Job failed on first run, rerun with "replace dataset collection elements" selected. Discovered output dataset collection elements were added to original collection, while new output dataset collection is not populated. This probably makes the job ineligible for the job cache / job search.
New HDCA without elements: b4248c8d761ed2ce Old HDCA with new elements: f65cf3bbc799b185
Change dataset_collection_id on dataset collection elements of old dataset collection to new one.
galaxy_main=> select * from dataset_collection_element as dce where dce.dataset_collection_id = 10074352;
id | dataset_collection_id | hda_id | ldda_id | child_collection_id | element_index | element_identifier
----+-----------------------+--------+---------+---------------------+---------------+--------------------
(0 rows)
galaxy_main=> select * from dataset_collection_element as dce where dce.dataset_collection_id = 10010723;
id | dataset_collection_id | hda_id | ldda_id | child_collection_id | element_index | element_identifier
----------+-----------------------+-----------+---------+---------------------+---------------+-----------------------------
75340757 | 10010723 | 158125270 | | | 0 | output.hic.a_ctg.noseq
75340758 | 10010723 | 158125271 | | | 1 | output.hic.hap1.p_ctg.noseq
75340759 | 10010723 | 158125272 | | | 2 | output.hic.hap2.p_ctg.noseq
75340760 | 10010723 | 158125273 | | | 3 | output.hic.p_ctg.noseq
75340761 | 10010723 | 158125274 | | | 4 | output.hic.p_utg.noseq
75340762 | 10010723 | 158125275 | | | 5 | output.hic.r_utg.noseq
(6 rows)Now change stuff:
galaxy_main=> start transaction
;
START TRANSACTION
galaxy_main=*> update dataset_collection_element set dataset_collection_id=10074352 where dataset_collection_id=10010723;
UPDATE 6
galaxy_main=*> update dataset_collection SET populated_state='ok' where id=10074352;
UPDATE 1
galaxy_main=*> update dataset_collection SET element_count=6 where id=10074352;
UPDATE 1
galaxy_main=*> commit;
COMMITnow shows up in job search:
import json
import requests
url = "https://usegalaxy.org/api/jobs/search"
api_key = os.getenv("GALAXY_API_KEY")
s = requests.Session()
s.headers["x-api-key"] = api_key
request_json = """{
"history_id": "bbd44e69cb8906b5e4b0d71318d67fc6",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0",
"tool_version": "0.25.0+galaxy0",
"inputs": {
"mode|mode_selector": "standard",
"mode|reads": {
"batch": false,
"product": false,
"values": [
{
"id": "1acbf043cb05ced3",
"src": "hdca",
"map_over_type": null
}
]
},
"filter_bits": "37",
"assembly_options|assembly_selector": "set",
"assembly_options|cleaning_rounds": "4",
"assembly_options|adapter_length": "0",
"assembly_options|pop_contigs": "10000000",
"assembly_options|pop_unitigs": "100000",
"assembly_options|remove_tips": "3",
"assembly_options|max_overlap": "0.8",
"assembly_options|min_overlap": "0.2",
"assembly_options|disable_post_join": false,
"assembly_options|ignore_error_corrected": false,
"assembly_options|hom_cov": "12",
"purge_options|purge_selector": "blank",
"hic_partition|hic_partition_selector": "set",
"hic_partition|h1": {
"batch": false,
"product": false,
"values": [
{
"id": "f9cad7b01a472135dcfffbe105500651",
"src": "hda",
"map_over_type": null
}
]
},
"hic_partition|h2": {
"batch": false,
"product": false,
"values": [
{
"id": "f9cad7b01a4721353d880d23d3fea0a1",
"src": "hda",
"map_over_type": null
}
]
},
"hic_partition|seed": "",
"hic_partition|n_weight": "",
"hic_partition|n_perturb": "",
"hic_partition|f_perturb": "",
"hic_partition|l_msjoin": "500000",
"ont_integration|ont_integration_selector": "blank",
