Merge branch 'master' into metrics-to-json

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 55.0.0
+current_version = 55.2.1
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "55.0.0"
+__version__ = "55.2.1"

cg/apps/crunchy/crunchy.py

@@ -64,25 +64,24 @@ def is_compression_pending(compression_obj: CompressionData) -> bool:
     def is_fastq_compression_possible(compression_obj: CompressionData) -> bool:
         """Check if FASTQ compression is possible.
 
-        There are three possible answers to this question:
-
-         - Compression is running          -> Compression NOT possible
-         - SPRING archive exists           -> Compression NOT possible
-         - Data is external                -> Compression NOT possible
-         - Not compressed and not running  -> Compression IS possible
+        - Compression is running          -> Compression NOT possible
+        - SPRING file exists on Hasta     -> Compression NOT possible
+        - Data is external                -> Compression NOT possible
+        - Not compressed and
+           not running  -> Compression IS possible
         """
         if CrunchyAPI.is_compression_pending(compression_obj):
             return False
 
         if compression_obj.spring_exists():
-            LOG.info("SPRING file found")
+            LOG.debug("SPRING file found")
             return False
 
         if "external-data" in str(compression_obj.fastq_first):
-            LOG.info("File is external data and should not be compressed")
+            LOG.debug("File is external data and should not be compressed")
             return False
 
-        LOG.info("FASTQ compression is possible")
+        LOG.debug("FASTQ compression is possible")
 
         return True
 

cg/apps/tb/api.py

@@ -91,20 +91,6 @@ def is_latest_analysis_completed(self, case_id: str) -> bool:
     def is_latest_analysis_qc(self, case_id: str) -> bool:
         return self.get_latest_analysis_status(case_id=case_id) == AnalysisStatus.QC
 
-    def mark_analyses_deleted(self, case_id: str) -> list | None:
-        """Mark all analyses for case deleted without removing analysis files"""
-        request_body = {
-            "case_id": case_id,
-        }
-        response = self.query_trailblazer(
-            command="mark-analyses-deleted", request_body=request_body
-        )
-        if response:
-            if isinstance(response, list):
-                return [TrailblazerAnalysis.model_validate(analysis) for analysis in response]
-            if isinstance(response, dict):
-                return [TrailblazerAnalysis.model_validate(response)]
-
     def add_pending_analysis(
         self,
         case_id: str,

cg/constants/delivery.py

@@ -124,14 +124,7 @@
     {"salmon-quant"},
 ]
 
-MICROSALT_ANALYSIS_CASE_TAGS: list[set[str]] = [
-    {"microsalt-qc"},
-    {"microsalt-type"},
-    {"assembly"},
-    {"trimmed-forward-reads"},
-    {"trimmed-reverse-reads"},
-    {"reference-alignment-deduplicated"},
-]
+MICROSALT_ANALYSIS_CASE_TAGS = [{"qc-report"}, {"typing-report"}]
 
 MICROSALT_ANALYSIS_SAMPLE_TAGS: list[set[str]] = []
 

cg/meta/compress/compress.py

@@ -14,7 +14,7 @@
 from cg.constants import SequencingFileTag
 from cg.meta.backup.backup import SpringBackupAPI
 from cg.meta.compress import files
-from cg.models import CompressionData, FileData
+from cg.models import CompressionData
 from cg.store.models import Sample
 
 LOG = logging.getLogger(__name__)
@@ -73,16 +73,11 @@ def compress_fastq(self, sample_id: str) -> bool:
         for run_name in sample_fastq:
             LOG.info(f"Check if compression possible for run {run_name}")
             compression: CompressionData = sample_fastq[run_name]["compression_data"]
-            if FileData.is_empty(compression.fastq_first):
-                LOG.warning(f"Fastq files are empty for {sample_id}: {compression.fastq_first}")
-                self.delete_fastq_housekeeper(
-                    hk_fastq_first=sample_fastq[run_name]["hk_first"],
-                    hk_fastq_second=sample_fastq[run_name]["hk_second"],
-                )
-                all_ok = False
-                continue
-
-            if not self.crunchy_api.is_fastq_compression_possible(compression_obj=compression):
+            is_compression_possible: bool = self._is_fastq_compression_possible(
+                compression=compression,
+                sample_id=sample_id,
+            )
+            if not is_compression_possible:
                 LOG.warning(f"FASTQ to SPRING not possible for {sample_id}, run {run_name}")
                 all_ok = False
                 continue
@@ -93,6 +88,20 @@ def compress_fastq(self, sample_id: str) -> bool:
             self.crunchy_api.fastq_to_spring(compression_obj=compression, sample_id=sample_id)
         return all_ok
 
+    def _is_fastq_compression_possible(self, compression: CompressionData, sample_id: str) -> bool:
+        if self._is_spring_archived(compression):
+            LOG.debug(f"Found archived Spring file for {sample_id} - compression not possible")
+            return False
+        return self.crunchy_api.is_fastq_compression_possible(compression_obj=compression)
+
+    def _is_spring_archived(self, compression_data: CompressionData) -> bool:
+        spring_file: File | None = self.hk_api.get_file_insensitive_path(
+            path=compression_data.spring_path
+        )
+        if (not spring_file) or (not spring_file.archive):
+            return False
+        return bool(spring_file.archive.archived_at)
+
     def decompress_spring(self, sample_id: str) -> bool:
         """Decompress SPRING archive for a sample.
 

cg/meta/workflow/analysis.py

@@ -207,7 +207,6 @@ def get_analysis_finish_path(self, case_id: str) -> Path:
 
     def add_pending_trailblazer_analysis(self, case_id: str) -> None:
         self.check_analysis_ongoing(case_id)
-        self.trailblazer_api.mark_analyses_deleted(case_id)
         self.trailblazer_api.add_pending_analysis(
             case_id=case_id,
             email=environ_email(),

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "55.0.0"
+version = "55.2.1"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"