Created more verbose error messages, using custom messages. Added an …

…option to attempt to fix the v2 primernames to v3

README.md

@@ -281,6 +281,7 @@ $ primal-page create [OPTIONS] SCHEMEPATH
 * `--links-homepage TEXT`: Optional link to homepage
 * `--link-vendor TEXT`: Optional link to vendors
 * `--link-misc TEXT`: Optional miscellaneous link
+* `--fix / --no-fix`: Attempt to fix the scheme  [default: no-fix]
 * `--help`: Show this message and exit.
 
 
@@ -559,7 +560,7 @@ $ primal-page modify change-status [OPTIONS] SCHEMEINFO [SCHEMESTATUS]:[withdraw
 **Arguments**:
 
 * `SCHEMEINFO`: The path to info.json  [required]
-* `[SCHEMESTATUS]:[withdrawn|deprecated|autogenerated|draft|tested|validated]`: The scheme class  [default: SchemeStatus.DRAFT]
+* `[SCHEMESTATUS]:[withdrawn|deprecated|autogenerated|draft|tested|validated]`: The scheme class  [default: draft]
 
 **Options**:
 
@@ -677,5 +678,4 @@ $ primal-page remove [OPTIONS] SCHEMEINFO
 
 **Options**:
 
-* `--help`: Show this message and exit.
-
+* `--help`: Show this message and exit.

primal_page/__init__.py

@@ -1 +1 @@
-__version__ = "1.6.0"
+__version__ = "1.7.0"

primal_page/bedfiles.py

@@ -2,29 +2,98 @@
 import re
 from enum import Enum
 
+from primal_page.errors import InvalidBedFileLine, PrimerNameError, PrimerVersionError
+
 # Primername versions
 V2_PRIMERNAME = r"^[a-zA-Z0-9\-]+_[0-9]+_(LEFT|RIGHT)_[0-9]+$"
 V1_PRIMERNAME = r"^[a-zA-Z0-9\-]+_[0-9]+_(LEFT|RIGHT)(_ALT[0-9]*|_alt[0-9]*)*$"
 
+# Bedfile versions
+## This doesn't parse the contents just the structure
+BEDFILE_LINE = r"^\S+\t\d+\t\d+\t\S+\t\d+\t(\+|\-)\t[a-zA-Z]+$"
+
+
+# bedfile versions
+class BedfileVersion(Enum):
+    """
+    V1 bedfiles use a 6 col system
+    V2 bedfiles use a 7 col system and V1 primernames
+    V3 bedfiles use a 7 col system and V2 primernames
+    """
+
+    V1 = "v1.0"
+    V2 = "v2.0"
+    V3 = "v3.0"
+    INVALID = "invalid"  # Not applicable
+
+
+class BEDFileResult(Enum):
+    VALID = 0
+    INVALID_VERSION = 1
+    INVALID_STRUCTURE = 2
+
 
 class PrimerNameVersion(Enum):
     V1 = "v1"
     V2 = "v2"
     INVALID = "invalid"  # Not applicable
 
 
+class BedLine:
+    def __init__(
+        self,
+        chrom: str,
+        start: int,
+        end: int,
+        primername: str,
+        pool: int,
+        strand: str,
+        seq: str,
+    ):
+        self.chrom = chrom
+        self.start = start
+        self.end = end
+        self.primername = primername
+        self.pool = pool
+        self.strand = strand
+        self.seq = seq
+
+        # Validate the primername
+        if determine_primername_version(primername) == PrimerNameVersion.INVALID:
+            raise PrimerNameError(f"{primername}")
+
+        # Autogenerated fields
+        self.prefix = primername.split("_")[0]
+        self.amplicon_number = int(primername.split("_")[1])
+        self.pn_direction = primername.split("_")[2]
+        self.primernumber: int | None = None
+
+    def __str__(self):
+        return f"{self.chrom}\t{self.start}\t{self.end}\t{self.primername}\t{self.pool}\t{self.strand}\t{self.seq}"
+
+    def parsed_primername(self, primernumber: int) -> str:
+        return "_".join(
+            [
+                self.prefix,
+                str(self.amplicon_number),
+                self.pn_direction,
+                str(primernumber),
+            ]
+        )
+
+    def parsed_bedline(self) -> str:
+        return f"{self.chrom}\t{self.start}\t{self.end}\t{self.primername if self.primernumber is None else self.parsed_primername(self.primernumber)}\t{self.pool}\t{self.strand}\t{self.seq}"
+
+
 def determine_primername_version(primername: str) -> PrimerNameVersion:
     """
     Determines the version of the primer name.
 
