Added tooling for working with the alias file

README.md

@@ -218,13 +218,71 @@ $ primal-page [OPTIONS] COMMAND [ARGS]...
 
 **Commands**:
 
+* `aliases`: Manage aliases
 * `build-index`: Build an index.json file from all schemes...
 * `create`: Create a new scheme in the required format
-* `dev`: Development commands
 * `download`: Download schemes from the index.json
 * `modify`: Modify an existing scheme's metadata...
 * `remove`: Remove a scheme's version from the repo,...
 
+## `primal-page aliases`
+
+Manage aliases
+
+**Usage**:
+
+```console
+$ primal-page aliases [OPTIONS] COMMAND [ARGS]...
+```
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+**Commands**:
+
+* `add`: Add an alias:schemeid to the alias file
+* `remove`: Remove an alias from the alias file
+
+### `primal-page aliases add`
+
+Add an alias:schemeid to the alias file
+
+**Usage**:
+
+```console
+$ primal-page aliases add [OPTIONS] ALIASES_FILE ALIAS SCHEMEID
+```
+
+**Arguments**:
+
+* `ALIASES_FILE`: The path to the alias file to write to  [required]
+* `ALIAS`: The alias to add  [required]
+* `SCHEMEID`: The schemeid to add the alias refers to. In the form of 'schemename/ampliconsize/schemeversion'  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
+### `primal-page aliases remove`
+
+Remove an alias from the alias file
+
+**Usage**:
+
+```console
+$ primal-page aliases remove [OPTIONS] ALIASES_FILE ALIAS
+```
+
+**Arguments**:
+
+* `ALIASES_FILE`: The path to the alias file to write to  [required]
+* `ALIAS`: The alias to add  [required]
+
+**Options**:
+
+* `--help`: Show this message and exit.
+
 ## `primal-page build-index`
 
 Build an index.json file from all schemes in the directory
@@ -284,7 +342,6 @@ $ primal-page create [OPTIONS] SCHEMEPATH
 * `--fix / --no-fix`: Attempt to fix the scheme  [default: no-fix]
 * `--help`: Show this message and exit.
 
-
 ## `primal-page download`
 
 Download schemes from the index.json
@@ -301,17 +358,17 @@ $ primal-page download [OPTIONS] COMMAND [ARGS]...
 
 **Commands**:
 
-* `download-all`: Download all schemes from the index.json
-* `download-scheme`: Download a scheme from the index.json
+* `all`: Download all schemes from the index.json
+* `scheme`: Download a scheme from the index.json
 
-### `primal-page download download-all`
+### `primal-page download all`
 
 Download all schemes from the index.json
 
 **Usage**:
 
 ```console
-$ primal-page download download-all [OPTIONS]
+$ primal-page download all [OPTIONS]
 ```
 
 **Options**:
@@ -320,14 +377,14 @@ $ primal-page download download-all [OPTIONS]
 * `--index-url TEXT`: The URL to the index.json  [default: https://raw.githubusercontent.com/quick-lab/primerschemes/main/index.json]
 * `--help`: Show this message and exit.
 
-### `primal-page download download-scheme`
+### `primal-page download scheme`
 
 Download a scheme from the index.json
 
 **Usage**:
 
 ```console
-$ primal-page download download-scheme [OPTIONS] SCHEMENAME AMPLICONSIZE SCHEMEVERSION
+$ primal-page download scheme [OPTIONS] SCHEMENAME AMPLICONSIZE SCHEMEVERSION
 ```
 
 **Arguments**:

primal_page/aliases.py

@@ -0,0 +1,113 @@
+import json
+import pathlib
+import re
+
+import typer
+from typing_extensions import Annotated
+
+from primal_page.schemas import validate_scheme_id
+
+app = typer.Typer(no_args_is_help=True)
+
+ALIASES_PATTERN = r"^[a-z0-9][a-z0-9-.]*[a-z0-9]$"
+
+
+def validate_alias(alias: str) -> str:
+    if not re.match(ALIASES_PATTERN, alias):
+        raise typer.BadParameter(
+            f"({alias}). Must only contain a-z, 0-9, and -. Cannot start or end with -"
+        )
+    return alias
+
+
+@app.command(no_args_is_help=True)
+def remove(
+    aliases_file: Annotated[
+        pathlib.Path,
+        typer.Argument(
+            help="The path to the alias file to write to",
+            exists=True,
+            file_okay=True,
+            writable=True,
+        ),
+    ],
+    alias: Annotated[
+        str,
+        typer.Argument(
+            help="The alias to add",
+            # No callback here because we don't want to validate removing the alias
+        ),
+    ],
+):
+    """
+    Remove an alias from the alias file
+    """
+    # Read in the info.json file
+    with open(aliases_file) as f:
+        aliases = json.load(f)
+
+    # Remove the alias, if it exists
+    aliases.pop(alias, None)
+
+    # Write the new info.json file
+    with open(aliases_file, "w") as f:
+        json.dump(aliases, f, indent=4, sort_keys=True)
+
+
+@app.command(no_args_is_help=True)
+def add(
+    aliases_file: Annotated[
+        pathlib.Path,
+        typer.Argument(
+            help="The path to the alias file to write to",
+            exists=True,
+            file_okay=True,
+            writable=True,
+        ),
+    ],
+    alias: Annotated[
+        str,
+        typer.Argument(
+            help="The alias to add",
+            callback=validate_alias,
+        ),
+    ],
+    schemeid: Annotated[
+        str,
+        typer.Argument(
+            help="The schemeid to add the alias refers to. In the form of 'schemename/ampliconsize/schemeversion'"
+        ),
+    ],
+):
+    """
+    Add an alias:schemeid to the alias file
+    """
+    # Parse the schemeid
+    schemename, ampliconsize, schemeversion = validate_scheme_id(schemeid)
+
+    # Read in the info.json file
+    with open(aliases_file) as f:
+        aliases = json.load(f)
+
+    # Check if the alias already exists
+    if alias in aliases:
+        raise typer.BadParameter(f"({alias}) already exists in the alias file")
+
+    # Add the alias
+    aliases[alias] = "/".join([schemename, ampliconsize, schemeversion])
+
+    # Write the new info.json file
+    with open(aliases_file, "w") as f:
+        json.dump(aliases, f, indent=4, sort_keys=True)
+
+
+def parse_alias(aliases_file: pathlib.Path, alias: str) -> str:
+    with open(aliases_file) as f:
+        aliases = json.load(f)
+    if alias not in aliases:
+        raise typer.BadParameter(f"({alias}) does not exist in the alias file")
+    return aliases[alias]
+
+
+if __name__ == "__main__":
+    app()