"advanced_options|advanced_selector": "blank",
"scaffolding_options|scaffold_selector": "blank",
"log_out": true,
"bins_out": true
}
}"""
r = s.post(url, json=d)
r.json()
[{'model_class': 'Job',
'id': 'bbd44e69cb8906b54e6a4a7bd8a8a0b1',
'history_id': 'bbd44e69cb8906b5e4b0d71318d67fc6',
'tool_id': 'toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0',
'state': 'ok',
'exit_code': 0,
'create_time': '2025-08-15T14:47:56.401554',
'update_time': '2025-08-21T20:52:06.511452',
'galaxy_version': '25.0',
'external_id': None,
'handler': None,
'job_runner_name': None,
'command_line': None,
'user_email': None,
'user_id': 'cbb47ba6d7091fac',
'command_version': '0.25.0-r726',
'params': {'mode': '{"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 4140536, "src": "hdca"}]}}',
'filter_bits': '"37"',
'assembly_options': '{"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "12", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"}',
'purge_options': '{"__current_case__": 0, "purge_selector": "blank"}',
'hic_partition': '{"__current_case__": 1, "f_perturb": "", "h1": {"values": [{"id": 157434293, "src": "hda"}]}, "h2": {"values": [{"id": 157434294, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": "", "n_weight": "", "seed": ""}',
'ont_integration': '{"__current_case__": 0, "ont_integration_selector": "blank"}',
'advanced_options': '{"__current_case__": 0, "advanced_selector": "blank"}',
'scaffolding_options': '{"__current_case__": 0, "scaffold_selector": "blank"}',
'log_out': 'true',
'bins_out': 'true',
'chromInfo': '"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"',
'dbkey': '"?"',
'__input_ext': '"fastqsanger.gz"'},
'inputs': {'mode|reads': {'id': 'f9cad7b01a472135d5b84b4fb6b02024',
'src': 'hda',
'uuid': '7e2e4df2-8076-430f-b586-c37a1868d761'},
'mode|reads1': {'id': 'f9cad7b01a472135d5b84b4fb6b02024',
'src': 'hda',
'uuid': '7e2e4df2-8076-430f-b586-c37a1868d761'},
'mode|reads2': {'id': 'f9cad7b01a47213570f5f3e0276d4685',
'src': 'hda',
'uuid': '572c4743-f8ec-42db-8599-d1e44cccecc0'},
'mode|reads3': {'id': 'f9cad7b01a472135ab06719319a67da6',
'src': 'hda',
'uuid': 'e8449582-17cf-49f8-b4e3-47b96d6d875b'},
'hic_partition|h2': {'id': 'f9cad7b01a4721353d880d23d3fea0a1',
'src': 'hda',
'uuid': '5d590fb8-ecd8-4bf5-8434-b12791f982b6'},
'hic_partition|h21': {'id': 'f9cad7b01a4721353d880d23d3fea0a1',
'src': 'hda',
'uuid': '5d590fb8-ecd8-4bf5-8434-b12791f982b6'},
'mode|reads4': {'id': 'f9cad7b01a4721354295104c45246ee7',
'src': 'hda',
'uuid': '4b76bd06-0599-43d0-8184-38c5f98f82b8'},
'mode|reads5': {'id': 'f9cad7b01a472135821d0f71295512af',
'src': 'hda',
'uuid': 'e139ff9a-6ff4-4bb8-943b-e671964b35d9'},
'mode|reads6': {'id': 'f9cad7b01a4721356504f55ce902d977',
'src': 'hda',
'uuid': '47d82e5c-f915-4579-8b66-c1f74d6c65a2'},
'mode|reads7': {'id': 'f9cad7b01a4721350c173c4c10f51905',
'src': 'hda',
'uuid': '3297578a-6c2e-44b4-8bc0-736966ad2a69'},
'mode|reads8': {'id': 'f9cad7b01a4721355f0d2f478db47cd4',
'src': 'hda',
'uuid': 'a698a01e-e92a-4d1b-b6ce-26ba7f0223a2'},
'mode|reads9': {'id': 'f9cad7b01a472135c6e8173ebd3ddbba',
'src': 'hda',
'uuid': 'd08a5da0-b556-4e65-bcb2-6630435dbe46'},
'mode|reads10': {'id': 'f9cad7b01a4721350086b32d6f9b68d0',
'src': 'hda',
'uuid': '1a371c27-9bbf-483d-b4e1-6898c1cc42fe'},
'mode|reads11': {'id': 'f9cad7b01a472135656745858bc2b22c',
'src': 'hda',
'uuid': 'c62b1d11-45d5-408c-b3bc-7a491247ed8c'},
'mode|reads12': {'id': 'f9cad7b01a472135e3f94f2f342b8a1f',
'src': 'hda',
'uuid': '65fa1293-9d2d-4602-83ae-dd14f85c9e19'},
'mode|reads13': {'id': 'f9cad7b01a472135d75635b7240c5d8b',
'src': 'hda',
'uuid': '82934c65-1aca-4825-8a31-2c4f701c55e2'},
