Added updated for PH2 and PAD datasets.

setup.py

@@ -55,7 +55,11 @@
     "packaging",
     "pandas",
     "PyYAML",
-    "tabulate"
+    "tabulate",
+    "alive-progress",
+    "requests",
+    "patool",
+    "fuzzywuzzy"
 ]
 
 CWD = os.path.abspath(os.path.dirname(__file__))

sla_cli/__init__.py

@@ -3,4 +3,4 @@
 Date:       08 April 2021
 """
 
-__version__ = '0.2.1'
+__version__ = '0.2.2'

sla_cli/entry.py

@@ -85,4 +85,4 @@ def cli(ctx: Context, params: CliParameters):
     cli.add_command(command)
 
 if __name__ == '__main__':
-    cli()
+    cli(prog_name="sla-cli")

sla_cli/src/cli/commands/download.py

@@ -46,6 +46,30 @@ class DownloadParameters:
 @kwargs_to_dataclass(DownloadParameters)
 @click.pass_context
 def download(ctx: Context, params: DownloadParameters):
+    """Download
+
+    Responsible for downloading datasets from various endpoints using the dataset name as
+    a key.
+
+    \b
+    Command flow:
+        1) Dataset archives are downloaded from a data repository endpoint specific to a given dataset.
+        2) Once downloaded, archives are extracted and the contents are moved to the 'data' directory specified.
+        3) A custom wrapper, specific to the given dataset, is used to restructure and format the dataset content into a uniform layout.
+
+    \b
+    Available datasets:
+        bcn_20000 | bcn_2020_challenge | brisbane_isic_challenge_2020 | dermoscopedia_cc_by ham10000
+        isic_2020_challenge_mskcc_contribution | isic_2020_vienna_part_1 | isic_2020_vienna_part_2
+        jid_editorial_images_2018 | mclass_d | mclass_nd | mednode | msk_1 | msk_2 | msk_3 | msk_4
+        msk_5 | pad_ufes_20 | ph2 | sonic | sydney_mia_smdc_2020_isic_challenge_contribution
+        uda_1 | uda_2
+
+    \b
+    Example:
+        $ sla-cli download -d ./data/ mednode ph2 uda_1
+
+    """
     datasets = AccessorFactory.create_datasets()
 
     # Remove datasets that dont exist in the tool before continuing.

sla_cli/src/common/console.py

@@ -33,7 +33,8 @@ def init_progress_bars_wrapper(*args, **kwargs):
             title_length=40,
             spinner="classic",
             unknown="classic",
-            bar="classic"
+            bar="classic",
+            enrich_print=False
         )
 
         return func(*args, **kwargs)

sla_cli/src/download/pad_ufes_20/download.py

@@ -38,9 +38,6 @@ def _extract(self):
             with ZipFile(archive, "r") as fh:
                 fh.extractall(images_dir)
 
-            # Remove archive after extraction.
-            os.remove(archive)
-
     def _format_metadata(self):
         pass
 
@@ -73,4 +70,4 @@ def _move_images(self):
     def _clean_up(self):
         """Clean up any stray files."""
         for i in range(1, 4):
-            os.remove(os.path.join(self.images_path, f"imgs_part_{i}"))
+            shutil.rmtree(os.path.join(self.images_path, f"imgs_part_{i}"))

sla_cli/src/download/ph2/download.py

@@ -31,6 +31,8 @@ def _download(self):
     def _extract(self):
         """Extracts the downloaded archive."""
         try:
+            if not os.path.exists(self.extracted_path):
+                os.makedirs(self.extracted_path)
             patoolib.extract_archive(self.archive_path, outdir=self.extracted_path, verbosity=-1)
         except Exception as err:
             logger.error(f"You may have to install a 3rd-party application to unpack '.rar' files.")