2020.11 (#3048)

* changes after deploy for 2020.11

* fix test

* addressing @ElDeveloper commenets

* minor doc changes that we missed

Author: antgonza

CHANGELOG.md

@@ -1,5 +1,19 @@
 # Qiita changelog
 
+
+Version 2020.11
+---------------
+
+* Deprecated the automatic creation of the per template QIIME1 mapping file. If you want to merge a preparation and a BIOM table you must first create a meta-analysis.
+* Added a new autoloaded boolean flag to the Study object so we can control if a study was autoloaded via an automatic EBI-ENA or SRA loading job.
+* We stopped adding the CRC32 information from mod_zip, which should remove the warnings about CRC incorrect checksums.
+* Removed the show/hide button from an analysis while the analysis was being built to avoid possible confusion.
+* A new per-sample, fast, bowtie2 and Woltka plugin for WGS and Metatrascriptomics processing has been added, deprecating the Shogun plugin and moving the rest of the commands to a new qp-meta plugin.
+* Added the possibility for plugins to submit and control their own jobs vs. Qiita automatically submitting for them. For specifics of this new functionality, visit (![#3040](https://github.com/biocore/qiita/pull/3040/files))
+* We increased the number of workers in qiita.ucsd.edu for the web interface (from eight to twenty), redbiom (from eight to ten), and the plugin interactions (from eight to twenty). This should speed up responses and improve general performance.
+* For the qp-qiime2 plugin, we removed some unsupported alpha rarefaction metrics from the options, following QIIME2 guidelines.
+* For the qp-qiime2 plugin, if the user selects a tree but it doesn't exist, it will not try to parse and skip it.
+
 Version 092020
 --------------
 

qiita_core/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "092020"
+__version__ = "2020.11"

qiita_db/__init__.py

@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "092020"
+__version__ = "2020.11"
 
 __all__ = ["analysis", "artifact",  "archive", "base", "commands",
            "environment_manager", "exceptions", "investigation", "logger",

qiita_pet/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "092020"
+__version__ = "2020.11"

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__ = "092020"
+__version__ = "2020.11"
 
 __all__ = ['prep_template_summary_get_req', 'data_types_get_req',
            'study_get_req', 'sample_template_filepaths_get_req',

qiita_pet/handlers/api_proxy/prep_template.py

@@ -141,18 +141,13 @@ def prep_template_ajax_get_req(user_id, prep_id):
     investigation_type = pt.investigation_type
 
     download_prep_id = None
-    download_qiime_id = None
     other_filepaths = []
     for fp_id, fp in pt.get_filepaths():
         fp = basename(fp)
-        if 'qiime' in fp:
-            if download_qiime_id is None:
-                download_qiime_id = fp_id
+        if download_prep_id is None:
+            download_prep_id = fp_id
         else:
-            if download_prep_id is None:
-                download_prep_id = fp_id
-            else:
-                other_filepaths.append(fp)
+            other_filepaths.append(fp)
 
     ontology = _get_ENA_ontology()
 
@@ -165,7 +160,6 @@ def prep_template_ajax_get_req(user_id, prep_id):
             'name': name,
             'files': files,
             'download_prep_id': download_prep_id,
-            'download_qiime_id': download_qiime_id,
             'other_filepaths': other_filepaths,
             'num_samples': num_samples,
             'num_columns': num_columns,

qiita_pet/handlers/api_proxy/tests/test_prep_template.py

@@ -74,8 +74,9 @@ def test_prep_template_ajax_get_req(self):
                'name': "Prep information 1",
                'files': ["uploaded_file.txt"],
                'download_prep_id': 24,
-               'download_qiime_id': 21,
-               'other_filepaths': ['1_prep_1_19700101-000000.txt',
+               'other_filepaths': ['1_prep_1_qiime_19700101-000000.txt',
+                                   '1_prep_1_19700101-000000.txt',
+                                   '1_prep_1_qiime_19700101-000000.txt',
                                    '1_prep_1_19700101-000000.txt'],
                'num_samples': 27,
                'num_columns': 22,

qiita_pet/static/js/networkVue.js

@@ -352,7 +352,7 @@ Vue.component('processing-graph', {
       })
         .fail(function(object, status, error_msg) {
           bootstrapAlert("Error submitting workflow: " + object.statusText, "danger");
-        });
+        })
         .always(function() {
           // return button to regular state
           $('#run-btn').attr('disabled', false);

qiita_pet/support_files/doc/source/analyzingsamples/index.rst

@@ -12,6 +12,9 @@ Thanks to this, we've got new layout of the analysis panel and the following new
 * `Filter Samples <https://docs.qiime2.org/2020.2/plugins/available/feature-table/>`__
 * `Taxa Summary <https://docs.qiime2.org/2020.2/plugins/available/taxa/barplot/>`__ (example `here <https://view.qiime2.org/visualization/?type=html&src=https%3A%2F%2Fdocs.qiime2.org%2F2020.2%2Fdata%2Ftutorials%2Fmoving-pictures%2Ftaxa-bar-plots.qzv>`__)
 
+
+.. _creating_a_new_analysis:
+
 Creating A New Analysis
 -----------------------
 

qiita_pet/support_files/doc/source/faq.rst

@@ -244,6 +244,18 @@ etc; for more information check
 `this 3 minute read about Markdown <https://guides.github.com/features/mastering-markdown/>`__.
 
 
+Where's my QIIME1 mapping file?
+-------------------------------
+
+During the 2020.11 deployment we removed the functionality that automatically created
+the merged preparation and sample information file per preparation. This change will allow us
+to make faster information file updates allow for future multi-site operations.
+
+If you want to create a merged and validated mapping file (merged sample and preparation
+information file) please create an analysis by following these instructions:
+:ref:`creating_a_new_analysis`.
+
+
 I want to transfer a lot of files to Qiita, is there an easy way?
 -----------------------------------------------------------------