Fix/use

.gitignore

@@ -179,3 +179,4 @@ venv/
 
 # output logging file for content 
 output.log
+.g3t

README.md

@@ -22,8 +22,8 @@ git clone repo
 cd fhirizer
 # create virtual env ex. 
 # NOTE: package_data folders must be in python path in virtual envs 
-python -m venv venv-fhirizer
-source venv-fhirizer/bin/activate
+python -m venv venv
+source venv/bin/activate
 pip install . 
 ```
 
@@ -128,6 +128,26 @@ fhirizer case_init
 fhirizer file_init 
 ```
 
+### FHIR data validation 
+
+#### disable gen3-client
+```
+mv ~/.gen3/gen3_client_config.ini ~/.gen3/gen3_client_config.ini-xxx
+mv ~/.gen3/gen3-client ~/.gen3/gen3-client-xxx
+```
+
+#### Run validate
+```
+fhirizer validate --path <path_to_META_folder_with_fhir_ndjson_files>
+```
+
+#### Restore gen3-client
+
+```
+mv ~/.gen3/gen3-client-xxx ~/.gen3/gen3-client
+mv ~/.gen3/gen3_client_config.ini-xxx ~/.gen3/gen3_client_config.ini
+
+```
 
 ### Testing 
 ```

fhirizer/__init__.py

@@ -0,0 +1,4 @@
+from fhirizer.patcher import apply_patches
+
+apply_patches()
+

fhirizer/cli.py

@@ -1,6 +1,16 @@
+import sys
+import os
+import json
+from gen3_tracker.common import ERROR_COLOR, INFO_COLOR
 from fhirizer import utils, mapping, entity2fhir, icgc2fhir, htan2fhir
 import click
 from pathlib import Path
+import importlib.resources
+import warnings
+from halo import Halo
+
+
+warnings.filterwarnings("ignore", category=SyntaxWarning)
 
 
 class NotRequiredIf(click.Option):
@@ -159,33 +169,87 @@ def convert(name, in_path, out_path, verbose):
 @click.option('--convert', is_flag=True, help='Boolean indicating to write converted keys to directory')
 @click.option('--verbose', is_flag=True)
 def generate(name, out_dir, entity_path, icgc, has_files, atlas, convert, verbose):
-    name_list = ['project', 'case', 'file', 'cellosaurus', 'icgc', 'htan']
+    name_list = ['case', 'file', 'cellosaurus', 'icgc', 'htan']
     assert name in name_list, f'--name is not in {name_list}.'
     if name != 'htan':
         assert Path(out_dir).is_dir(), f"Path {out_dir} is not a valid directory path."
         assert Path(entity_path).is_file(), f"Path {entity_path} is not a valid file path."
     else:
         assert Path("./projects/HTAN").is_dir()
 
-    if name in 'project':
-        entity2fhir.project_gdc_to_fhir_ndjson(out_dir=out_dir, projects_path=entity_path, convert=convert, verbose=verbose)
+    spinner = Halo(text="🔥 Transforming data", spinner='dots', placement='right', color='white')
+
     if name in 'case':
-        entity2fhir.case_gdc_to_fhir_ndjson(out_dir=out_dir, name=name, cases_path=entity_path, convert=convert, verbose=verbose)
+        spinner.start()
+        entity2fhir.case_gdc_to_fhir_ndjson(out_dir=out_dir, name=name, cases_path=entity_path, convert=convert, verbose=verbose, spinner=spinner)
     if name in 'file':
-        entity2fhir.file_gdc_to_fhir_ndjson(out_dir=out_dir, name=name, files_path=entity_path, convert=convert, verbose=verbose)
+        spinner.start()
+        entity2fhir.file_gdc_to_fhir_ndjson(out_dir=out_dir, name=name, files_path=entity_path, convert=convert, verbose=verbose, spinner=spinner)
     if name in 'cellosaurus':
-        entity2fhir.cellosaurus2fhir(out_dir=out_dir, path=entity_path)
+        spinner.start()
+        entity2fhir.cellosaurus2fhir(out_dir=out_dir, path=entity_path, spinner=spinner)
     if name in 'icgc' and icgc:
         icgc2fhir.icgc2fhir(project_name=icgc, has_files=has_files)
     if name in 'htan':
+
         if isinstance(atlas, str):
             if "," in atlas:
                 atlas = atlas.split(",")
                 atlas = [a.strip() for a in atlas]
             else:
                 atlas = [atlas]
 
-        htan2fhir.htan2fhir(entity_atlas_name=atlas, verbose=verbose)
+        spinner.start()
+        htan2fhir.htan2fhir(entity_atlas_name=atlas, verbose=verbose, spinner=spinner)
+
+
+
+@cli.command('validate')
+@click.option("-d", "--debug", is_flag=True, default=False,
+              help="Run in debug mode.")
+@click.option("-p", "--path", default=None,
+              help="Path to read the FHIR NDJSON files.")
+def validate(debug: bool, path):
+    """Validate the output FHIR ndjson files."""
+    from gen3_tracker.git import run_command
+
+    if not path:
+        path = str(Path(importlib.resources.files('cda2fhir').parent / 'data' / 'META'))
+    if not os.path.isdir(path):
+        raise ValueError(f"Path: '{path}' is not a valid directory.")
+
+    try:
+        from gen3_tracker.meta.validator import validate as validate_dir
+        from halo import Halo
+        with Halo(text='Validating', spinner='line', placement='right', color='white'):
+            result = validate_dir(path)
+        click.secho(result.resources, fg=INFO_COLOR, file=sys.stderr)
+        # print exceptions, set exit code to 1 if there are any
+        for _ in result.exceptions:
+            click.secho(f"{_.path}:{_.offset} {_.exception} {json.dumps(_.json_obj, separators=(',', ':'))}", fg=ERROR_COLOR, file=sys.stderr)
+        if result.exceptions:
+            sys.exit(1)
+    except Exception as e:
+        click.secho(str(e), fg=ERROR_COLOR, file=sys.stderr)
+        if debug:
+            raise
+
+
+@cli.command('study_group')
+@click.option("-p", '--path', required=True,
+              default='./META',
+              show_default=True,
+              help='Directory path to META folder.')
+@click.option("-o", '--output_path', required=True,
+              show_default=True,
+              help='Directory path to folder to save the Group.ndjson file.')
+def study_group(path, output_path):
+    """Adds a FHIR ndjson Group file as a post-processing metadata that captures ResearchSubject or Participants to a
+    ResearchStudy."""
+    assert Path(path).is_dir(), f"Path {path} is not a valid directory path."
+    assert Path(output_path).is_dir(), f"Path {output_path} is not a valid directory path."
+
+    utils.study_groups(meta_path=path, out_path=output_path)
 
 
 if __name__ == '__main__':