Mercurial > repos > tduigou > save_to_db
changeset 5:f934215bdb78 draft default tip
planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 02 Jun 2025 10:29:28 +0000 |
| parents | c7a7520afb4b |
| children | |
| files | output.html output.json save_to_db.py save_to_db.xml test-data/test-JSON_arg.json test-data/test-JSON_arg_block.json |
| diffstat | 6 files changed, 251 insertions(+), 35 deletions(-) [+] |
line wrap: on
line diff
--- a/output.html Mon Jun 02 09:48:14 2025 +0000 +++ b/output.html Mon Jun 02 10:29:28 2025 +0000 @@ -285,7 +285,7 @@ var md = window.markdownit({ html: true, }); - target.innerHTML = md.render(atob('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')); + target.innerHTML = md.render(atob('## Test Summary

<div class="progress">
  <div class="progress-bar progress-bar-success" style="width: 50.0%" aria-valuenow="1" aria-valuemin="0" aria-valuemax="2" data-toggle="tooltip" title="1 Passed">
  </div>
  <div class="progress-bar progress-bar-warning" style="width: 0.0%" aria-valuenow="0" aria-valuemin="0" aria-valuemax="2" data-toggle="tooltip" title="0 Skipped">
  </div>
  <div class="progress-bar progress-bar-danger" style="width: 50.0%" aria-valuenow="1" aria-valuemin="0" aria-valuemax="2" title="1 Failed or Errored">
  </div>
</div>

| Test State | Count |
| ---------- | ----- |
| Total      | 2 |
| Passed     | 1 |
| Error      | 0 |
| Failure    | 1 |
| Skipped    | 0 |


<details open><summary>Failed Tests</summary>

* <details class="rcorners light-red"><summary class="light-red">&#10060; save_to_db (Test # 1)</summary><div class="padded">

    **Problems**:
    * ```
      Output output:  different than expected
      Expected 5+-0 lines in the output found 0
      ```
    **Command Line:**

    * ```console
      python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpgfe8mdmw/files/a/5/a/dataset_a5a56a5c-573a-4b34-8c98-27b2edff54f3.dat,/tmp/tmpgfe8mdmw/files/1/7/7/dataset_1779bfb3-ff31-4b6d-8c6f-82172c987fee.dat,/tmp/tmpgfe8mdmw/files/4/c/c/dataset_4cc83056-e7b7-4dcd-9360-cde2bc1978f1.dat,/tmp/tmpgfe8mdmw/files/9/6/9/dataset_969b7b35-4f05-48bc-92f5-4e2f5ce375ca.dat,/tmp/tmpgfe8mdmw/files/7/b/4/dataset_7b47f46b-3e00-4a65-9c9a-6a25e3c30b04.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpgfe8mdmw/job_working_directory/000/7/outputs/dataset_89f2f3f4-04a0-4998-a3f6-d065b9e1f365.dat' --file_name_mapping '/tmp/tmpgfe8mdmw/files/a/5/a/dataset_a5a56a5c-573a-4b34-8c98-27b2edff54f3.dat:p7_L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/1/7/7/dataset_1779bfb3-ff31-4b6d-8c6f-82172c987fee.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpgfe8mdmw/files/4/c/c/dataset_4cc83056-e7b7-4dcd-9360-cde2bc1978f1.dat:p6_Kozak-ATG.gb,/tmp/tmpgfe8mdmw/files/9/6/9/dataset_969b7b35-4f05-48bc-92f5-4e2f5ce375ca.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/7/b/4/dataset_7b47f46b-3e00-4a65-9c9a-6a25e3c30b04.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpgfe8mdmw/files/b/3/e/dataset_b3e3a95b-dd84-41de-b53b-ea44d034e11b.dat'
      ```
    **Exit Code:**

    * ```console
      0
      ```
    **Standard Output:**

    * ```console
      Execution was blocked by config (execution = false)

      ```
    **Traceback:**

    * ```console
      
      ```
   **Job Parameters:**

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | genbank\_files | ` {"values": [{"id": 1, "src": "hdca"}]} ` |
       | table | ` None ` |
       | sequence\_column | ` None ` |
       | annotation\_column | ` None ` |
       | fragment\_column | ` None ` |
       | db\_uri | ` None ` |
       | adv | ` {"json_conf": {"values": [{"id": 6, "src": "hda"}]}} ` |
       | chromInfo | ` "/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
       | dbkey | ` "?" ` |
       | \_\_input\_ext | ` "input" ` |



