Improve the implement of the spec.

README.md

@@ -21,9 +21,20 @@ python setup.py install
 ### Usage
 
 ```bash
-Usage: metadata_validator [OPTIONS]
+Usage: metav [OPTIONS] COMMAND [ARGS]...
 
-  Console script for metadata_validator.
+Options:
+  --help  Show this message and exit.
+
+Commands:
+  generate-template  Generate metadata template as a xlsx file.
+  validate           Metadata Validator
+```
+
+```bash
+Usage: metav validate [OPTIONS]
+
+  Metadata Validator
 
 Options:
   -i, --input FILE                Input file path, only support xlsx file.
@@ -37,22 +48,50 @@ Options:
   --help                          Show this message and exit.
 ```
 
+```bash
+Usage: metav generate-template [OPTIONS]
+
+  Generate metadata template as a xlsx file.
+
+Options:
+  -o, --output TEXT               Output metadata template as a file.
+                                  [required]
+  -t, --template-type [DNAseq|RNAseq|Proteomics|Metabolomics]
+                                  It support the following metadata tables:
+                                  'DNAseq', 'RNAseq', 'Proteomics,
+                                  'Metabolomics'  [required]
+  --help                          Show this message and exit.
+```
+
 ### Example
 
-Validate your metadata file of DNAseq template with the following command:
+#### Generate metadata template
 
 ```bash
-metadata_validator -i your_metadata_file.xlsx -o output.log -t DNAseq
+metav generate-template -t Metabolomics -o metabolomics_metadata.xlsx
+```
+
+![metabolomics_metadata](./assets/metabolomics-metadata-table.png)
+
+#### Validate metadata
+
+Validate your metadata file of Metabolomics template with the following command:
+
+```bash
+metav validate -i your_metadata_file.xlsx -o output.log -t Metabolomics
 ```
 
 ### Metada
 
 * Free software: MIT license
 * Documentation: https://metadata-validator.readthedocs.io.
 
-
 ### Features
 
+- Generate metadata template as a xlsx file.
+
+- Validate metadata file.
+
 ### TODO
 
 ### Credits

metadata_validator/cli.py

@@ -2,21 +2,42 @@
 import os
 import sys
 import click
+
 from metadata_validator.validator import DNAseqMetadataValidator
+from metadata_validator.specs import spec_dict
 
 validator_dict = {
     "DNAseq": DNAseqMetadataValidator,
     "RNAseq": None,
     "Proteomics": None,
-    "Metabolomics": None
+    "Metabolomics": None,
 }
 
-@click.command("Metadata Validator")
-@click.option("--input", "-i", required=True, type=click.Path(exists=True, file_okay=True, dir_okay=False),
-              help="Input file path, only support xlsx file.")
-@click.option("--output", "-o", required=True, help="Output error and warning messages as a file.")
-@click.option("--template-type", "-t", required=True, help="It support the following metadata tables: 'DNAseq', 'RNAseq', 'Proteomics, 'Metabolomics'", type=click.Choice(['DNAseq', 'RNAseq', 'Proteomics', 'Metabolomics']))
-def main(input, output, template_type):
+
+@click.group()
+def cli():
+    pass
+
+
+@cli.command(help="Metadata Validator")
+@click.option(
+    "--input",
+    "-i",
+    required=True,
+    type=click.Path(exists=True, file_okay=True, dir_okay=False),
+    help="Input file path, only support xlsx file.",
+)
+@click.option(
+    "--output", "-o", required=True, help="Output error and warning messages as a file."
+)
+@click.option(
+    "--template-type",
+    "-t",
+    required=True,
+    help="It support the following metadata tables: 'DNAseq', 'RNAseq', 'Proteomics, 'Metabolomics'",
+    type=click.Choice(["DNAseq", "RNAseq", "Proteomics", "Metabolomics"]),
+)
+def validate(input, output, template_type):
     """Console script for metadata_validator."""
     if template_type in validator_dict.keys():
         validator = validator_dict[template_type](input)
@@ -25,18 +46,44 @@ def main(input, output, template_type):
         error_msg = validator.errors
         warning_msg = validator.warnings
 
-        if os.path.exists(output):
-            raise FileExistsError("The output file already exists.")
+        if output:
+            if os.path.exists(output):
+                raise FileExistsError("The output file already exists.")
+            else:
+                with open(output, "w") as f:
+                    f.write(error_msg)
+                    f.write("\n")
+                    f.write(warning_msg)
         else:
-            with open(output, "w") as f:
-                f.write(error_msg)
-                f.write("\n")
-                f.write(warning_msg)
+            print(error_msg)
+            print("\n")
+            print(warning_msg)
+    else:
+        click.echo("The template type is not supported.")
+
+    return 0
+
+
+@cli.command(help="Generate metadata template as a xlsx file.")
+@click.option(
+    "--output", "-o", required=True, help="Output metadata template as a file."
+)
+@click.option(
+    "--template-type",
+    "-t",
+    required=True,
+    help="It support the following metadata tables: 'DNAseq', 'RNAseq', 'Proteomics, 'Metabolomics'",
+    type=click.Choice(["DNAseq", "RNAseq", "Proteomics", "Metabolomics"]),
+)
+def generate_template(output, template_type):
+    if template_type in spec_dict.keys():
+        template = spec_dict[template_type]()
+        template.generate_template(output)
     else:
         click.echo("The template type is not supported.")
 
     return 0
 
 
 if __name__ == "__main__":
-    sys.exit(main())  # pragma: no cover
+    sys.exit(cli())  # pragma: no cover

metadata_validator/specs/__init__.py

@@ -0,0 +1,20 @@
+from .dnaseq_spec import DNAseqSpec
+from .rnaseq_spec import RNAseqSpec
+from .metabolomics_spec import MetabolomicsSpec
+
+from .spec import ExpectedColumnItem
+
+spec_dict = {
+    "DNAseq": DNAseqSpec,
+    "RNAseq": RNAseqSpec,
+    "Metabolomics": MetabolomicsSpec,
+}
+
+
+__all__ = [
+    "DNAseqSpec",
+    "RNAseqSpec",
+    "MetabolomicsSpec",
+    "ExpectedColumnItem",
+    "spec_dict",
+]