From c0e715ba16569a768e04508f944aef458daf59d3 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Sat, 12 Oct 2024 07:56:48 -0600 Subject: [PATCH 1/2] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d29e6491d..33fb0303a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ Deployed on October 14th, 2024 * `Woltka v0.1.7, paired-end` superseded `Woltka v0.1.6` in `qp-woltka`; [more information](https://qiita.ucsd.edu/static/doc/html/processingdata/woltka_pairedend.html). Thank you to @qiyunzhu for the benchmarks! * Other general fixes, like [#3424](https://github.com/qiita-spots/qiita/pull/3424), [#3425](https://github.com/qiita-spots/qiita/pull/3425), [#3439](https://github.com/qiita-spots/qiita/pull/3439), [#3440](https://github.com/qiita-spots/qiita/pull/3440). * General SPP improvements, like: [NuQC modified to preserve metadata in fastq files](https://github.com/biocore/mg-scripts/pull/155), [use squeue instead of sacct](https://github.com/biocore/mg-scripts/pull/152), , [job aborts if Qiita study contains sample metadata columns reserved for prep-infos](https://github.com/biocore/mg-scripts/pull/151), [metapool generates OverrideCycles value](https://github.com/biocore/metagenomics_pooling_notebook/pull/225). +* We updated the available parameters for `Filter features against reference [filter_features]`, `Non V4 16S sequence assessment [non_v4_16s]` and all the phylogenetic analytical commands so they can use `Greengenes2 2024.09`. From 769e3829012baf56ca88b30738cac6b4f20d5a31 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 11 Mar 2025 23:30:01 +0100 Subject: [PATCH 2/2] multiple validation jobs should be submitted as lead and dependent jobs, but the later must also made known by the DB --- qiita_db/processing_job.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/qiita_db/processing_job.py b/qiita_db/processing_job.py index 27192bab7..c773ff927 100644 --- a/qiita_db/processing_job.py +++ b/qiita_db/processing_job.py @@ -1105,13 +1105,23 @@ def submit(self, parent_job_id=None, dependent_jobs_list=None): # organized into n 'queues' or 'chains', and # will all run simultaneously. for dependent in dependent_jobs_list: + # register dependent job as queued to make qiita + # aware of this child process + dependent._set_status('queued') + + dep_software = dependent.command.software + dep_job_dir = join(qdb.util.get_work_base_dir(), + dependent.id) p = Process(target=launcher['function'], - args=(plugin_env_script, - plugin_start_script, + args=(dep_software.environment_script, + dep_software.start_script, url, - self.id, - job_dir)) + dependent.id, + dep_job_dir)) p.start() + # assign the child process ID as external id to + # the dependent + dependent.external_id = p.pid else: error = ("execute_in_process must be defined", "as either true or false")