Fix BED example. Revert last change

Author: sveinugu

src/omnipy_examples/bed.py

@@ -2,7 +2,7 @@
 
 from omnipy import (Chain2, Chain3, convert_dataset, Dataset, HttpUrlDataset, LinearFlowTemplate,
                     MatchItemsModel, Model, PandasDataset, SplitToItemsModel, SplitToLinesModel,
-                    TableOfPydanticRecordsModel, TaskTemplate)
+                    TableOfPydanticRecordsModel, TaskTemplate, StrDataset)
 from omnipy_examples.util import get_github_repo_urls
 from pydantic import BaseModel, conint, constr
 
@@ -36,7 +36,7 @@ class BedRecordModel(BaseModel):
     strand: constr(regex='[-+\.]') | None
     thickStart: GenomeCoord | None
     thickEnd: GenomeCoord | None
-    itemRgb: SplitOnComma2RgbColorModel | Literal[0] | None
+    itemRgb: SplitOnComma2RgbColorModel | Literal['0'] | None
     blockCount: conint(ge=0) | None
     blockSizes: SplitOnComma2ListOfIntsModel | None
     blockStarts: SplitOnComma2ListOfIntsModel | None
@@ -56,8 +56,8 @@ class BedDataset(Dataset[BedModel]):
 
 # Omnipy tasks
 @TaskTemplate()
-def fetch_bed_dataset(url_list: HttpUrlDataset) -> BedDataset:
-    bed_raw_dataset = BedDataset()
+def fetch_bed_dataset(url_list: HttpUrlDataset) -> StrDataset:
+    bed_raw_dataset = StrDataset()
     bed_raw_dataset.load(url_list)
     return bed_raw_dataset
 
@@ -66,15 +66,11 @@ def fetch_bed_dataset(url_list: HttpUrlDataset) -> BedDataset:
 @LinearFlowTemplate(
     get_github_repo_urls,
     fetch_bed_dataset,
+    convert_dataset.refine(name='parse_bed', fixed_params={'dataset_cls': BedDataset}),
     convert_dataset.refine(
         name='convert_to_dataframe', fixed_params={'dataset_cls': PandasDataset}),
 )
 def import_bed_files_to_pandas(owner: str, repo: str, branch: str, path: str,
                                file_suffix: str) -> PandasDataset:
     ...
 
-
-# Running the flow
-if __name__ == '__main__':
-    import_bed_files_to_pandas.run(
-        owner='arq5x', repo='bedtools2', branch='master', path='data', file_suffix='bed')

src/omnipy_examples/main.py

@@ -23,11 +23,11 @@ def get_path_to_example_data() -> Path:
 
 @app.command()
 def bed(
-    owner: str = 'sunyumail93',
-    repo: str = 'Bed12Processing',
+    owner: str = 'arq5x',
+    repo: str = 'bedtools2',
     branch: str = 'master',
     path: str = 'data',
-    file_suffix: str = 'bed12',
+    file_suffix: str = 'bed',
 ) -> PandasDataset:
     from omnipy_examples.bed import import_bed_files_to_pandas
     return import_bed_files_to_pandas.run(
@@ -71,6 +71,12 @@ def chatgpt() -> object:
     return get_chatgpt_interpretation_of_biorxiv_entries_and_commit_loop.run()
 
 
+@app.command()
+def seqcol() -> object:
+    from omnipy_examples.seqcol import seqcol_tests
+    return seqcol_tests.run()
+
+
 @app.callback()
 def main(output_dir: str = runtime.config.job.output_storage.local.persist_data_dir_path,
          engine: EngineChoice = 'local',