From 3332573d07acdc18d18eac3bfaf8f6f2afd57206 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 11 Dec 2024 15:35:31 +0100
Subject: [PATCH] Option to parse coordinates from filename
---
model_server/clients/batch_runner.py | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/model_server/clients/batch_runner.py b/model_server/clients/batch_runner.py
index 91fac94a..6492726e 100644
--- a/model_server/clients/batch_runner.py
+++ b/model_server/clients/batch_runner.py
@@ -1,6 +1,7 @@
from collections import OrderedDict
import json
from pathlib import Path
+import re
import shutil
import pandas as pd
@@ -142,11 +143,17 @@ class FileBatchRunnerClient(HttpClient):
where_remote = Path(self.remote_paths['input']) / inp['directory']
def _get_file_info(filename):
- return {
+ info = {
'remote_path': (where_remote / filename).as_posix(),
'local_path': where_local / filename,
'is_multiposition': is_multiposition,
}
+ if (coord_regex := inp.get('coord_regex')) is not None:
+ for coord_k, coord_v in re.search(coord_regex, filename).groupdict().items():
+ if coord_k.lower() not in ['well', 'position', 'time']:
+ raise InvalidStackCoordinateKeyError(f'Cannot interpret coordinate {coord_k}')
+ info[f'coord_{coord_k.lower()}'] = int(coord_v)
+ return info
paths = paths + [_get_file_info(f) for f in files]
if max_count is not None:
df = pd.DataFrame(paths).head(min(max_count, len(paths)))
@@ -269,4 +276,7 @@ class WatchPathVerificationError(Error):
pass
class TasksRemainingError(Error):
+ pass
+
+class InvalidStackCoordinateKeyError(Error):
pass
\ No newline at end of file
--
GitLab