Merge branch 'master' into fix-demultiplex-tests

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 55.0.0
+current_version = 55.1.0
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "55.0.0"
+__version__ = "55.1.0"

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/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.
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "55.0.0"
+version = "55.1.0"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"

tests/apps/crunchy/test_crunchy.py

@@ -56,7 +56,7 @@ def test_is_fastq_compression_possible(
     assert not spring_file.exists()
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_fastq_compression_possible(compression_object)
+    result = crunchy_api.is_fastq_compression_possible(compression_obj=compression_object)
 
     # THEN result should be True
     assert result is True
@@ -83,7 +83,7 @@ def test_is_fastq_compression_possible_compression_pending(
     assert not spring_file.exists()
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_fastq_compression_possible(compression_object)
+    result = crunchy_api.is_fastq_compression_possible(compression_obj=compression_object)
 
     # THEN result should be False since the compression flag exists
     assert result is False
@@ -107,7 +107,7 @@ def test_is_fastq_compression_possible_spring_exists(
     assert spring_file.exists()
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_fastq_compression_possible(compression_object)
+    result = crunchy_api.is_fastq_compression_possible(compression_obj=compression_object)
 
     # THEN result should be False since the compression flag exists
     assert result is False
@@ -116,22 +116,21 @@ def test_is_fastq_compression_possible_spring_exists(
 
 
 def test_is_compression_done(
-    crunchy_config: dict[str, dict[str, Any]],
+    real_crunchy_api,
     spring_metadata_file: Path,
     compression_object: CompressionData,
     caplog,
 ):
     """Test if compression is done when everything is correct"""
     caplog.set_level(logging.DEBUG)
     # GIVEN a crunchy-api, and FASTQ paths
-    crunchy_api = CrunchyAPI(crunchy_config)
     # GIVEN no SPRING file exists
     compression_object.spring_path.touch()
     assert spring_metadata_file == compression_object.spring_metadata_path
     assert spring_metadata_file.exists()
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_fastq_compression_done(compression_object)
+    result = real_crunchy_api.is_fastq_compression_done(compression_object)
 
     # THEN result should be True
     assert result is True
@@ -140,18 +139,17 @@ def test_is_compression_done(
 
 
 def test_is_compression_done_no_spring(
-    crunchy_config: dict[str, dict[str, Any]], compression_object: CompressionData, caplog
+    real_crunchy_api: CrunchyAPI, compression_object: CompressionData, caplog
 ):
     """Test if compression is done when no SPRING archive"""
     caplog.set_level(logging.DEBUG)
     # GIVEN a crunchy-api, and FASTQ paths
-    crunchy_api = CrunchyAPI(crunchy_config)
     # GIVEN no SPRING file exists
     spring_file = compression_object.spring_path
     assert not spring_file.exists()
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_fastq_compression_done(compression_object)
+    result = real_crunchy_api.is_fastq_compression_done(compression_object)
 
     # THEN result should be false
     assert not result
@@ -160,20 +158,19 @@ def test_is_compression_done_no_spring(
 
 
 def test_is_compression_done_no_flag_spring(
-    crunchy_config: dict[str, dict[str, Any]], compression_object: CompressionData, caplog
+    real_crunchy_api: CrunchyAPI, compression_object: CompressionData, caplog
 ):
     """Test if SPRING compression is done when no metadata file"""
     caplog.set_level(logging.DEBUG)
     # GIVEN a crunchy-api, and FASTQ paths
-    crunchy_api = CrunchyAPI(crunchy_config)
     # GIVEN a existing SPRING file
     compression_object.spring_path.touch()
     assert compression_object.spring_path.exists()
-    # GIVEN a non existing flag file
+    # GIVEN a non-existing flag file
     assert not compression_object.spring_metadata_path.exists()
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_fastq_compression_done(compression_object)
+    result = real_crunchy_api.is_fastq_compression_done(compression_object)
 
