PyPI - geoseeq - Versions diffs - 0.6.14.dev2__tar.gz → 0.6.14.dev3__tar.gz - Mend

@@ -378,6 +378,30 @@ def cli_download_ids(state, cores, target_dir, file_name, yes, download, head, i
         download_manager.download_files()
+def _get_sample_result_files_with_names(sample, module_name=None, first=False):
+    for read_type, folder in sample.get_all_fastqs().items():
+        if module_name and module_name != read_type:
+            continue
+        result_files_with_names = []
+        for folder_name, result_files in folder.items():
+            for result_file in result_files:
+                if read_type in ["short_read::paired_end"]:
+                    result_files_with_names.append(
+                        (result_file[0], result_file[0].get_referenced_filename())
+                    )
+                    result_files_with_names.append(
+                        (result_file[1], result_file[1].get_referenced_filename())
+                    )
+                else:
+                    result_files_with_names.append(
+                        (result_file, result_file.get_referenced_filename())
+                    )
+            if first:
+                break
+    return result_files_with_names
 @cli_download.command("fastqs")
 @use_common_state
 @cores_option
@@ -455,24 +479,12 @@ def cli_download_fastqs(state,
     result_files_with_names = []
     for sample in samples:
-        for read_type, folder in sample.get_all_fastqs().items():
-            if module_name and module_name != read_type:
-                continue
-            for folder_name, result_files in folder.items():
-                for result_file in result_files:
-                    if read_type in ["short_read::paired_end"]:
-                        result_files_with_names.append(
-                            (result_file[0], result_file[0].get_referenced_filename())
-                        )
-                        result_files_with_names.append(
-                            (result_file[1], result_file[1].get_referenced_filename())
-                        )
-                    else:
-                        result_files_with_names.append(
-                            (result_file, result_file.get_referenced_filename())
-                        )
-                if first:
-                    break
+        try:
+            result_files_with_names += _get_sample_result_files_with_names(sample, module_name, first)
+        except Exception as e:
+            logger.error(f"Error fetching fastq files for sample {sample.name}: {e}")
+            if not ignore_errors:
+                raise e
     if len(result_files_with_names) == 0:
         click.echo("No suitable fastq files found.")

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.14.dev2
+Version: 0.6.14.dev3
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

@@ -55,7 +55,7 @@ def version():
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
     Run `geoseeq eula show` to view the EULA.
     """
-    click.echo('0.6.14dev2')  # remember to update pyproject.toml
+    click.echo('0.6.14dev3')  # remember to update pyproject.toml
 @main.group('advanced')

@@ -200,7 +200,6 @@ class Sample(RemoteObject):
         """
         url = f"data/samples/{self.uuid}/all-fastqs"
         blob = self.knex.get(url)
-        print(blob)
         files = {}
         for read_type, folders in blob.items():
             files[read_type] = {}

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.14.dev2
+Version: 0.6.14.dev3
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "geoseeq"
-version = "0.6.14dev2"
+version = "0.6.14dev3"
 authors = [
   { name="David C. Danko", email="dcdanko@biotia.io" },
 ]

geoseeq 0.6.14.dev2__tar.gz → 0.6.14.dev3__tar.gz

geoseeq 0.6.14.dev2tar.gz → 0.6.14.dev3tar.gz