Changes to the code that runs locally

s3 path gives an error
broadinstitute · Sep 3, 2024 · f082f89 · f082f89
1 parent 62804e1
commit f082f89
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Showing 2 changed files with 20 additions and 10 deletions.
diff --git a/src/pe2loaddata/__main__.py b/src/pe2loaddata/__main__.py
@@ -68,7 +68,8 @@ def headless(
             os.makedirs(output_path)  
 
     # Strip spaces because XML parser is broken
-    channels = dict([(str(k).replace(" ", ""), v) for (k, v) in channels.items()])
+    if channels != '':
+        channels = dict([(str(k).replace(" ", ""), v) for (k, v) in channels.items()])
 
 
     if "s3" in index_directory:
@@ -101,8 +102,8 @@ def headless(
                 return
 
     else:
-        index_file = glob.glob(f"{index_directory}" + "/*.xml")
-
+        index_file = glob.glob(f"{index_directory}" + "/*.xml")[0]
+    #__import__("IPython").embed()
     print(index_file)
     index_file 
 
@@ -115,7 +116,7 @@ def headless(
     wells = handler.root.wells.wells
 
     paths = {}  
-
+    #print(paths)
     if not illum_only:
         if search_subdirectories:
             if remote:
@@ -130,6 +131,7 @@ def headless(
                             path, filename = fullpath.rsplit("/", 1)
                             if filename.endswith(".tiff"):
                                 paths[filename] = path
+                                print(fullpath)
                 except KeyError:
                     print("Listing files in s3 directory failed.")
                     return
@@ -142,7 +144,7 @@ def headless(
         else:
             for filename in os.listdir(index_directory):
                 paths[filename] = index_directory
-
+        print(paths)
         with open(output, "w") as fd:
             writer = csv.writer(fd, lineterminator="\n")
 

diff --git a/src/pe2loaddata/transformer.py b/src/pe2loaddata/transformer.py
@@ -139,7 +139,9 @@ def write_csv(writer, images, plates, wells, channels, channelid, metadata, path
                     else:
                         fields[field_id][channel] = image
                 except Exception as e:
-                    print(e)
+                    #print(image.channel_name)
+                    print('error at image step')
+                    #print(e)
 
             for field in sorted(fields):
                 d = fields[field]
@@ -154,10 +156,12 @@ def write_csv(writer, images, plates, wells, channels, channelid, metadata, path
                             file_name = image.metadata["URL"]
 
                             row += [file_name, paths[file_name]]
+                            print(channels)
                         except Exception as e:
                             logging.debug("Channel = {}; Field = {}; Plate = {}".format(channel, field, plate_name))
-
-                            print(e)
+                            #print(file_name)
+                            #print('error at field step')
+                            #print(e)
 
                             row = []
 
@@ -187,8 +191,11 @@ def write_csv(writer, images, plates, wells, channels, channelid, metadata, path
                             row += [file_name, paths[file_name]]
                         except Exception as e:
                             logging.debug("Channel = {}; Field = {}; Plate = {}".format(channel, field, plate_name))
-
-                            print(e)
+                            print(channelid.keys())
+                            #print(paths[file_name])
+                            #print(image.metadata["URL"])
+                            #print('error at else step')
+                            #print(e)
 
                             row = []
 
@@ -209,3 +216,4 @@ def write_csv(writer, images, plates, wells, channels, channelid, metadata, path
 
                     writer.writerow(row)
 
+    #__import__("IPython").embed()