     # THEN result should be false
     assert not result
@@ -182,15 +179,14 @@ def test_is_compression_done_no_flag_spring(
 
 
 def test_is_compression_done_spring(
-    crunchy_config: dict[str, dict[str, Any]],
+    real_crunchy_api: CrunchyAPI,
     compression_object: CompressionData,
     spring_metadata_file: Path,
     caplog,
 ):
     """Test if compression is done when SPRING files exists"""
     caplog.set_level(logging.DEBUG)
     # GIVEN a crunchy-api, and FASTQ paths
-    crunchy_api = CrunchyAPI(crunchy_config)
     # GIVEN a existing SPRING file
     compression_object.spring_path.touch()
     assert compression_object.spring_path.exists()
@@ -199,7 +195,7 @@ def test_is_compression_done_spring(
     assert compression_object.spring_metadata_path.exists()
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_fastq_compression_done(compression_object)
+    result = real_crunchy_api.is_fastq_compression_done(compression_object)
 
     # THEN result should be True
     assert result
@@ -208,7 +204,7 @@ def test_is_compression_done_spring(
 
 
 def test_is_compression_done_spring_new_files(
-    crunchy_config: dict[str, dict[str, Any]],
+    real_crunchy_api: CrunchyAPI,
     compression_object: CompressionData,
     spring_metadata_file: Path,
     caplog,
@@ -219,7 +215,6 @@ def test_is_compression_done_spring_new_files(
     """
     caplog.set_level(logging.DEBUG)
     # GIVEN a crunchy-api, and FASTQ paths
-    crunchy_api = CrunchyAPI(crunchy_config)
     # GIVEN a existing SPRING file
     compression_object.spring_path.touch()
     assert compression_object.spring_path.exists()
@@ -237,7 +232,7 @@ def test_is_compression_done_spring_new_files(
         assert "updated" in file_info
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_fastq_compression_done(compression_object)
+    result = real_crunchy_api.is_fastq_compression_done(compression_object)
 
     # THEN result should be False since the updated date < 3 weeks
     assert result is False
@@ -246,7 +241,7 @@ def test_is_compression_done_spring_new_files(
 
 
 def test_is_compression_done_spring_old_files(
-    crunchy_config: dict[str, dict[str, Any]],
+    real_crunchy_api: CrunchyAPI,
     compression_object: CompressionData,
     spring_metadata_file: Path,
     caplog,
@@ -257,7 +252,6 @@ def test_is_compression_done_spring_old_files(
     """
     caplog.set_level(logging.DEBUG)
     # GIVEN a crunchy-api, and FASTQ paths
-    crunchy_api = CrunchyAPI(crunchy_config)
     # GIVEN a existing SPRING file
     compression_object.spring_path.touch()
     assert compression_object.spring_path.exists()
@@ -277,7 +271,7 @@ def test_is_compression_done_spring_old_files(
     )
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_fastq_compression_done(compression_object)
+    result = real_crunchy_api.is_fastq_compression_done(compression_object)
 
     # THEN result should be True since the updated date > 3 weeks
     assert result is True
@@ -286,15 +280,14 @@ def test_is_compression_done_spring_old_files(
 
 
 def test_is_spring_decompression_possible_no_fastq(
-    crunchy_config: dict[str, dict[str, Any]], compression_object: CompressionData, caplog
+    real_crunchy_api: CrunchyAPI, compression_object: CompressionData, caplog
 ):
     """Test if decompression is possible when there are no FASTQ files
 
     The function should return true since there are no FASTQ files
     """
     caplog.set_level(logging.DEBUG)
     # GIVEN a crunchy-api
-    crunchy_api = CrunchyAPI(crunchy_config)
     # GIVEN a existing SPRING file
     compression_object.spring_path.touch()
     assert compression_object.spring_path.exists()
@@ -305,7 +298,7 @@ def test_is_spring_decompression_possible_no_fastq(
     assert not compression_object.fastq_second.exists()
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_spring_decompression_possible(compression_object)
+    result = real_crunchy_api.is_spring_decompression_possible(compression_object)
 
