Add --embedded-mode param to parse (#278)

* bump version

* added param

* linted

setup.cfg

@@ -3,7 +3,7 @@
 ##########################
 [metadata]
 name = sssom
-version = 0.3.12.dev
+version = 0.3.12
 description = Operations on SSSOM mapping tables
 long_description = file: README.md
 long_description_content_type = text/markdown

sssom/cli.py

@@ -157,6 +157,15 @@ def convert(input: str, output: TextIO, output_format: str):
     required=True,
     help="If True (default), records with unknown prefixes are removed from the SSSOM file.",
 )
+@click.option(
+    "-E",
+    "--embedded-mode",
+    default=True,
+    is_flag=True,
+    help="If False, the resultant SSSOM file will be saved\
+        in the 'filename'.tsv provided by -o/--output option\
+        AND the metadata gets saved in the 'filename'.yml.",
+)
 @predicate_filter_option
 @output_option
 def parse(
@@ -166,17 +175,18 @@ def parse(
     prefix_map_mode: str,
     clean_prefixes: bool,
     output: TextIO,
+    embedded_mode: bool,
     mapping_predicate_filter: Optional[tuple],
 ):
     """Parse a file in one of the supported formats (such as obographs) into an SSSOM TSV file."""
-    # TODO: add "--embedded-mode" - boolean
     parse_file(
         input_path=input,
         output=output,
         input_format=input_format,
         metadata_path=metadata,
         prefix_map_mode=prefix_map_mode,
         clean_prefixes=clean_prefixes,
+        embedded_mode=embedded_mode,
         mapping_predicate_filter=mapping_predicate_filter,
     )
 

sssom/io.py

@@ -59,6 +59,7 @@ def parse_file(
     metadata_path: Optional[str] = None,
     prefix_map_mode: Optional[str] = None,
     clean_prefixes: bool = True,
+    embedded_mode: bool = True,
     mapping_predicate_filter: tuple = None,
 ) -> None:
     """Parse an SSSOM metadata file and write to a table.
@@ -71,6 +72,7 @@ def parse_file(
     :param prefix_map_mode: Defines whether the prefix map in the metadata should be extended or replaced with
         the SSSOM default prefix map. Must be one of metadata_only, sssom_default_only, merged
     :param clean_prefixes: If True (default), records with unknown prefixes are removed from the SSSOM file.
+    :param embedded_mode:If True (default), the dataframe and metadata are exported in one file (tsv), else two separate files (tsv and yaml).
     :param mapping_predicate_filter: Optional list of mapping predicates or filepath containing the same.
     """
     raise_for_bad_path(input_path)
@@ -101,8 +103,7 @@ def parse_file(
     if clean_prefixes:
         # We do this because we got a lot of prefixes from the default SSSOM prefixes!
         doc.clean_prefix_map()
-    write_table(doc, output)
-    # TODO: add "--embedded-mode" - boolean to write_table which is optional.
+    write_table(doc, output, embedded_mode)
 
 
 def validate_file(

sssom/writers.py

@@ -46,9 +46,13 @@
 MSDFWriter = Callable[[MappingSetDataFrame, TextIO], None]
 
 
-def write_table(msdf: MappingSetDataFrame, file: TextIO, serialisation="tsv") -> None:
+def write_table(
+    msdf: MappingSetDataFrame,
+    file: TextIO,
+    embedded_mode: bool = True,
+    serialisation="tsv",
+) -> None:
     """Write a mapping set dataframe to the file as a table."""
-    # TODO: based on "--embedded-mode" parameter save file a certain way.
     if msdf.df is None:
         raise TypeError
 
@@ -65,9 +69,18 @@ def write_table(msdf: MappingSetDataFrame, file: TextIO, serialisation="tsv") ->
     lines = yaml.safe_dump(meta).split("\n")
     lines = [f"# {line}" for line in lines if line != ""]
     s = msdf.df.to_csv(sep=sep, index=False)
-    lines = lines + [s]
-    for line in lines:
-        print(line, file=file)
+
+    if embedded_mode:
+        lines = lines + [s]
+        for line in lines:
+            print(line, file=file)
+    else:
+        # Export MSDF as tsv
+        msdf.df.to_csv(file, sep=sep, index=False)
+        # Export Metadata as yaml
+        yml_filepath = file.name.replace("tsv", "yaml")
+        with open(yml_filepath, "w") as y:
+            yaml.safe_dump(meta, y)
 
 
 def write_rdf(