    </div></details>


</details>
<details ><summary>Passed Tests</summary>

* <details class="rcorners light-green"><summary class="light-green">&#9989; save_to_db (Test # 2)</summary><div class="padded">

    **Command Line:**

    * ```console
      python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpgfe8mdmw/files/3/6/2/dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat,/tmp/tmpgfe8mdmw/files/4/e/0/dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat,/tmp/tmpgfe8mdmw/files/6/d/a/dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat,/tmp/tmpgfe8mdmw/files/8/0/b/dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat,/tmp/tmpgfe8mdmw/files/3/8/7/dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat' --file_name_mapping '/tmp/tmpgfe8mdmw/files/3/6/2/dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat:p7_L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/4/e/0/dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpgfe8mdmw/files/6/d/a/dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat:p6_Kozak-ATG.gb,/tmp/tmpgfe8mdmw/files/8/0/b/dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/3/8/7/dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpgfe8mdmw/files/8/3/d/dataset_83ddd986-5a07-406e-91f8-fcc403a6e927.dat'
      ```
    **Exit Code:**

    * ```console
      0
      ```
    **Standard Output:**

    * ```console
      Container 'test_fragments_db' is already running.
      Connected to database.
      Processing file: dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat(p7_L7Ae-Weiss)
      Processing file: dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat(p6_Nt-IgKLsequence)
      Processing file: dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat(p6_Kozak-ATG)
      Processing file: dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat(p4_Kt-L7Ae-Weiss)
      Processing file: dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat(HC_Amp_ccdB)
      Inserted 5 fragments.
      Fragment names written to '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat'.

      ```
    **Traceback:**

    * ```console
      
      ```
   **Job Parameters:**

   *   | Job parameter | Parameter value |
       | ------------- | --------------- |
       | genbank\_files | ` {"values": [{"id": 2, "src": "hdca"}]} ` |
       | table | ` None ` |
       | sequence\_column | ` None ` |
       | annotation\_column | ` None ` |
       | fragment\_column | ` None ` |
       | db\_uri | ` None ` |
       | adv | ` {"json_conf": {"values": [{"id": 13, "src": "hda"}]}} ` |
       | chromInfo | ` "/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
       | dbkey | ` "?" ` |
       | \_\_input\_ext | ` "input" ` |



