desc for deprecated software (#3339)

* adding the software desction to the GUI for deprecated software

* clean docs

* add workflow not active message

* Update qiita_pet/support_files/doc/source/processingdata/qp-fastp-minimap2.rst

Co-authored-by: Daniel McDonald <d3mcdonald@eng.ucsd.edu>

---------

Co-authored-by: Charles Cowart <42684307+charles-cowart@users.noreply.github.com>
Co-authored-by: Daniel McDonald <d3mcdonald@eng.ucsd.edu>

qiita_pet/handlers/artifact_handlers/base_handlers.py

@@ -228,6 +228,7 @@ def artifact_summary_get_request(user, artifact_id):
             'processing_parameters': proc_params.values,
             'command_active': cmd.active,
             'software_deprecated': sw.deprecated,
+            'software_description': sw.description
             }
     else:
         processing_info = {}

qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py

@@ -243,6 +243,12 @@ def test_artifact_summary_get_request(self):
                            private_download_button % 2),
                'processing_info': {
                  'command_active': True, 'software_deprecated': False,
+                 'software_description': ('Quantitative Insights Into '
+                                          'Microbial Ecology (QIIME) is an '
+                                          'open-source bioinformatics '
+                                          'pipeline for performing '
+                                          'microbiome analysis from raw DNA '
+                                          'sequencing data'),
                  'command': 'Split libraries FASTQ',
                  'processing_parameters': {
                    'max_barcode_errors': '1.5', 'sequence_max_n': '0',

qiita_pet/handlers/software.py

@@ -146,7 +146,7 @@ def _default_parameters_parsing(node):
 
         workflows.append(
             {'name': w.name, 'id': w.id, 'data_types': w.data_type,
-             'description': w.description,
+             'description': w.description, 'active': w.active,
              'parameters_sample': wparams['sample'],
              'parameters_prep': wparams['prep'],
              'nodes': nodes, 'edges': edges})

qiita_pet/support_files/doc/source/processingdata/processing-recommendations.rst

@@ -77,6 +77,12 @@ subsequent meta-analyses. We currently provide the several options for your conv
 - auto-detect adapters and **rat** + phix filtering. Includes Norway rat (*Rattus norvegicus*) reference `GCF_000001895.5 (Rnor_6.0) <https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000001895.5/>`_. `GCF_000001895.5 fna <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/895/GCA_000001895.4_Rnor_6.0/GCA_000001895.4_Rnor_6.0_genomic.fna.gz>`_
 - auto-detect adapters only filtering. Only includes the two adapter sequences noted above.
 
+For more information about the versions in this plugin, visit:
+
+.. toctree::
+
+   qp-fastp-minimap2.rst
+
 Note that the command produces up to 6 output artifacts based on the aligner and database selected:
 
 - Alignment Profile: contains the raw alignment file and the no rank classification BIOM table

qiita_pet/support_files/doc/source/processingdata/qp-fastp-minimap2.rst

@@ -0,0 +1,37 @@
+Adapter and host filtering
+==========================
+
+At the end of August 2023, we discovered that the parameters used by
+qp-fastp-minimap2 did not trigger application of adapter filtering. By default,
+fastp performs autodetection of adapters and filtering for single-end data. By
+default, fastp does not perform these operations on paired-end data. This behavior
+was not expected by us. It was discovered when manually assessing replicated
+sequences, which on examination by BLAST against NT reported to be adapters.
+
+Adapter filtering for paired-end data with fastp requires specifying either the
+exact adapters to remove (i.e., no autodetection), or to explicitly specify “--detect_adapter_for_pe”. Qiita previously indicated to users that the
+qp-fastp-minimap2 plugin was performing adapter autodetection and filtering.
+However, because this flag was not specified, that behavior did not occur.
+
+In the metagenomic dataset the adapters were discovered in, we observed a few
+sequences with high replication, with assignments to a few genomes in RS210.
+The coverage of those genomes, using all metagenomic short reads, was constrained
+to very specific regions. The replicated sequences exhibited high identity to
+known adapters. As such, we suspect the replicated sequences we observed were
+adapters. We suspect the observed genomes either suffer from adapter contamination
+themselves, or the constructs used in the samples we examined were derived from
+real organisms. Although we cannot differentiate this definitively in the data
+we examined, in either case these short reads are likely artifactual.
+
+For the dataset we examined, removal of these false positives was important
+for the biological interpretation of the results. However, whether the removal
+is important likely depends on the dataset and question.
+
+qp-fastp-minimap2 has been updated to perform adapter filtering on paired-end data.
+The fastp autodetection is compile-time limited to `the first 256k sequences <https://github.com/OpenGene/fastp/blob/7784d047fdf0a8df4211967156f5c97920c6d2e8/src/evaluator.cpp#L410-L417>`_.
+Because of this, we opted for a more conservative approach of not relying on
+autodetection and instead we now test all adapters that fastp is aware of. Specifically,
+we now provide fastp a known adapters FASTA which is a serialized representation
+of their `known adapter list <https://github.com/OpenGene/fastp/blob/7784d047fdf0a8df4211967156f5c97920c6d2e8/src/knownadapters.h#L11>`_.
+
+The new command is named: `Adapter and host filtering v2023.12`.

