Check for errors in the 'phenose' file.

4 files changed, 68 insertions, 17 deletions

diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
index 1650a79..524282b 100644
--- a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
@@ -90,6 +90,14 @@
 {{errors_table("tbl-errors-pheno", errorspheno[0:50])}}
 {%endif%}
 
+{%if errorsphenose | length > 0%}
+<h2 class="heading">Phenose Errors ({{errorsphenose | length}})</h3>
+<div class="explainer">
+  We found the following errors in the 'phenose' file in your R/qtl2 bundle:
+</div>
+{{errors_table("tbl-errors-phenose", errorsphenose[0:50])}}
+{%endif%}
+
 {%if errorsphenocovar | length > 0%}
 <h2 class="heading">Phenocovar Errors ({{errorsphenocovar | length}})</h3>
 <div class="explainer">
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index c45952c..66b219d 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -211,6 +211,8 @@ def rqtl2_bundle_qc_status(jobid: UUID):
                                            thejob.get("errors-geno", "[]")),
                                        errorspheno=json.loads(
                                            thejob.get("errors-pheno", "[]")),
+                                       errorsphenose=json.loads(
+                                           thejob.get("errors-phenose", "[]")),
                                        errorsphenocovar=json.loads(
                                            thejob.get("errors-phenocovar", "[]")),
                                        messages=logmessages)
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index a41c442..f62f142 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -97,6 +97,22 @@ def pheno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]:
             zfile, "pheno", (__min_3_decimal_places__,))
         if error is not None)
 
+def phenose_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]:
+    """Check for and retrieve phenose errors."""
+    def __min_6_decimal_places__(
+            lineno: int, field: str, value: str) -> Optional[InvalidValue]:
+        if not (re.search(r"^([0-9]+\.[0-9]{6,}|[0-9]+\.?0*)$", value)
+                or re.search(r"^0\.0+$", value)
+                or re.search("^0+$", value)):
+            return InvalidValue(lineno, field, value, (
+                f"Invalid value '{value}'. Expected numerical value "
+                "with at least 6 decimal places."))
+        return None
+    return (
+        error for error in retrieve_errors(
+            zfile, "phenose", (__min_6_decimal_places__,))
+        if error is not None)
+
 def retrieve_errors(zfile: ZipFile, filetype: str, checkers: tuple[Callable]) -> Iterator[
         Union[InvalidValue, MissingFile]]:
     """Check for and retrieve errors from files of type `filetype`."""
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py
index aea1baa..c3e8b66 100644
--- a/scripts/qc_on_rqtl2_bundle.py
+++ b/scripts/qc_on_rqtl2_bundle.py
@@ -14,6 +14,7 @@ from qc_app import jobs
 from qc_app.db_utils import database_connection
 from qc_app.check_connections import check_db, check_redis
 
+from r_qtl import r_qtl2 as rqtl2
 from r_qtl import r_qtl2_qc as rqc
 from r_qtl import fileerrors as rqfe
 
@@ -59,31 +60,54 @@ def qc_missing_files(rconn: Redis,
 def qc_geno_errors(rconn, fqjobid, zfile, logger) -> bool:
     """Check for errors in `geno` file(s)."""
     logger.info("Checking for errors in the 'geno' file…")
-    gerrs = tuple(rqc.geno_errors(zfile))
-    add_to_errors(rconn, fqjobid, "errors-generic", tuple(
-        err for err in gerrs if isinstance(err, rqfe.MissingFile)))
-    add_to_errors(rconn, fqjobid, "errors-geno", tuple(
-        err for err in gerrs if not isinstance(err, rqfe.MissingFile)))
-    if len(gerrs) > 0:
-        logger.error("The 'geno' file has errors.")
-        return True
+    cdata = rqtl2.control_data(zfile)
+    if "geno" in cdata:
+        gerrs = tuple(rqc.geno_errors(zfile))
+        add_to_errors(rconn, fqjobid, "errors-generic", tuple(
+            err for err in gerrs if isinstance(err, rqfe.MissingFile)))
+        add_to_errors(rconn, fqjobid, "errors-geno", tuple(
+            err for err in gerrs if not isinstance(err, rqfe.MissingFile)))
+        if len(gerrs) > 0:
+            logger.error("The 'geno' file has errors.")
+            return True
+
     logger.info("No errors found in the 'geno' file.")
     return False
 
 def qc_pheno_errors(rconn, fqjobid, zfile, logger) -> bool:
     """Check for errors in `pheno` file(s)."""
-    logger.info("Checking for errors in the 'pheno' file …")
-    perrs = tuple(rqc.pheno_errors(zfile))
-    add_to_errors(rconn, fqjobid, "errors-generic", tuple(
-        err for err in perrs if isinstance(err, rqfe.MissingFile)))
-    add_to_errors(rconn, fqjobid, "errors-pheno", tuple(
-        err for err in perrs if not isinstance(err, rqfe.MissingFile)))
-    if len(perrs) > 0:
-        logger.error("The 'pheno' file has errors.")
-        return True
+    logger.info("Checking for errors in the 'pheno' file…")
+    cdata = rqtl2.control_data(zfile)
+    if "pheno" in cdata:
+        perrs = tuple(rqc.pheno_errors(zfile))
+        add_to_errors(rconn, fqjobid, "errors-generic", tuple(
+            err for err in perrs if isinstance(err, rqfe.MissingFile)))
+        add_to_errors(rconn, fqjobid, "errors-pheno", tuple(
+            err for err in perrs if not isinstance(err, rqfe.MissingFile)))
+        if len(perrs) > 0:
+            logger.error("The 'pheno' file has errors.")
+            return True
+
     logger.info("No errors found in the 'pheno' file.")
     return False
 
+def qc_phenose_errors(rconn, fqjobid, zfile, logger) -> bool:
+    """Check for errors in `phenose` file(s)."""
+    logger.info("Checking for errors in the 'phenose' file…")
+    cdata = rqtl2.control_data(zfile)
+    if "phenose" in cdata:
+        perrs = tuple(rqc.phenose_errors(zfile))
+        add_to_errors(rconn, fqjobid, "errors-generic", tuple(
+            err for err in perrs if isinstance(err, rqfe.MissingFile)))
+        add_to_errors(rconn, fqjobid, "errors-phenose", tuple(
+            err for err in perrs if not isinstance(err, rqfe.MissingFile)))
+        if len(perrs) > 0:
+            logger.error("The 'phenose' file has errors.")
+            return True
+
+    logger.info("No errors found in the 'phenose' file.")
+    return False
+
 def qc_phenocovar_errors(_rconn, _fqjobid, _zfile, _logger) -> bool:
     """Check for errors in `phenocovar` file(s)."""
     return False
@@ -104,6 +128,7 @@ def run_qc(rconn: Redis,
             1 if any((
                 qc_geno_errors(rconn, fqjobid, zfile, logger),
                 qc_pheno_errors(rconn, fqjobid, zfile, logger),
+                qc_phenose_errors(rconn, fqjobid, zfile, logger),
                 qc_phenocovar_errors(rconn, fqjobid, zfile, logger)))
             else 0)