Hi Greg, Another small patch for cleanup_datasets.py, that makes the output messages slightly more informative. The changes are: 1. If a dataset is skipped (because it's shared/cloned and was already process), no message is printed at all. 2. If a dataset can not be deleted because it is shared, and one instance is not marked as "deleted", a proper message is printed. 3. If a dataset has metadata files, the message is changed depending on "info_only" and "remove_from_disk" flags. 4. The final summary message is slightly changed. The main goal is for the "delete_datasets.sh" script (with "-i" or without) to display exactly what's going on. comments are welcomed, -gordon Example of items 1,2: Without patch: ===== ... ######### Processing dataset id: 1782 ######### Processing dataset id: 1782 ######### Processing dataset id: 1782 ######### Processing dataset id: 1783 Dataset 1783 will be deleted (without 'info_only' mode) ######### Processing dataset id: 1801 Dataset 1801 will be deleted (without 'info_only' mode) ====== Which shows that dataset 1782 seems to be processed three times, but still not deleted, without giving a reason. With this patch, the output will be: ====== ######### Processing dataset id: 1782 Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted) ######### Processing dataset id: 1783 Dataset 1783 will be deleted (without 'info_only' mode) ######### Processing dataset id: 1801 Dataset 1801 will be deleted (without 'info_only' mode) ====== Example of item 3: Without patch: ========== ######### Processing dataset id: 1404 The following metadata files attached to associations of Dataset '1404' have been purged: /localdata1/galaxy/database_prod/files/_metadata_files/000/metadata_102.dat Dataset 1404 will be deleted (without 'info_only' mode) ========== With patch: ========== ######### Processing dataset id: 1404 The following metadata files attached to associations of Dataset '1404' will be marked as deleted (without 'info_only' mode): /localdata1/galaxy/database_prod/files/_metadata_files/000/metadata_102.dat Dataset 1404 will be deleted (without 'info_only' mode) =========== Example of item 4: Without patch: ==== Examined 606 datasets, marked 589 as deleted and purged 595 dataset instances ==== With patch: === Examined 606 datasets, marked 589 datasets and 595 dataset instances (HDA) as deleted ===
Hello Assaf, Thanks very much for the patch - I've applied it in change set 5788:b2f7abd50f6a Greg On Jul 12, 2011, at 3:18 PM, Assaf Gordon wrote:
Hi Greg,
Another small patch for cleanup_datasets.py, that makes the output messages slightly more informative.
The changes are: 1. If a dataset is skipped (because it's shared/cloned and was already process), no message is printed at all. 2. If a dataset can not be deleted because it is shared, and one instance is not marked as "deleted", a proper message is printed. 3. If a dataset has metadata files, the message is changed depending on "info_only" and "remove_from_disk" flags. 4. The final summary message is slightly changed.
The main goal is for the "delete_datasets.sh" script (with "-i" or without) to display exactly what's going on.
comments are welcomed, -gordon
Example of items 1,2: Without patch: ===== ... ######### Processing dataset id: 1782 ######### Processing dataset id: 1782 ######### Processing dataset id: 1782 ######### Processing dataset id: 1783 Dataset 1783 will be deleted (without 'info_only' mode) ######### Processing dataset id: 1801 Dataset 1801 will be deleted (without 'info_only' mode) ======
Which shows that dataset 1782 seems to be processed three times, but still not deleted, without giving a reason.
With this patch, the output will be: ====== ######### Processing dataset id: 1782 Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted) ######### Processing dataset id: 1783 Dataset 1783 will be deleted (without 'info_only' mode) ######### Processing dataset id: 1801 Dataset 1801 will be deleted (without 'info_only' mode) ======
Example of item 3: Without patch: ========== ######### Processing dataset id: 1404 The following metadata files attached to associations of Dataset '1404' have been purged: /localdata1/galaxy/database_prod/files/_metadata_files/000/metadata_102.dat Dataset 1404 will be deleted (without 'info_only' mode) ==========
With patch: ========== ######### Processing dataset id: 1404 The following metadata files attached to associations of Dataset '1404' will be marked as deleted (without 'info_only' mode): /localdata1/galaxy/database_prod/files/_metadata_files/000/metadata_102.dat Dataset 1404 will be deleted (without 'info_only' mode) ===========
Example of item 4: Without patch: ==== Examined 606 datasets, marked 589 as deleted and purged 595 dataset instances ====
With patch: === Examined 606 datasets, marked 589 datasets and 595 dataset instances (HDA) as deleted ===
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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Greg Von Kuster