    </div></details>


</details>
')); </script> </body> </html> \ No newline at end of file
--- a/output.json Mon Jun 02 09:48:14 2025 +0000 +++ b/output.json Mon Jun 02 10:29:28 2025 +0000 @@ -1,65 +1,65 @@ { "summary": { "num_errors": 0, - "num_failures": 0, + "num_failures": 1, "num_skips": 0, - "num_tests": 1 + "num_tests": 2 }, "tests": [ { "data": { "inputs": { "adv|json_conf": { - "id": "1895a93fdf3c72e9", + "id": "c9e99bc7539b08e5", "src": "hda" }, "genbank_files": { - "id": "c0d7a43ba58f94b5", + "id": "c804608f95de6282", "src": "hdca" } }, "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpxct9x70x/files/3/0/f/dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat,/tmp/tmpxct9x70x/files/b/f/b/dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat,/tmp/tmpxct9x70x/files/1/e/5/dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat,/tmp/tmpxct9x70x/files/a/b/a/dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat,/tmp/tmpxct9x70x/files/7/b/7/dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat' --file_name_mapping '/tmp/tmpxct9x70x/files/3/0/f/dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat:p7_L7Ae-Weiss.gb,/tmp/tmpxct9x70x/files/b/f/b/dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpxct9x70x/files/1/e/5/dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat:p6_Kozak-ATG.gb,/tmp/tmpxct9x70x/files/a/b/a/dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpxct9x70x/files/7/b/7/dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpxct9x70x/files/f/4/f/dataset_f4fd59e8-f8d6-4be2-8b00-9e12ca8319ef.dat'", + "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpgfe8mdmw/files/a/5/a/dataset_a5a56a5c-573a-4b34-8c98-27b2edff54f3.dat,/tmp/tmpgfe8mdmw/files/1/7/7/dataset_1779bfb3-ff31-4b6d-8c6f-82172c987fee.dat,/tmp/tmpgfe8mdmw/files/4/c/c/dataset_4cc83056-e7b7-4dcd-9360-cde2bc1978f1.dat,/tmp/tmpgfe8mdmw/files/9/6/9/dataset_969b7b35-4f05-48bc-92f5-4e2f5ce375ca.dat,/tmp/tmpgfe8mdmw/files/7/b/4/dataset_7b47f46b-3e00-4a65-9c9a-6a25e3c30b04.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpgfe8mdmw/job_working_directory/000/7/outputs/dataset_89f2f3f4-04a0-4998-a3f6-d065b9e1f365.dat' --file_name_mapping '/tmp/tmpgfe8mdmw/files/a/5/a/dataset_a5a56a5c-573a-4b34-8c98-27b2edff54f3.dat:p7_L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/1/7/7/dataset_1779bfb3-ff31-4b6d-8c6f-82172c987fee.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpgfe8mdmw/files/4/c/c/dataset_4cc83056-e7b7-4dcd-9360-cde2bc1978f1.dat:p6_Kozak-ATG.gb,/tmp/tmpgfe8mdmw/files/9/6/9/dataset_969b7b35-4f05-48bc-92f5-4e2f5ce375ca.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/7/b/4/dataset_7b47f46b-3e00-4a65-9c9a-6a25e3c30b04.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpgfe8mdmw/files/b/3/e/dataset_b3e3a95b-dd84-41de-b53b-ea44d034e11b.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-06-02T09:46:35.368351", + "create_time": "2025-06-02T10:25:46.744304", "dependencies": [], "exit_code": 0, - "external_id": "129989", + "external_id": "148807", "galaxy_version": "24.2", "handler": null, - "history_id": "c0d7a43ba58f94b5", - "id": "92e9df4c7abf24ab", + "history_id": "c804608f95de6282", + "id": "91a273dde5f46de6", "inputs": { "adv|json_conf": { - "id": "1895a93fdf3c72e9", + "id": "c9e99bc7539b08e5", "src": "hda", - "uuid": "f4fd59e8-f8d6-4be2-8b00-9e12ca8319ef" + "uuid": "b3e3a95b-dd84-41de-b53b-ea44d034e11b" }, "genbank_files1": { - "id": "c0d7a43ba58f94b5", + "id": "c804608f95de6282", "src": "hda", - "uuid": "30fc2017-6620-4a80-a60e-0c795c89f106" + "uuid": "a5a56a5c-573a-4b34-8c98-27b2edff54f3" }, "genbank_files2": { - "id": "1e3e46a5cbeec338", + "id": "dc78a71e9d46a610", "src": "hda", - "uuid": "bfb54321-8ad0-4e42-b307-f32e47e0618a" + "uuid": "1779bfb3-ff31-4b6d-8c6f-82172c987fee" }, "genbank_files3": { - "id": "81fab13a93a3da95", + "id": "32d06e9182be9fe5", "src": "hda", - "uuid": "1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3" + "uuid": "4cc83056-e7b7-4dcd-9360-cde2bc1978f1" }, "genbank_files4": { - "id": "a9ff23755d49e4b6", + "id": "a50e356be1f2db6f", "src": "hda", - "uuid": "aba8d5b4-a4f3-4487-803c-be5dee1445cd" + "uuid": "969b7b35-4f05-48bc-92f5-4e2f5ce375ca" }, "genbank_files5": { - "id": "2ca788c708559c16", + "id": "64d80998680b05e1", "src": "hda", - "uuid": "7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968" + "uuid": "7b47f46b-3e00-4a65-9c9a-6a25e3c30b04" } }, "job_messages": [], @@ -71,16 +71,16 @@ "output_collections": {}, "outputs": { "output": { - "id": "92e9df4c7abf24ab", + "id": "91a273dde5f46de6", "src": "hda", - "uuid": "41b844ab-5a85-46cd-8367-7ad1fbee7d3c" + "uuid": "89f2f3f4-04a0-4998-a3f6-d065b9e1f365" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}}", "annotation_column": null, - "chromInfo": "\"/tmp/tmpxct9x70x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "db_uri": null, "dbkey": "\"?