feat: add convert-to-zenodo in cli

Untested

_data/python-pfhub/pfhub/scripts/cli.py

@@ -8,14 +8,123 @@
 from toolz.curried import pipe, get
 from toolz.curried import map as map_
 
-from ..convert import download_zenodo, download_meta
+from ..convert import meta_to_zenodo, download_file
+from ..convert import download_zenodo as download_zenodo_
+from ..convert import download_meta as download_meta_
 from ..func import compact
 
+import tempfile
+import pykwalify
+import pykwalify.core
+import shutil
+
 
 EPILOG = "See the documentation at \
 https://github.com/usnistgov/pfhub/blob/master/CLI.md (under construction)"
 
 
+
+@click.group(epilog=EPILOG)
+def cli():
+    """Submit results to PFHub and manipulate PFHub data"""
+
+
+
+def output(local_filepaths):
+    def echo(local_filepath, newline, comma=","):
+        formatted_path = click.format_filename(local_filepath)
+        click.secho(message=f" {formatted_path}" + comma, fg="green", nl=newline)
+
+    click.secho(message="Writing:", fg="green", nl=False)
+    for local_filepath in local_filepaths[:-1]:
+        echo(local_filepath, False)
+    echo(local_filepaths[-1], True, comma="")
+
+
+@cli.command(epilog=EPILOG)
+@click.argument("url", type=click_params.URL)
+@click.option(
+    "--dest",
+    "-d",
+    help="destination directory",
+    default="./",
+    type=click.Path(exists=True),
+)
+def download_zenodo(url, dest):
+    """Download a Zenodo record
+
+    Works with any Zenodo link
+
+    Args:
+      url: the URL of either a meta.yaml or Zenodo record
+      dest: the destination directory
+    """
+    record_id = get_zenodo_record_id(url, zenodo_regexs())
+    sandbox = False
+    if record_id is None:
+        record_id = get_zenodo_record_id(url, zenodo_sandbox_regexs())
+        sandbox = True
+
+    if record_id is not None:
+        local_filepaths = download_zenodo_(record_id, sandbox=sandbox, dest=dest)
+        output(local_filepaths)
+    else:
+        click.secho(f"{url} does not match any expected regex for Zenodo", fg="red")
+
+
+@cli.command(epilog=EPILOG)
+@click.argument("url", type=click_params.URL)
+@click.option(
+    "--dest",
+    "-d",
+    help="destination directory",
+    default="./",
+    type=click.Path(exists=True),
+)
+def download_meta(url, dest):
+    """Download a record from pfhub
+
+    Download a meta.yaml from any URL
+
+    Args:
+      url: the URL of either a meta.yaml or Zenodo record
+      dest: the destination directory
+    """
+
+    is_meta = check_meta_url(url)
+    if is_meta:
+        local_filepaths = download_meta_(url, dest=dest)
+        output(local_filepaths)
+    else:
+        click.secho(f"{url} is not a valid PFHub meta.yaml", fg="red")
+
+
+@cli.command(epilog=EPILOG)
+@click.argument("file_path", type=click.Path(exists=True))
+@click.option(
+    "--dest",
+    "-d",
+    help="destination directory",
+    default="./",
+    type=click.Path(exists=False),
+)
+def convert_to_zenodo(file_path, dest):
+    """Convert a meta.yaml into a format suitable for Zenodo submission
+
+    Args:
+      file_path: the URL of the meta.yaml
+      dest: the destination directory
+
+    """
+    is_meta = check_meta(file_path)
+    if is_meta:
+        local_filepaths = [meta_to_zenodo(file_path)]
+        output(local_filepaths)
+    else:
+        click.secho(f"{file_path} is not a valid PFHub meta.yaml", fg="red")
+
+
+
 def zenodo_regexs():
     """Regular expression for acceptable Zenodo URLs"""
     return [
@@ -53,50 +162,29 @@ def get_zenodo_record_id(url, regexs):
     )
 
 
-@click.group(epilog=EPILOG)
-def cli():
-    """Submit results to PFHub and manipulate PFHub data"""
-
-
-@cli.command(epilog=EPILOG)
-@click.argument("url", type=click_params.URL)
-@click.option(
-    "--dest",
-    "-d",
-    help="destination directory",
-    default="./",
-    type=click.Path(exists=True),
-)
-def download(url, dest):
-    """Download a PFHub record
-
-    Download an old meta.yaml or a new PFHub record stored on Zenodo.
-
-    Args:
-      url: the URL of either a meta.yaml or Zenodo record
+def check_meta_url(url):
+    """Check that a file is a valid meta.yaml
     """
-
-    def output(local_filepaths):
-        def echo(local_filepath, newline, comma=","):
-            formatted_path = click.format_filename(local_filepath)
-            click.secho(message=f" {formatted_path}" + comma, fg="green", nl=newline)
-
-        click.secho(message="Writing:", fg="green", nl=False)
-        for local_filepath in local_filepaths[:-1]:
-            echo(local_filepath, False)
-        echo(local_filepaths[-1], True, comma="")
-
-    record_id = get_zenodo_record_id(url, zenodo_regexs())
-    sandbox = False
-    if record_id is None:
-        record_id = get_zenodo_record_id(url, zenodo_sandbox_regexs())
-        sandbox = True
-
-    if record_id is not None:
-        local_filepaths = download_zenodo(record_id, sandbox=sandbox, dest=dest)
-        output(local_filepaths)
-    elif re.fullmatch(r".*/meta.yaml", url):
-        local_filepaths = download_meta(url, dest=dest)
-        output(local_filepaths)
-    else:
-        click.secho(f"{url} does not match any expected regex", fg="red")
+    tmpdir = tempfile.mkdtemp()
+    file_path = download_file(url, dest=tmpdir)
+    result = check_meta(file_path)
+    shutil.rmtree(tmpdir)
+    return result
+
+
+def check_meta(path):
+    try:
+        c = pykwalify.core.Core(source_file=path, schema_files=["schema.yaml"])
+    except pykwalify.errors.CoreError:
+        return False
+    try:
+        c.validate(raise_exception=True)
+    except pykwalify.errors.SchemaError:
+        return False
+    return True
+
+
+def check_linkml(path):
+    """Check that a file has a valid linkml pfhub schema
+    """
+    pass