Version v1.0.0

README.md

@@ -27,3 +27,12 @@ This is the tooling for working with the primerschemes index
 
 The main purpose of info.json is to store vital metadata, which is parsed into the repo-manifest. 
 
+### Create 
+
+The create command has two main modes of use. 
+- Where the scheme directory is provided, and used to parse; --primerbed, --reference, --configpath, --algorithmversion.
+- The options are provided via the CLI
+
+If a field cannot be parsed via the scheme directory, it will require it to be spesified via the CLI.
+- CLI args always override the parsed args.
+

primal_page/build_index.py

@@ -56,7 +56,7 @@ def parse_version(
         repo_url, scheme_name, length, version.name, "info.json", pclass
     )
 
-    # Check the hashes in the config.json file match the generated hashes
+    # Check the hashes in the info.json file match the generated hashes
     if version_dict["primer_bed_md5"] != info_dict["primer_bed_md5"]:
         raise ValueError(
             f"Hash mismatch for {version_dict['primer_bed_md5']}. Expected {version_dict['primer_bed_md5']} but got {info_dict['primer_bed_md5']}"
@@ -165,15 +165,33 @@ def check_consistency(existing_json, new_json):
             )
 
 
-def create_index(server_url, repo_url):
+import json
+import pathlib
+
+
+def create_index(server_url, repo_url, parent_dir=pathlib.Path(".")):
+    """
+    Create an index JSON file for the given server and repository URLs.
+
+    Args:
+        server_url (str): The URL of the server.
+        repo_url (str): The URL of the repository.
+        parent_dir (str, optional): The parent directory path containing the primerscheme dir. index.json will be writem to parent_dir/index.json Defaults to ".".
+
+    Returns:
+        bool: True if the index JSON file is created successfully, False otherwise.
+    """
     # For any Scheme, we can generate a JSON file with the following format:
     json_dict = dict()
+    # Ensure the parent_dir is a pathlib.Path
+    if type(parent_dir) == str:
+        parent_dir = pathlib.Path(parent_dir)
     # Parse panels and schemes
     pclasses = ["primerschemes"]
     for pclass in pclasses:
         # Create a dict to hold all the pclass data
         pclass_dict = dict()
-        for path in pathlib.Path(pclass).iterdir():
+        for path in (parent_dir / pclass).iterdir():
             # Only add directories
             if not path.is_dir() or path.name.startswith("."):
                 continue
@@ -188,7 +206,6 @@ def create_index(server_url, repo_url):
     # Read in the existing index.json file
     with open("index.json") as f:
         existing_json_dict = json.load(f)
-
     # Check persistence of existing files
     check_consistency(existing_json_dict, json_dict)
 
@@ -201,4 +218,5 @@ def create_index(server_url, repo_url):
 if __name__ == "__main__":
     server_url = sys.argv[1]
     repo_url = sys.argv[2]
+
     create_index(server_url, repo_url)

primal_page/main.py

@@ -4,13 +4,18 @@
 import shutil
 import hashlib
 import json
-import github
-import os
+from typing import Optional
+import re
+
 from primal_page.build_index import create_index
-from primal_page.schemas import PrimerClass, SchemeStatus, Info
+from primal_page.schemas import (
+    PrimerClass,
+    SchemeStatus,
+    Info,
+    determine_primername_version,
+    PrimerNameVersion,
+)
 
-SCHEMENAME_PATTERN = r"^[a-z0-9][a-z0-9-]*[a-z0-9]$"
-VERSION_PATTERN = r"^v\d+\.\d+\.\d+$"
 
 # Create the typer app
 app = typer.Typer()
@@ -60,7 +65,7 @@ def hashfile(fname: pathlib.Path) -> str:
     return hash_md5.hexdigest()
 
 
-def validate_primer_bed(primer_bed: pathlib.Path, fix: bool = False):
+def validate_primer_bed(primer_bed: pathlib.Path, fix: bool = False) -> bool:
     """Validate a primer bed file"""
     with open(primer_bed, "r") as f:
         for lineindex, line in enumerate(f.readlines()):
@@ -73,14 +78,20 @@ def validate_primer_bed(primer_bed: pathlib.Path, fix: bool = False):
                 )
 
             # Check for valid primername
-            primername = data[3].split("_")
-            if len(primername) == 4 and primername[-1].isdigit():
-                # Valid name
-                pass
-            else:
-                raise ValueError(
-                    f"Line {lineindex} in {primer_bed} does not have a valid primername '{data[3]}'"
-                )
+            raw_primername = data[3].strip()
+
+            match determine_primername_version(raw_primername):
+                case PrimerNameVersion.V1:
+                    # Valid name
+                    pass
+                case PrimerNameVersion.V2:
+                    # Valid version 2 name
+                    pass
+                case PrimerNameVersion.INVALID:
+                    raise ValueError(
+                        f"Line {lineindex} in {primer_bed} does not have a valid primername '{raw_primername}'"
+                    )
+
     return True
 