\"", "fragment_column": null, @@ -90,22 +90,193 @@ }, "state": "ok", "stderr": "", - "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat\nProcessing file: dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat\nProcessing file: dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat\nProcessing file: dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat\nProcessing file: dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat'.\n", + "stdout": "Execution was blocked by config (execution = false)\n", "tool_id": "save_to_db", "tool_stderr": "", - "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat\nProcessing file: dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat\nProcessing file: dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat\nProcessing file: dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat\nProcessing file: dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat'.\n", - "update_time": "2025-06-02T09:46:41.929779", + "tool_stdout": "Execution was blocked by config (execution = false)\n", + "update_time": "2025-06-02T10:25:54.228017", "user_email": "planemo@galaxyproject.org", - "user_id": "c0d7a43ba58f94b5" + "user_id": "c804608f95de6282" }, - "status": "success", + "output_problems": [ + "Output output: different than expected\nExpected 5+-0 lines in the output found 0" + ], + "status": "failure", "test_index": 0, - "time_seconds": 29.02011752128601, + "time_seconds": 28.49768567085266, "tool_id": "save_to_db", - "tool_version": "0.1.0+galaxy1" + "tool_version": "0.2.0+galaxy2" }, "has_data": true, "id": "save_to_db-0" + }, + { + "data": { + "inputs": { + "adv|json_conf": { + "id": "ba5e0bd88cc3030c", + "src": "hda" + }, + "genbank_files": { + "id": "dc78a71e9d46a610", + "src": "hdca" + } + }, + "job": { + "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpgfe8mdmw/files/3/6/2/dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat,/tmp/tmpgfe8mdmw/files/4/e/0/dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat,/tmp/tmpgfe8mdmw/files/6/d/a/dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat,/tmp/tmpgfe8mdmw/files/8/0/b/dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat,/tmp/tmpgfe8mdmw/files/3/8/7/dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat' --file_name_mapping '/tmp/tmpgfe8mdmw/files/3/6/2/dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat:p7_L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/4/e/0/dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpgfe8mdmw/files/6/d/a/dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat:p6_Kozak-ATG.gb,/tmp/tmpgfe8mdmw/files/8/0/b/dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/3/8/7/dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpgfe8mdmw/files/8/3/d/dataset_83ddd986-5a07-406e-91f8-fcc403a6e927.dat'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-06-02T10:26:14.771419", + "dependencies": [ + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pandas", + "version": "2.2.3" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "sqlalchemy", + "version": "2.0.40" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "psycopg2", + "version": "2.9.9" + } + ], + "exit_code": 0, + "external_id": "149308", + "galaxy_version": "24.2", + "handler": null, + "history_id": "dc78a71e9d46a610", + "id": "c6ad8bbeb64086ff", + "inputs": { + "adv|json_conf": { + "id": "ba5e0bd88cc3030c", + "src": "hda", + "uuid": "83ddd986-5a07-406e-91f8-fcc403a6e927" + }, + "genbank_files1": { + "id": "4da6c37b755c621f", + "src": "hda", + "uuid": "362bcc57-3b7e-4089-b9c7-33155498d352" + }, + "genbank_files2": { + "id": "83933cf19817c19f", + "src": "hda", + "uuid": "4e03baea-fd7c-45b3-b808-4443adc60f91" + }, + "genbank_files3": { + "id": "33ff3c6dc742881e", + "src": "hda", + "uuid": "6da90158-c02d-457e-8908-56b532b4b3c2" + }, + "genbank_files4": { + "id": "8187d0d2b67e72bf", + "src": "hda", + "uuid": "80b64d26-b0b2-40df-ad9b-41446c172705" + }, + "genbank_files5": { + "id": "a744ea399046e427", + "src": "hda", + "uuid": "38751000-4953-44bb-b142-81b4bc41ad97" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output": { + "id": "c6ad8bbeb64086ff", + "src": "hda", + "uuid": "ee43072f-661d-47e0-b30f-d905aac37a4a" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"json_conf\": {\"values\": [{\"id\": 13, \"src\": \"hda\"}]}}", + "annotation_column": null, + "chromInfo": "\"/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": null, + "dbkey": "\"?