
+{% if "fastq" in case.data_analysis.data_delivery %}
+<table class="table w-auto align-middle" aria-describedby="uploaded-fastq-files-table">
+  <thead class="table-secondary">
     <tr>
-      <th scope="row" rowspan="{{ files | length + 1}}">{{ row_title }}</th>
+      <th scope="col" colspan="2">Fastq-filer</th>
     </tr>
-    {% for file in files %}
-      <tr>
-        <td>{{ file }}</td>
-      </tr>
+  </thead>
+  <tbody>
+    {% for sample in case.samples %}
+    <!-- Delivered files -->
+    {{ delivered_files(row_title=sample.name, files=sample.delivered_fastq_files) }}
     {% endfor %}
-  {% endif %}
+  </tbody>
+</table>
+{% endif %}
 {% endmacro %}
+
+{% macro delivered_files(row_title, files) %}
+{% if files != "N/A" %}
+<tr>
+  <th scope="row" rowspan="{{ files | length + 1}}">{{ row_title }}</th>
+</tr>
+{% for file in files %}
+<tr>
+  <td>{{ file }}</td>
+</tr>
+{% endfor %}
+{% endif %}
+{% endmacro %}

cg/meta/upload/scout/raredisease_config_builder.py

@@ -69,7 +69,7 @@ def build_load_config(self, hk_version: Version, analysis: Analysis) -> Raredise
         self.load_custom_image_sample(
             load_config=load_config, analysis=analysis, hk_version=hk_version
         )
-        load_config.human_genome_build = GenomeBuild.hg19
+        load_config.human_genome_build = GenomeBuild.hg38
         load_config.rank_score_threshold = RANK_MODEL_THRESHOLD
         load_config.rank_model_version = self.get_rank_model_version(
             variant_type=Variants.SNV, hk_version=hk_version

cg/meta/workflow/analysis.py

@@ -67,7 +67,7 @@ class AnalysisAPI(MetaAPI):
     def __init__(self, workflow: Workflow, config: CGConfig):
         super().__init__(config=config)
         self.workflow = workflow
-        if self.workflow == Workflow.NALLO:
+        if self.workflow in [Workflow.NALLO, Workflow.RAREDISEASE]:
             self.scout_api: ScoutAPI = self.scout_api_38
         else:
             self.scout_api: ScoutAPI = self.scout_api_37

cg/meta/workflow/raredisease.py

@@ -164,8 +164,8 @@ def get_scout_upload_case_tags(self) -> dict:
         return RAREDISEASE_CASE_TAGS
 
     def get_genome_build(self, case_id: str) -> GenomeVersion:
-        """Return reference genome for a raredisease case. Currently fixed for hg19."""
-        return GenomeVersion.HG19
+        """Return reference genome for a raredisease case."""
+        return GenomeVersion.HG38
 
     def parse_analysis(self, qc_metrics_raw: list[MetricsBase], **kwargs) -> NextflowAnalysis:
         """Parse Nextflow output analysis files and return an analysis model."""

cg/services/delivery_message/messages/utils.py

@@ -15,7 +15,7 @@ def get_scout_link(case: Case) -> str:
     case_name: str = case.name
     url: str = (
         "https://scout38.sys.scilifelab.se/"
-        if case.data_analysis == Workflow.NALLO
+        if case.data_analysis in [Workflow.NALLO, Workflow.RAREDISEASE]
         else "https://scout.scilifelab.se/"
     )
     return f"{url}{customer_id}/{case_name}"

tests/cli/upload/test_cli_scout.py

@@ -14,6 +14,7 @@
 from cg.meta.workflow.mip_dna import MipDNAAnalysisAPI
 from cg.meta.workflow.mip_rna import MipRNAAnalysisAPI
 from cg.meta.workflow.nallo import NalloAnalysisAPI
+from cg.meta.workflow.raredisease import RarediseaseAnalysisAPI
 from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
 from cg.meta.workflow.tomte import TomteAnalysisAPI
 from cg.models.cg_config import CGConfig
@@ -31,22 +32,24 @@
 ]
 
 ANALYSIS_API: list = [
-    (Workflow.BALSAMIC, BalsamicAnalysisAPI),
-    (Workflow.MIP_DNA, MipDNAAnalysisAPI),
-    (Workflow.MIP_RNA, MipRNAAnalysisAPI),
-    (Workflow.NALLO, NalloAnalysisAPI),
-    (Workflow.RNAFUSION, RnafusionAnalysisAPI),
-    (Workflow.TOMTE, TomteAnalysisAPI),
+    (Workflow.BALSAMIC, BalsamicAnalysisAPI, "scout_api_37"),
+    (Workflow.MIP_DNA, MipDNAAnalysisAPI, "scout_api_37"),
+    (Workflow.MIP_RNA, MipRNAAnalysisAPI, "scout_api_37"),
+    (Workflow.NALLO, NalloAnalysisAPI, "scout_api_38"),
+    (Workflow.RAREDISEASE, RarediseaseAnalysisAPI, "scout_api_38"),
+    (Workflow.RNAFUSION, RnafusionAnalysisAPI, "scout_api_37"),
+    (Workflow.TOMTE, TomteAnalysisAPI, "scout_api_37"),
 ]
 
