Mercurial > repos > ufz > omero_get_id
annotate omero_metadata_upload.py @ 2:c7b2650718fe draft default tip
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
author | ufz |
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date | Mon, 16 Dec 2024 20:55:50 +0000 |
parents | c23735b45a4a |
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rev | line source |
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c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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changeset
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1 import argparse |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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2 import json |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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3 from datetime import datetime |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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4 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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5 import ezomero as ez |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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6 import pandas as pd |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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7 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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8 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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9 def metadata_import_ezo(user, pws, host, port, obj_type, did=None, ann_type="table", ann_file=None, an_name=None, |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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10 log_file='metadata_import_log.txt'): |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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11 def upload_metadata(conn, obj_type, did, data_dict, df, ann_type, an_name): |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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12 try: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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13 if ann_type == "KV": |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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14 id_map_ann = ez.post_map_annotation(conn, obj_type, object_id=int(did), kv_dict=data_dict, ns=an_name) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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15 ma_dict = ez.get_map_annotation(conn, id_map_ann) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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16 return ma_dict |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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17 elif ann_type == "table": |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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18 id_tb_ann = ez.post_table(conn, df, object_type=obj_type, object_id=int(did), title=an_name, |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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19 headers=True) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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20 tb_dict = ez.get_table(conn, id_tb_ann) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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21 return tb_dict |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
changeset
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22 except Exception as e: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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23 log_error(f"Error uploading metadata for {obj_type} with ID {did}: {str(e)}") |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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24 return None |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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25 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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26 def log_error(message): |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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27 with open(log_file, 'w') as f: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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28 f.write(f"ERROR: {message}\n") |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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29 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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30 def log_success(message): |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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31 with open(log_file, 'w') as f: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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32 f.write(f"SUCCESS: {message}\n") |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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33 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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34 try: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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35 df = pd.read_csv(ann_file, delimiter='\t') |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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36 except FileNotFoundError as e: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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37 log_error(f"Annotation file not found: {str(e)}") |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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38 return |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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39 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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40 if ann_type == "table": |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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41 data_dict = df.to_dict(orient='records') |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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42 elif ann_type == "KV": |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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43 data_dict = {col: df[col].iloc[0] for col in df.columns} |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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44 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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45 try: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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46 with ez.connect(user, pws, "", host, port, secure=True) as conn: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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47 if obj_type == "project": |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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48 if did is None: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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49 did = ez.post_project(conn, project_name=str(datetime.now())) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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50 result = upload_metadata(conn, "Project", did, data_dict, df, ann_type, an_name) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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51 elif obj_type == "screen": |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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52 if did is None: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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53 did = ez.post_screen(conn, screen_name=str(datetime.now())) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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54 result = upload_metadata(conn, "Screen", did, data_dict, df, ann_type, an_name) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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55 elif obj_type == "dataset": |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
diff
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56 if did is None: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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57 did = ez.post_dataset(conn, dataset_name=str(datetime.now())) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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58 result = upload_metadata(conn, "Dataset", did, data_dict, df, ann_type, an_name) |
2
c7b2650718fe
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
ufz
parents:
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59 elif obj_type == "plate": |
c7b2650718fe
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
ufz
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60 result = upload_metadata(conn, "Plate", did, data_dict, df, ann_type, an_name) |
c7b2650718fe
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
ufz
parents:
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61 elif obj_type == "well": |
c7b2650718fe
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46
ufz
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62 result = upload_metadata(conn, "Well", did, data_dict, df, ann_type, an_name) |
0
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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63 elif obj_type == "image": |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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64 result = upload_metadata(conn, "Image", did, data_dict, df, ann_type, an_name) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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65 else: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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66 raise ValueError("Unsupported object type provided: {}".format(obj_type)) |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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67 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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68 if result is not None: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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69 log_success(f"Successfully uploaded metadata for {obj_type} with ID {did}. Result: {result}") |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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70 else: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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71 log_error(f"Failed to upload metadata for {obj_type} with ID {did}.") |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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72 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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73 conn.close() |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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74 |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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75 except Exception as e: |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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76 log_error(f"Connection error: {str(e)}") |
c23735b45a4a
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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77 |
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78 |
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79 if __name__ == "__main__": |
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80 parser = argparse.ArgumentParser(description='Import metadata into OMERO.') |
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81 parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, |
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82 help="Credential file (JSON file with username and password for OMERO)") |
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83 parser.add_argument('--host', required=True, help='OMERO host') |
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84 parser.add_argument('--port', required=True, type=int, help='OMERO port') |
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85 parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'plate', |
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86 'well ', 'image'], |
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87 help='Type of OMERO object') |
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88 parser.add_argument('--did', type=int, help='ID of the object (if it exists)') |
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89 parser.add_argument('--ann_type', required=True, choices=['table', 'KV'], help='Annotation type') |
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90 parser.add_argument('--ann_file', required=True, help='Path to the annotation file') |
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91 parser.add_argument('--an_name', required=True, help='Namespace or title for the annotation') |
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92 parser.add_argument('--log_file', default='metadata_import_log.txt', help='Path to the log file') |
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93 |
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94 args = parser.parse_args() |
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95 |
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96 with open(args.credential_file, 'r') as f: |
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97 crds = json.load(f) |
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98 |
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99 metadata_import_ezo(user=crds['username'], pws=crds['password'], host=args.host, port=args.port, |
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100 obj_type=args.obj_type, did=args.did, ann_type=args.ann_type, |
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101 ann_file=args.ann_file, an_name=args.an_name, log_file=args.log_file) |