Merge branch 'dev' of github.com:biocore/qiita

Author: antgonza

Diff for: CHANGELOG.md

@@ -1,5 +1,15 @@
 # Qiita changelog
 
+Version 2025.04
+---------------
+
+Deployed on April 11th, 2025
+
+* General improvements for automatic environment generation by @sjanssen2 (thank you!): [#3462](https://github.com/qiita-spots/qiita/pull/3462), [#3463](https://github.com/qiita-spots/qiita/pull/3463), [3464](https://github.com/qiita-spots/qiita/pull/3464), [#3465](https://github.com/qiita-spots/qiita/pull/3465).
+* When ProcessingJob.resource_allocation_info fails, it will now be [set as the error for the job](https://github.com/qiita-spots/qiita/pull/3466).
+* SPP: General updates and clean up: [#169](https://github.com/biocore/mg-scripts/pull/169), [#101](https://github.com/qiita-spots/qp-knight-lab-processing/pull/101).
+* `Remove SynDNA plasmid, insert, & CP026085 reads` superseded `Remove SynDNA inserts & plasmid reads`; which now removes SynDNA plasmids, inserts, and CP026085 reads, in this order.
+
 Version 2025.02
 ---------------
 
@@ -8,7 +18,7 @@ Deployed on February 24th, 2025
 * Replaced os.rename for shutil.move in the code to fix [#3455](https://github.com/qiita-spots/qiita/issues/3455).
 * Via qp-spades, replaced the legacy `spades` command for `cloudSPAdes` for TellSeq.
 * `FASTA_preprocessed` within qtp-sequencing now allows for results to be named using their sample-name, extra from run-prefix.
-* `Remove SynDNA inserts & plasmid reads` superseded `Remove SynDNA reads`, which now removes SynDna inserts and plasmids.
+* `Remove SynDNA inserts & plasmid reads` superseded `Remove SynDNA reads`, which now removes SynDNA inserts and plasmids.
 * `update_resource_allocation_redis` now relies on using equations stored in the database vs. hardcoded; thank you @Gossty!
 * SPP: Updated prep-info file generation to identify and report filtered fastq files that could not be matched to a sample-id instead of silently ignoring them.
 * SPP: Removed legacy test code and example files for amplicon processing. Some other tests updated and repurposed.

Diff for: qiita_core/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2025.02"
+__version__ = "2025.04"

Diff for: qiita_db/__init__.py

@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "2025.02"
+__version__ = "2025.04"
 
 __all__ = ["analysis", "artifact",  "archive", "base", "commands",
            "environment_manager", "exceptions", "investigation", "logger",

Diff for: qiita_db/processing_job.py

@@ -1049,7 +1049,13 @@ def submit(self, parent_job_id=None, dependent_jobs_list=None):
                 # before returning immediately, usually with a job ID that can
                 # be used to monitor the job's progress.
 
-                resource_params = self.resource_allocation_info
+                try:
+                    resource_params = self.resource_allocation_info
+                except qdb.exceptions.QiitaDBUnknownIDError as e:
+                    # this propagates the error to the job and using str(e)
+                    # should be fine as we just want the last calculation
+                    # error
+                    self._set_error(str(e))
 
                 # note that parent_job_id is being passed transparently from
                 # submit declaration to the launcher.
@@ -1105,13 +1111,23 @@ 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")

Diff for: qiita_db/software.py

@@ -1620,6 +1620,11 @@ def load(cls, command, json_str=None, values_dict=None):
             error_msg = ("The provided JSON string doesn't encode a "
                          "parameter set for command %s" % command.id)
         else:
+            if not isinstance(values_dict, dict):
+                raise qdb.exceptions.QiitaDBError(
+                    "The provided value_dict is %s (i.e. not None) but also "
+                    "not a dictionary for command %s" % (
+                        values_dict, command.id))
             parameters = deepcopy(values_dict)
             error_msg = ("The provided values dictionary doesn't encode a "
                          "parameter set for command %s" % command.id)

Diff for: qiita_pet/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2025.02"
+__version__ = "2025.04"

Diff for: qiita_pet/handlers/api_proxy/__init__.py

@@ -38,7 +38,7 @@
 from .user import (user_jobs_get_req)
 from .util import check_access, check_fp
 
-__version__ = "2025.02"
+__version__ = "2025.04"
 
 __all__ = ['prep_template_summary_get_req', 'data_types_get_req',
            'study_get_req', 'sample_template_filepaths_get_req',

Diff for: qiita_ware/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2025.02"
+__version__ = "2025.04"

Diff for: setup.py

@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "2025.02"
+__version__ = "2025.04"
 
 
 classes = """