\"", + "fragment_column": null, + "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}", + "sequence_column": null, + "table": null + }, + "state": "ok", + "stderr": "", + "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat(p6_Kozak-ATG)\nProcessing file: dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat'.\n", + "tool_id": "save_to_db", + "tool_stderr": "", + "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat(p6_Kozak-ATG)\nProcessing file: dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat'.\n", + "update_time": "2025-06-02T10:26:21.180586", + "user_email": "planemo@galaxyproject.org", + "user_id": "c804608f95de6282" + }, + "status": "success", + "test_index": 1, + "time_seconds": 26.70093870162964, + "tool_id": "save_to_db", + "tool_version": "0.2.0+galaxy2" + }, + "has_data": true, + "id": "save_to_db-1" } ], "version": "0.1"
--- a/save_to_db.py Mon Jun 02 09:48:14 2025 +0000 +++ b/save_to_db.py Mon Jun 02 10:29:28 2025 +0000 @@ -123,8 +123,9 @@ for gb_file in gb_files: # Extract base file name (just the file name, not the full path) real_file_name = os.path.basename(gb_file) + fragment_name = file_name_mapping_dict.get(real_file_name) - print(f"Processing file: {real_file_name}") # Debugging: Log the current file + print(f"Processing file: {real_file_name}({fragment_name})") # Debugging: Log the current file # Get the corresponding fragment name from the mapping fragment_name = file_name_mapping_dict.get(real_file_name) @@ -196,6 +197,9 @@ if args.json_conf != 'None' or '': with open(args.json_conf, "r") as f: json_config = json.load(f) + if "execution" in json_config and json_config["execution"] is False: + print("Execution was blocked by config (execution = false)") + return # Prefer user input; fallback to JSON_ values if not provided user_params = {
--- a/save_to_db.xml Mon Jun 02 09:48:14 2025 +0000 +++ b/save_to_db.xml Mon Jun 02 10:29:28 2025 +0000 @@ -39,6 +39,29 @@ </outputs> <tests> <!--Only 1 test can be execute because the fragment will be already saved for the second test and it will return error as the fragments are present in the DB (execut ../get_db_data/testMock.py to regenerate initial DB)--> + <!--test tool blocking from JSON --> + <test> + <param name="genbank_files"> + <collection type="list"> + <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" /> + <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" /> + <element name="p14_CMVp" value="p6_Kozak-ATG.gb" /> + <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" /> + <element name="p18_CMVp" value="HC_Amp_ccdB.gb" /> + </collection> + </param> + <param name="adv|json_conf" value="test-JSON_arg_block.json" /> + <output name="output" file="test_raport.txt" ftype="txt" > + <assert_contents> + <has_n_lines n="5" /> + <has_line_matching expression="p7_L7Ae-Weiss" /> + <has_line_matching expression="p6_Nt-IgKLsequence" /> + <has_line_matching expression="p6_Kozak-ATG" /> + <has_line_matching expression="p4_Kt-L7Ae-Weiss" /> + <has_line_matching expression="HC_Amp_ccdB" /> + </assert_contents> + </output> + </test> <!--test DB config in the tool --> <test> <param name="genbank_files"> @@ -90,7 +113,7 @@ </output> </test> </tests> - + <help><![CDATA[ Save Data To DB =================== @@ -106,6 +129,14 @@ * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file. * **DB IDs Column Name**: Column holding the unique fragment IDs. * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name). +* **DB config as a json file**: JSON file contains the DB configuration: + - "JSON_table": will be the key to the table name. + - "JSON_sequence_column": will be the key to the sequence column. + - "JSON_annotation_column": will be the key to the annotation column. + - "JSON_fragment_column": will be the key to the fragment column. + - "JSON_db_uri": will be the key to the URI. + - "execution": It is the key to execute or block the tool during a workflow ("True" or "False"). +* NOTE: the JSON file can be generated using the json_db_config_generating tool. ]]></help> <citations> <citation type="bibtex">
--- a/test-data/test-JSON_arg.json Mon Jun 02 09:48:14 2025 +0000 +++ b/test-data/test-JSON_arg.json Mon Jun 02 10:29:28 2025 +0000 @@ -3,6 +3,7 @@ "JSON_sequence_column": "sequence", "JSON_annotation_column": "annotation", "JSON_fragment_column": "fragment", - "JSON_db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db" + "JSON_db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", + "execution": true } \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-JSON_arg_block.json Mon Jun 02 10:29:28 2025 +0000 @@ -0,0 +1,9 @@ +{ + "JSON_table": "sample", + "JSON_sequence_column": "sequence", + "JSON_annotation_column": "annotation", + "JSON_fragment_column": "fragment", + "JSON_db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", + "execution": false +} + \ No newline at end of file