-    Args:
-        primername (str): The primer name to check.
-
-    Returns:
-        PrimerNameVersion: The version of the primer name.
-
-    Raises:
-        None.
+    :param primername: The primer name to check.
+    :type primername: str
+    :return: The version of the primer name.
+    :rtype: PrimerNameVersion
+    :raises: None
     """
     if re.search(V2_PRIMERNAME, primername):
         return PrimerNameVersion.V2
@@ -34,11 +103,17 @@ def determine_primername_version(primername: str) -> PrimerNameVersion:
         return PrimerNameVersion.INVALID
 
 
-def convert_v1_primernames_to_v2(primername: str) -> str:
+def convert_v1_primernames_to_v2(primername: str, primernumber=1) -> str:
     """
-    Convert a v1 primername to a v2 primername. Cannot handle alt primers
-    :param primername: The v1 primername
-    :return: The v2 primername
+    Convert a v1 primername to a v2 primername. Cannot convert alt primers.
+
+    :param primername: The v1 primername to convert.
+    :type primername: str
+    :param primernumber: The primernumber to add to the primername.
+    :type primernumber: int
+    :return: The v2 primername.
+    :rtype: str
+    :raises: ValueError
     """
     # Check if this is a v1 primername
     if determine_primername_version(primername) != PrimerNameVersion.V1:
@@ -47,34 +122,21 @@ def convert_v1_primernames_to_v2(primername: str) -> str:
     # Split the primername
     data = primername.split("_")
     # Remove the alt
-    if data[-1] == "alt" or data[-1] == "ALT":
+    if "alt" in data[-1].lower():
         raise ValueError(f"{primername} is a v1 alt primername, cannot convert")
 
-    data.append("0")
-    # Join back together
+    # Add primernumber and return
+    data.append(str(primernumber))
     return "_".join(data)
 
 
-# Bedfile versions
-## This doesn't parse the contents just the structure
-BEDFILE_LINE = r"^\S+\t\d+\t\d+\t\S+\t\d+\t(\+|\-)\t[a-zA-Z]+$"
-
-
-class BEDFileResult(Enum):
-    VALID = 0
-    INVALID_VERSION = 1
-    INVALID_STRUCTURE = 2
-
-
 def validate_bedfile_line_structure(line: str) -> bool:
     """
-    This function validates the structure of a bedfile line, but not the contents.
-
-    Args:
-        line (str): The line to be validated.
-
-    Returns:
-        bool: True if the line structure is valid, False otherwise.
+    This function validates the structure of a bedfile line, but not the contents. Empty lines will error.
+    :param line: The line to validate.
+    :type line: str
+    :return: Whether the line is valid or not.
+    :rtype: bool
     """
     line = line.strip()
     if line.startswith("#"):
@@ -103,8 +165,13 @@ def validate_bedfile(bedfile: pathlib.Path) -> BEDFileResult:
 
     # Check each line
     for line in bedlines:
+        # Skip empty lines
+        if not line:
+            continue
         if not validate_bedfile_line_structure(line):
-            return BEDFileResult.INVALID_STRUCTURE
+            raise InvalidBedFileLine(
+                f"Invalid line in bedfile:\n{line}\nShould contain 7 columns separated by tabs."
+            )
 
     # Check the bedfile names.
     match determine_bedfile_version(bedfile):
@@ -114,25 +181,14 @@ def validate_bedfile(bedfile: pathlib.Path) -> BEDFileResult:
             return BEDFileResult.VALID
 
 
-# bedfile versions
-class BedfileVersion(Enum):
-    """
-    V1 bedfiles use a 6 col system
-    V2 bedfiles use a 7 col system and V1 primernames
-    V3 bedfiles use a 7 col system and V2 primernames
-    """
-
-    V1 = "v1.0"
-    V2 = "v2.0"
-    V3 = "v3.0"
-    INVALID = "invalid"  # Not applicable
-
-
 def determine_bedfile_version(input: list[list] | pathlib.Path) -> BedfileVersion:
     """
     Determine the bedfile version
     :param input: Either the bedfile lines as a list or the bedfile path
     :return: The bedfile version
+    :raises:
+        - PrimerNameError: If there are invalid primer names
+        - PrimerVersionError: If there is a mix of primernames
     """
     if isinstance(input, pathlib.Path):
         bedlines, _ = read_bed_file(input)
@@ -146,60 +202,30 @@ def determine_bedfile_version(input: list[list] | pathlib.Path) -> BedfileVersio
     # If 7 cols then v2 or v3
     # Check from primername
     primernames = [x[3] for x in bedlines]
-    primer_name_versions = {determine_primername_version(x) for x in primernames}
+    primer_name_versions_dict = {
+        x: determine_primername_version(x) for x in primernames
+    }
+    primer_name_versions = set(primer_name_versions_dict.values())
+
     if primer_name_versions == {PrimerNameVersion.V1}:
         return BedfileVersion.V2
     elif primer_name_versions == {PrimerNameVersion.V2}:
         return BedfileVersion.V3
-    # Invalid if we get here
-    # Mix of v1, v2 or invalid
-    return BedfileVersion.INVALID
-
-
-class BedLine:
-    def __init__(
-        self,
-        chrom: str,
-        start: int,
-        end: int,
-        primername: str,
-        pool: int,
-        strand: str,
-        seq: str,
-    ):
-        self.chrom = chrom
-        self.start = start
-        self.end = end
-        self.primername = primername
-        self.pool = pool
-        self.strand = strand
-        self.seq = seq
 