     # THEN result should be True since there are no fastq files
     assert result is True
@@ -314,18 +307,17 @@ def test_is_spring_decompression_possible_no_fastq(
 
 
 def test_is_spring_decompression_possible_no_spring(
-    crunchy_config: dict[str, dict[str, Any]], compression_object: CompressionData, caplog
+    real_crunchy_api: CrunchyAPI, compression_object: CompressionData, caplog
 ):
     """Test if decompression is possible when there are no SPRING archive
 
     The function should return False since there is no SPRING archive
     """
     caplog.set_level(logging.DEBUG)
     # GIVEN a crunchy-api, and FASTQ paths
-    crunchy_api = CrunchyAPI(crunchy_config)
 
     # WHEN checking if SPRING compression is done
-    result = crunchy_api.is_spring_decompression_possible(compression_object)
+    result = real_crunchy_api.is_spring_decompression_possible(compression_object)
 
     # THEN result should be False since there is no SPRING archive
     assert result is False
@@ -334,23 +326,22 @@ def test_is_spring_decompression_possible_no_spring(
 
 
 def test_is_spring_decompression_possible_fastq(
-    crunchy_config: dict[str, dict[str, Any]], compression_object: CompressionData, caplog
+    real_crunchy_api: CrunchyAPI, compression_object: CompressionData, caplog
 ):
     """Test if decompression is possible when there are existing FASTQ files
 
     The function should return False since there are decompressed FASTQ files
     """
     caplog.set_level(logging.DEBUG)
     # GIVEN a crunchy-api, and FASTQ paths
-    crunchy_api = CrunchyAPI(crunchy_config)
     # GIVEN a existing SPRING file
     compression_object.spring_path.touch()
     # GIVEN that the FASTQ files exists
     compression_object.fastq_first.touch()
     compression_object.fastq_second.touch()
 
     # WHEN checking if SPRING decompression is possible
-    result = crunchy_api.is_spring_decompression_possible(compression_object)
+    result = real_crunchy_api.is_spring_decompression_possible(compression_object)
 
     # THEN result should be False since the FASTQ files already exists
     assert result is False
@@ -359,31 +350,29 @@ def test_is_spring_decompression_possible_fastq(
 
 
 def test_is_not_pending_when_no_flag_file(
-    crunchy_config: dict[str, dict[str, Any]], compression_object: CompressionData
+    real_crunchy_api: CrunchyAPI, compression_object: CompressionData
 ):
     """Test if SPRING compression is pending when no flag file"""
     # GIVEN a crunchy-api, and a FASTQ file
-    crunchy_api = CrunchyAPI(crunchy_config)
-    # GIVEN a non existing pending flag
+    # GIVEN a non-existing pending flag
     assert not compression_object.pending_path.exists()
 
     # WHEN checking if SPRING compression is ongoing
-    result = crunchy_api.is_compression_pending(compression_object)
+    result = real_crunchy_api.is_compression_pending(compression_object)
 
     # THEN result should be False since the pending flag is not there
     assert result is False
 
 
-def test_is_pending(crunchy_config: dict[str, dict[str, Any]], compression_object: CompressionData):
+def test_is_pending(real_crunchy_api: CrunchyAPI, compression_object: CompressionData):
     """Test if SPRING compression is pending when pending file exists"""
     # GIVEN a crunchy-api, and FASTQ files
-    crunchy_api = CrunchyAPI(crunchy_config)
     # GIVEN a existing pending flag
     compression_object.pending_path.touch()
     assert compression_object.pending_path.exists()
 
     # WHEN checking if SPRING compression is pending
-    result = crunchy_api.is_compression_pending(compression_object)
+    result = real_crunchy_api.is_compression_pending(compression_object)
 
     # THEN result should be True since the pending_path exists
     assert result is True