primal_page/errors.py

@@ -43,3 +43,31 @@ class InvalidReference(UsageError):
 
     def __init__(self, message: str):
         super().__init__(message)
+
+
+class InvalidSchemeID(UsageError):
+    """Raised when a schemeid is invalid"""
+
+    def __init__(self, message: str):
+        super().__init__(message)
+
+
+class InvalidSchemeName(UsageError):
+    """Raised when a schemename is invalid"""
+
+    def __init__(self, message: str):
+        super().__init__(message)
+
+
+class InvalidAmpliconSize(UsageError):
+    """Raised when a schemeversion is invalid"""
+
+    def __init__(self, message: str):
+        super().__init__(message)
+
+
+class InvalidSchemeVersion(UsageError):
+    """Raised when a schemeversion is invalid"""
+
+    def __init__(self, message: str):
+        super().__init__(message)

primal_page/main.py

@@ -9,6 +9,7 @@
 from typing_extensions import Annotated
 
 from primal_page.__init__ import __version__
+from primal_page.aliases import app as aliases_app
 from primal_page.bedfiles import (
     BEDFileResult,
     BedfileVersion,
@@ -50,6 +51,7 @@ class FindResult(Enum):
     help="Download schemes from the index.json",
 )
 app.add_typer(dev_app, name="dev", help="Development commands", hidden=True)
+app.add_typer(aliases_app, name="aliases", help="Manage aliases")
 
 
 def typer_callback_version(value: bool):

primal_page/schemas.py

@@ -6,6 +6,11 @@
 from pydantic.functional_validators import AfterValidator
 
 from primal_page.bedfiles import BedfileVersion
+from primal_page.errors import (
+    InvalidSchemeID,
+    InvalidSchemeName,
+    InvalidSchemeVersion,
+)
 
 INFO_SCHEMA = "v2.0.0"
 
@@ -27,17 +32,58 @@ class SchemeStatus(Enum):
     VALIDATED = "validated"
 
 
+def validate_scheme_id(schemeid) -> tuple[str, str, str]:
+    """
+    Parse the schemeid into its components
+    :raises InvalidSchemeID: if the schemeid is invalid
+    """
+    try:
+        (
+            schemename,
+            ampliconsize,
+            schemeversion,
+        ) = schemeid.split("/")
+    except ValueError as e:
+        raise InvalidSchemeID(
+            f"{schemeid} needs to be in the form (schemename)/(ampliconsize)/(schemeversion)"
+        ) from e
+
+    # Validate each part separately
+    try:
+        schemename = validate_schemename(schemename)
+        schemeversion = validate_schemeversion(schemeversion)
+        ampliconsize = int(ampliconsize)
+    except InvalidSchemeName as e:
+        raise InvalidSchemeID(
+            f"{schemename} is an invalid schemename in {schemeid}"
+        ) from e
+    except InvalidSchemeVersion as e:
+        raise InvalidSchemeID(
+            f"{schemeversion} is an invalid schemeversion in {schemeid}"
+        ) from e
+    except ValueError as e:
+        raise InvalidSchemeID(
+            f"{ampliconsize} is an invalid ampliconsize in {schemeid}"
+        ) from e
+
+    return schemename, str(ampliconsize), schemeversion
+
+
 def validate_schemeversion(version: str) -> str:
     if not re.match(VERSION_PATTERN, version):
-        raise ValueError(
+        raise InvalidSchemeVersion(
             f"Invalid version: {version}. Must match be in form of v(int).(int).(int)"
         )
     return version
 
 
 def validate_schemename(schemename: str) -> str:
+    """
+    Validate the schemename
+    :raises InvalidSchemeName: if the schemename is invalid
+    """
     if not re.match(SCHEMENAME_PATTERN, schemename):
-        raise ValueError(
+        raise InvalidSchemeName(
             f"Invalid schemename: {schemename}. Must only contain a-z, 0-9, and -. Cannot start or end with -"
         )
     return schemename