qiita_pet/templates/artifact_ajax/artifact_summary.html

@@ -125,6 +125,7 @@ <h4>
         {% if processing_info['software_deprecated'] %}
           <div class="alert alert-danger" role="alert">
             Danger, the software that generated this artifact was produced by a software version with a known bug and the results are wrong, please re-run with the newer version.
+            {% raw processing_info['software_description'] %}
           </div>
         {% elif not processing_info['command_active'] %}
           <div class="alert alert-warning" role="alert">

qiita_pet/templates/workflows.html

@@ -87,6 +87,11 @@ <h5>Hover on the spheres to get more information</h5>
         <div class="row">
           <div class="col-sm-7" style="background-color: #DCDCDC; height: 650px" id="workflow_{{i}}"></div>
           <div class="col-sm-5">
+            {% if not w['active'] %}
+              <h3 style="color:red">
+                ~~ NOT ACTIVE ~~
+              </h3>
+            {% end %}
             <h4>
               Application: {{', '.join(w['data_types'])}} ->
               {% if w['parameters_sample'] or w['parameters_prep'] %}

qiita_pet/test/test_software.py

@@ -175,7 +175,7 @@ def test_retrive_workflows(self):
     {'name': 'FASTQ upstream workflow', 'id': 1, 'data_types': ['16S', '18S'],
      'description': 'This accepts html <a href="https://qiita.ucsd.edu">Qiita!'
                     '</a><br/><br/><b>BYE!</b>',
-     'parameters_sample': {}, 'parameters_prep': {},
+     'active': True, 'parameters_sample': {}, 'parameters_prep': {},
      'nodes': [
         ['params_1', 1, 'Split libraries FASTQ', 'Defaults', {
             'max_bad_run_length': '3', 'min_per_read_length_fraction': '0.75',
@@ -199,7 +199,7 @@ def test_retrive_workflows(self):
         ['params_2', 'output_params_2_OTU table | BIOM']]},
     {'name': 'FASTA upstream workflow', 'id': 2, 'data_types': ['18S'],
      'description': 'This is another description',
-     'parameters_sample': {}, 'parameters_prep': {},
+     'active': False, 'parameters_sample': {}, 'parameters_prep': {},
      'nodes': [
         ['params_3', 2, 'Split libraries', 'Defaults with Golay 12 barcodes', {
             'min_seq_len': '200', 'max_seq_len': '1000',
@@ -226,7 +226,7 @@ def test_retrive_workflows(self):
         ['params_4', 'output_params_4_OTU table | BIOM']]},
     {'name': 'Per sample FASTQ upstream workflow', 'id': 3,
      'data_types': ['ITS'], 'description': None,
-     'parameters_sample': {}, 'parameters_prep': {},
+     'active': True, 'parameters_sample': {}, 'parameters_prep': {},
      'nodes': [
         ['params_5', 1, 'Split libraries FASTQ', 'per sample FASTQ defaults', {
             'max_bad_run_length': '3', 'min_per_read_length_fraction': '0.75',