 
 @pytest.mark.parametrize(
-    "workflow,analysis_api",
+    "workflow,analysis_api, scout_instance",
     ANALYSIS_API,
 )
 def test_get_upload_api(
     cg_context: CGConfig,
     case_id: str,
+    scout_instance: str,
     helpers: StoreHelpers,
     workflow: Workflow,
     analysis_api: AnalysisAPI,
@@ -63,6 +66,7 @@ def test_get_upload_api(
 
     # THEN assert that the type of upload API is correct
     assert isinstance(upload_api.analysis_api, analysis_api)
+    assert upload_api.analysis_api.scout_api is getattr(upload_api.analysis_api, scout_instance)
 
 
 @pytest.mark.parametrize(

tests/cli/upload/test_utils.py

@@ -1,36 +1,36 @@
+import pytest
+
 from cg.cli.upload.utils import get_scout_api_by_case, get_scout_api_by_genome_build
 from cg.constants import Workflow
 from cg.models.cg_config import CGConfig
 from cg.store.models import Case
 from tests.store_helpers import StoreHelpers
 
 
-def test_get_scout_api_by_case_38(upload_context: CGConfig, helpers: StoreHelpers):
-
-    # GIVEN a Nallo case
-    nallo_case: Case = helpers.ensure_case(
-        store=upload_context.status_db, data_analysis=Workflow.NALLO
-    )
-
-    # WHEN getting the corresponding ScoutAPI
-    scout_api = get_scout_api_by_case(cg_config=upload_context, case_id=nallo_case.internal_id)
-
-    # THEN the ScoutAPI should be towards the hg38 instance
-    assert scout_api == upload_context.scout_api_38
-
-
-def test_get_scout_api_by_case_37(upload_context: CGConfig, helpers: StoreHelpers):
-
-    # GIVEN a MIP-DNA case
-    nallo_case: Case = helpers.ensure_case(
-        store=upload_context.status_db, data_analysis=Workflow.MIP_DNA
-    )
+@pytest.mark.parametrize(
+    "workflow,scout_instance",
+    [
+        (Workflow.BALSAMIC, "scout_api_37"),
+        (Workflow.BALSAMIC_UMI, "scout_api_37"),
+        (Workflow.MIP_DNA, "scout_api_37"),
+        (Workflow.MIP_RNA, "scout_api_37"),
+        (Workflow.NALLO, "scout_api_38"),
+        (Workflow.RAREDISEASE, "scout_api_38"),
+        (Workflow.TOMTE, "scout_api_37"),
+    ],
+)
+def test_get_scout_api_by_case(
+    workflow: Workflow, scout_instance: str, upload_context: CGConfig, helpers: StoreHelpers
+):
+
+    # GIVEN a case
+    case: Case = helpers.ensure_case(store=upload_context.status_db, data_analysis=workflow)
 
     # WHEN getting the corresponding ScoutAPI
-    scout_api = get_scout_api_by_case(cg_config=upload_context, case_id=nallo_case.internal_id)
+    scout_api = get_scout_api_by_case(cg_config=upload_context, case_id=case.internal_id)
 
-    # THEN the ScoutAPI should be towards the hg37 instance
-    assert scout_api == upload_context.scout_api_37
+    # THEN the ScoutAPI should be towards the correct scout instance
+    assert scout_api == getattr(upload_context, scout_instance)
 
 
 def test_get_scout_api_by_reference_genome_hg19(upload_context: CGConfig):

tests/conftest.py

@@ -2904,7 +2904,6 @@ def raredisease_context(
         last_sequenced_at=datetime.now(),
         reads=total_sequenced_reads_pass,
         application_tag=wgs_application_tag,
-        reference_genome=GenomeVersion.HG19,
     )
 
     another_sample_enough_reads: Sample = helpers.add_sample(
@@ -2914,7 +2913,6 @@ def raredisease_context(
         last_sequenced_at=datetime.now(),
         reads=total_sequenced_reads_pass,
         application_tag=wgs_application_tag,
-        reference_genome=GenomeVersion.HG19,
     )
 
     helpers.add_relationship(