Merge pull request #11 from DOED-DAAD/dev

updated cli error handling

.gitignore

@@ -1,4 +1,5 @@
 .pytest**
 .ruff_cache
 __pycache__
-.vscode
+.vscode
+errors.txt

pyproject.toml

@@ -11,7 +11,7 @@ requires-python = ">=3.8"
 license = "MIT"
 keywords = []
 authors = [
-  { name = "Matthew Wells", email = "[email protected]" },
+  { name = "Matthew Wells", email = "[email protected]" },
 ]
 classifiers = [
   "Development Status :: 4 - Beta",
@@ -36,7 +36,7 @@ Issues = "https://github.com/unknown/mikrokondo-tools/issues"
 Source = "https://github.com/unknown/mikrokondo-tools"
 
 [project.scripts]
-mikrokondo-tools = "mikrokondo_tools.cli:mikrokondo_tools"
+mikrokondo-tools = "mikrokondo_tools.cli:safe_entry_point"
 
 [tool.hatch.version]
 path = "src/mikrokondo_tools/__about__.py"

src/mikrokondo_tools/__main__.py

@@ -1,25 +1,10 @@
-# SPDX-FileCopyrightText: 2024-present Matthew Wells <[email protected]>
+# SPDX-FileCopyrightText: 2024-present Matthew Wells <[email protected]>
 #
 # SPDX-License-Identifier: MIT
 import sys
-import traceback
-import mikrokondo_tools.utils as u
+
 
 if __name__ == "__main__":
     #from mikrokondo_tools.cli import mikrokondo_tools
     from mikrokondo_tools.cli import main
-    logger = u.get_logger(__name__)
-
-    try:
-        main()
-    except Exception as e:
-        errors_out = "errors.txt"
-        logger.warning("Error encountered appending traceback to %s", errors_out)
-        with open(errors_out, 'r') as output:
-            output.write(traceback.format_exc())
-        error_number = e.errno if hasattr(e, "errno") else -1
-        SystemExit(error_number)
-    else:
-        logger.info("Program finished.")
-
-    sys.exit(0)
+    sys.exit(main())

src/mikrokondo_tools/cli/__init__.py

@@ -3,6 +3,9 @@
 # SPDX-License-Identifier: MIT
 import click
 
+import traceback
+import mikrokondo_tools.utils as u
+
 from mikrokondo_tools.__about__ import __version__
 from mikrokondo_tools.cli.download import download
 from mikrokondo_tools.cli.samplesheet import samplesheet
@@ -17,6 +20,20 @@ def mikrokondo_tools():
 mikrokondo_tools.add_command(samplesheet)
 
 
+def safe_entry_point():
+    logger = u.get_logger(__name__)
+    try:
+        mikrokondo_tools(prog_name='mikrokondo-tools')
+    except Exception as e:
+        errors_out = "errors.txt"
+        logger.warning("Error encountered appending traceback to %s for debugging.", errors_out)
+        with open(errors_out, 'a') as output:
+            output.write(traceback.format_exc())
+        error_number = e.errno if hasattr(e, "errno") else -1
+        SystemExit(error_number)
+    else:
+        logger.info("Program finished.")
 
 def main():
-    return mikrokondo_tools(prog_name='mikrokondo-tools')
+    return safe_entry_point
+

src/mikrokondo_tools/cli/samplesheet/__init__.py

@@ -21,4 +21,4 @@ def samplesheet(output_sheet, read_1, read_2, input_directory, schema_input):
 
     data = ss.get_samples(p.Path(input_directory))
     ngs_data = ss.NGSData(data[0], data[1], read_1, read_2, output_sheet, schema_input)
-    return ngs_data.create_sample_sheet()
+    ngs_data.create_sample_sheet()

src/mikrokondo_tools/samplesheet/samplesheet.py

@@ -30,6 +30,9 @@ class DuplicateFilesException(Exception):
 class MissingSchemaException(Exception):
     pass
 
+class NoFilesFoundException(Exception):
+    pass
+
 @dataclass
 class SampleRow:
     sample: str
@@ -189,10 +192,11 @@ def organize_data(self) -> t.Dict[str, t.List[SampleRow]]:
         pe_reads, se_reads, assemblies = self.get_ngs_data()
         sample_sheet: t.Dict[str, t.List[SampleRow]] = dict()
 
-        for k, v in pe_reads.items():
-            sample_sheet[k] = []
-            for idx in range(len(v[0])):
-                sample_sheet[k].append(SampleRow(sample=k, fastq_1=v[0][idx], fastq_2=v[1][idx]))
+        if pe_reads:
+            for k, v in pe_reads.items():
+                sample_sheet[k] = []
+                for idx in range(len(v[0])):
+                    sample_sheet[k].append(SampleRow(sample=k, fastq_1=v[0][idx], fastq_2=v[1][idx]))
         if se_reads:
             self.update_sample_sheet_se(sample_sheet, se_reads.items(), SampleRow.longreads_key())
         if assemblies:
@@ -294,7 +298,7 @@ def get_samples(directory: p.Path) -> t.Tuple[t.List[p.Path], t.List[p.Path]]:
             try:
                 sfx = file.suffixes[-2] # get second last file extension
             except IndexError:
-                logger.error("File: %s is inappropriately no other extension is present besides %s", file, sfx)
+                logger.error("File: %s is inappropriately named no other extension is present besides %s", file, sfx)
                 sys.exit(-1)
         if sfx in __FASTQ_EXTENSIONS__:
             reads.append(file.absolute())
@@ -303,5 +307,8 @@ def get_samples(directory: p.Path) -> t.Tuple[t.List[p.Path], t.List[p.Path]]:
         else:
             logger.warning("Miscellaneous file present in sample directory: %s", file)
 
+    if not reads and not fastas:
+        logger.error("No files found in: %s", directory)
+        raise NoFilesFoundException
     return reads, fastas