-        # Validate the primername
-        if determine_primername_version(primername) == PrimerNameVersion.INVALID:
-            raise ValueError(f"Invalid primername: {primername}")
+    if PrimerNameVersion.INVALID in primer_name_versions:
+        # Raise an error if there are invalid primer names
+        invalid_primer_names = {
+            pn
+            for pn, pv in primer_name_versions_dict.items()
+            if pv == PrimerNameVersion.INVALID
+        }
+        raise PrimerNameError(f"{invalid_primer_names}")
 
-        # Autogenerated fields
-        self.prefix = primername.split("_")[0]
-        self.amplicon_number = int(primername.split("_")[1])
-        self.pn_direction = primername.split("_")[2]
-        self.primernumber: int | None = None
-
-    def __str__(self):
-        return f"{self.chrom}\t{self.start}\t{self.end}\t{self.primername}\t{self.pool}\t{self.strand}\t{self.seq}"
-
-    def parsed_primername(self, primernumber: int) -> str:
-        return "_".join(
-            [
-                self.prefix,
-                str(self.amplicon_number),
-                self.pn_direction,
-                str(primernumber),
-            ]
-        )
+    if primer_name_versions == {PrimerNameVersion.V1, PrimerNameVersion.V2}:
+        raise PrimerVersionError("Mix of v1 and v2 primer names")
 
-    def parsed_bedline(self) -> str:
-        return f"{self.chrom}\t{self.start}\t{self.end}\t{self.primername if self.primernumber is None else self.parsed_primername(self.primernumber)}\t{self.pool}\t{self.strand}\t{self.seq}"
+    # This should not be reached
+    return BedfileVersion.INVALID
 
 
 def read_bedlines(bedfilepath: pathlib.Path) -> tuple[list[BedLine], list[str]]:
@@ -307,4 +333,4 @@ def regenerate_v3_bedfile(bedfile: pathlib.Path) -> str:
                 # Add the line to the bedfile
                 bedfile_str_list.append(line.parsed_bedline())
 
-    return "\n".join(bedfile_str_list)
+    return "\n".join(bedfile_str_list) + "\n"

primal_page/dev.py

@@ -1,9 +1,9 @@
-from Bio import SeqIO
 import hashlib
 import json
 import pathlib
 
 import typer
+from Bio import SeqIO
 from typing_extensions import Annotated
 
 from primal_page.bedfiles import (
@@ -53,7 +53,9 @@ def regenerate(
     # Hash the reference.fasta file
     # If the hash is different, rewrite the file
     ref_hash = hashfile(scheme_path / "reference.fasta")
-    ref_str = "".join((x.format("fasta") for x in SeqIO.parse(scheme_path / "reference.fasta", "fasta")))
+    ref_str = "".join(
+        x.format("fasta") for x in SeqIO.parse(scheme_path / "reference.fasta", "fasta")
+    )
     if ref_hash != hashlib.md5(ref_str.encode()).hexdigest():
         with open(scheme_path / "reference.fasta", "w") as ref_file:
             ref_file.write(ref_str)

primal_page/errors.py

@@ -0,0 +1,45 @@
+from click import UsageError
+
+
+class PrimerNameError(UsageError):
+    """Raised when a primername is invalid"""
+
+    def __init__(self, primername: str):
+        super().__init__(
+            f"Invalid primernames: {primername}. Please use format (name)_(amplicon-number)_(LEFT|RIGHT) with optional _(primer-number)"
+        )
+
+
+class PrimerVersionError(UsageError):
+    """Raised when a primername is unexpected"""
+
+    def __init__(self, message: str):
+        super().__init__(message)
+
+
+class InvalidBedFileLine(UsageError):
+    """Raised when a bedline is invalid"""
+
+    def __init__(self, message: str):
+        super().__init__(message)
+
+
+class SchemeExists(UsageError):
+    """Raised when a Scheme already exists"""
+
+    def __init__(self, message: str):
+        super().__init__(message)
+
+
+class FileNotFound(UsageError):
+    """Raised when a file is not found"""
+
+    def __init__(self, message: str):
+        super().__init__(message)
+
+
+class InvalidReference(UsageError):
+    """Raised when a file is not found"""
+
+    def __init__(self, message: str):
+        super().__init__(message)