'mode|reads14': {'id': 'f9cad7b01a472135ee79849c534c718c',
'src': 'hda',
'uuid': '7e354309-bf86-46f9-a07f-f6cd778e2221'},
'mode|reads15': {'id': 'f9cad7b01a4721358149be310f0a61c2',
'src': 'hda',
'uuid': '510a268d-5869-48c3-b83b-6a7c9f6b0e22'},
'mode|reads16': {'id': 'f9cad7b01a4721350d22aa4abdab36e4',
'src': 'hda',
'uuid': 'cd7158a6-ed1d-43d7-8101-e55528eeb3a7'},
'mode|reads17': {'id': 'f9cad7b01a47213502da18194fe2409b',
'src': 'hda',
'uuid': '10ef1b9b-fcd2-4fed-8f53-e24aff4d07ee'},
'mode|reads18': {'id': 'f9cad7b01a472135144fd535613621ef',
'src': 'hda',
'uuid': '282856df-15aa-4802-ba01-5d965abbd049'},
'hic_partition|h1': {'id': 'f9cad7b01a472135dcfffbe105500651',
'src': 'hda',
'uuid': 'e026a60c-ba5f-450a-894a-6ffc3d0e6a0f'},
'hic_partition|h11': {'id': 'f9cad7b01a472135dcfffbe105500651',
'src': 'hda',
'uuid': 'e026a60c-ba5f-450a-894a-6ffc3d0e6a0f'}},
'outputs': {'hic_pcontig_graph': {'id': 'f9cad7b01a4721352ba3401768f39167',
'src': 'hda',
'uuid': '3f90395a-cdd9-4145-b86b-3d5f756d6e9e'},
'hic_acontig_graph': {'id': 'f9cad7b01a472135dde747f00948f322',
'src': 'hda',
'uuid': 'ce6b221d-6e81-4622-940f-73a940fd4aad'},
'hic_balanced_contig_hap1_graph': {'id': 'f9cad7b01a4721351c87b379b645b8ba',
'src': 'hda',
'uuid': '30762353-8adc-4c62-b179-75e42d5079e9'},
'hic_balanced_contig_hap2_graph': {'id': 'f9cad7b01a472135a553b080efa9bad8',
'src': 'hda',
'uuid': '68f195bc-f872-452f-af25-ceedded3921d'},
'hic_raw_initig': {'id': 'f9cad7b01a472135441b7ef3314a4c98',
'src': 'hda',
'uuid': 'b573cce8-302d-45d2-9d1a-d3e436f3f0cc'},
'log_file': {'id': 'f9cad7b01a47213598f51d345976d5b7',
'src': 'hda',
'uuid': '224ea3e8-eca2-4e8c-81f5-0c9d4149dba6'},
'__new_primary_file_noseq_files|output.hic.a_ctg.noseq__': {'id': 'f9cad7b01a4721354eb801756cd95462',
'src': 'hda',
'uuid': 'c5803bbd-d7a5-46f4-b3c6-59ddad57f84d'},
'__new_primary_file_noseq_files|output.hic.hap1.p_ctg.noseq__': {'id': 'f9cad7b01a472135826658cd08b90cf3',
'src': 'hda',
'uuid': '3c051a78-bdee-439a-87fe-0b30b394cd1d'},
'__new_primary_file_noseq_files|output.hic.hap2.p_ctg.noseq__': {'id': 'f9cad7b01a472135c8e4e9c8067ad8e6',
'src': 'hda',
'uuid': '9a7abb16-6d5c-4ed7-88d3-4e6a8355d187'},
'__new_primary_file_noseq_files|output.hic.p_ctg.noseq__': {'id': 'f9cad7b01a472135150792445f6b78a6',
'src': 'hda',
'uuid': 'bdb8b3cf-9d47-4ea1-8032-b5c44d7667fc'},
'__new_primary_file_noseq_files|output.hic.p_utg.noseq__': {'id': 'f9cad7b01a472135468948773eb6443d',
'src': 'hda',
'uuid': '97143174-554a-4fb3-ab79-7e946f317b74'},
'__new_primary_file_noseq_files|output.hic.r_utg.noseq__': {'id': 'f9cad7b01a472135b79c5badabfe0de9',
'src': 'hda',
'uuid': '75d600d6-bd1f-4c25-bc48-0a2b3775685f'},
'__new_primary_file_bin_files|output.ec__': {'id': 'f9cad7b01a472135afa8bfa2508f5f5f',
'src': 'hda',
'uuid': '19355375-15ed-4a88-81ca-5ac1a301b5c0'},
'__new_primary_file_bin_files|output.hic.lk__': {'id': 'f9cad7b01a472135a0b327269e3851fd',
'src': 'hda',
'uuid': '698623c4-8e55-4ac4-8412-4d20f13544c7'},
'__new_primary_file_bin_files|output.hic.tlb__': {'id': 'f9cad7b01a472135f390f15e6f7c69ef',
'src': 'hda',
'uuid': '84579f2c-8f80-4703-a313-646a3a3c1ac2'},
'__new_primary_file_bin_files|output.ovlp.reverse__': {'id': 'f9cad7b01a472135f7caa3620204087d',
'src': 'hda',
'uuid': '96dff50b-d8e3-4b5a-9743-e00cb5f2e9f3'},
'__new_primary_file_bin_files|output.ovlp.source__': {'id': 'f9cad7b01a4721355dc7019a701115bc',
'src': 'hda',
'uuid': '628087c3-6e9e-45fc-b21f-4fe9adc26d35'}},
'copied_from_job_id': None,
'output_collections': {'noseq_files': {'src': 'hdca',
'id': 'f65cf3bbc799b185'},
'bin_files': {'src': 'hdca', 'id': '61cc550ab754accb'}}}]