 
@@ -219,14 +230,14 @@ def create(
         "artic network",
     ],
     primerbed: Annotated[
-        pathlib.Path,
+        Optional[pathlib.Path],
         typer.Option(
             help="Manually specify the primer bed file, default is *primer.bed",
             readable=True,
         ),
     ] = None,
     reference: Annotated[
-        pathlib.Path,
+        Optional[pathlib.Path],
         typer.Option(
             help="Manually specify the referance.fasta file, default is *.fasta",
             readable=True,
@@ -237,19 +248,20 @@ def create(
         typer.Option(help="Where to output the scheme", writable=True),
     ] = pathlib.Path("primerschemes"),
     configpath: Annotated[
-        pathlib.Path,
+        Optional[pathlib.Path],
         typer.Option(
             help="Where the config.json file is located", readable=True, exists=True
         ),
     ] = None,
     algorithmversion: Annotated[
-        str, typer.Option(help="The version of primalscheme or other")
+        Optional[str], typer.Option(help="The version of primalscheme or other")
     ] = None,
     description: Annotated[
-        str, typer.Option(help="A description of the scheme")
+        Optional[str], typer.Option(help="A description of the scheme")
     ] = None,
     derivedfrom: Annotated[
-        str, typer.Option(help="Which scheme has this scheme been derived from")
+        Optional[str],
+        typer.Option(help="Which scheme has this scheme been derived from"),
     ] = None,
     primerclass: Annotated[
         PrimerClass, typer.Option(help="The primer class")
@@ -555,16 +567,19 @@ def remove_citation(
 def build_index(
     gitaccount: Annotated[
         str,
-        typer.Argument(help="The name of the github account"),
+        typer.Option(help="The name of the github account"),
     ] = "quick-lab",
     gitserver: Annotated[
         str,
-        typer.Argument(help="The name of the github server"),
+        typer.Option(help="The name of the github server"),
     ] = "https://github.com/",
+    parentdir: Annotated[
+        pathlib.Path, typer.Option(help="The parent directory")
+    ] = pathlib.Path("."),
 ):
     """Build an index.json file from all schemes in the directory"""
 
-    create_index(gitserver, gitaccount)
+    create_index(gitserver, gitaccount, parentdir)
 
 
 @app.command()

primal_page/schemas.py

@@ -7,6 +7,51 @@
 SCHEMENAME_PATTERN = r"^[a-z0-9][a-z0-9-]*[a-z0-9]$"
 VERSION_PATTERN = r"^v\d+\.\d+\.\d+$"
 
+# Primername versions
+V2_PRIMERNAME = r"^[a-zA-Z0-9\-]+_[0-9]+_(LEFT|RIGHT)_[0-9]+$"
+V1_PRIMERNAME = r"^[a-zA-Z0-9\-]+_[0-9]+_(LEFT|RIGHT)(_ALT|_alt)*$"
+
+
+class PrimerNameVersion(Enum):
+    V1 = "v1"
+    V2 = "v2"
+    INVALID = "invalid"  # Not applicable
+
+
+def determine_primername_version(primername: str) -> PrimerNameVersion:
+    """
+    Determine the primername version
+    :param primername: The primername to check
+    :return: The primername version
+    """
+    if re.search(V2_PRIMERNAME, primername):
+        return PrimerNameVersion.V2
+    elif re.search(V1_PRIMERNAME, primername):
+        return PrimerNameVersion.V1
+    else:
+        return PrimerNameVersion.INVALID
+
+
+def convert_v1_primernames_to_v2(primername: str) -> str:
+    """
+    Convert a v1 primername to a v2 primername. Cannot handle alt primers
+    :param primername: The v1 primername
+    :return: The v2 primername
+    """
+    # Check if this is a v1 primername
+    if determine_primername_version(primername) != PrimerNameVersion.V1:
+        raise ValueError(f"{primername} is not a valid v1 primername")
+
+    # Split the primername
+    data = primername.split("_")
+    # Remove the alt
+    if data[-1] == "alt" or data[-1] == "ALT":
+        raise ValueError(f"{primername} is a v1 alt primername, cannot convert")
+
+    data.append("0")
+    # Join back together
+    return "_".join(data)
+
 
 class PrimerClass(Enum):
     PRIMERSCHEMES = "primerschemes"

pyproject.toml

@@ -15,6 +15,7 @@ typer = {extras = ["all"], version = "^0.9.0"}
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.3"
+typer-cli = {path = "../typer-cli"} # https://github.com/Patarimi/typer-cli/commit/f44b547a0b9ea71e5c7b2dc7d4c1ab1212394e5e
 
 [build-system]
 requires = ["poetry-core"]