From eec94ddb35a1c2619761ce1d56549cb6187c1aed Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Thu, 7 Apr 2022 06:29:20 -0600
Subject: [PATCH 1/6] fixes for 2022.04

---
 CHANGELOG.md                                   | 12 ++++++++++++
 qiita_core/__init__.py                         |  2 +-
 qiita_db/__init__.py                           |  2 +-
 qiita_db/analysis.py                           |  4 ++--
 qiita_pet/__init__.py                          |  2 +-
 .../analysis_handlers/base_handlers.py         |  3 +++
 qiita_pet/handlers/api_proxy/__init__.py       |  2 +-
 qiita_pet/templates/analysis_selected.html     | 18 +++++++++++-------
 qiita_ware/__init__.py                         |  2 +-
 setup.py                                       |  2 +-
 10 files changed, 34 insertions(+), 15 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5c142b0e6..de4d9e070 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,17 @@
 # Qiita changelog
 
+Version 2022.04
+---------------
+
+* Moved from Python 3.6 to 3.9.
+* Added support for Pandas 1.4.0, [details here](https://github.com/qiita-spots/qiita/pull/3174).
+* Updated all available JavaScript libraries, [details here](https://github.com/qiita-spots/qiita/pull/3177).
+* User can select which metadata to use when creating a new analysis, by default only overlapping metadata in all studies is selected.
+* Now we can fully delete users in the backend.
+* Fixed outstanding issues to add default workflow to a preparation, [details here](https://github.com/qiita-spots/qiita/issues/3158).
+* Fixed the following issues: [3183](https://github.com/qiita-spots/qiita/issues/3183), [3182](https://github.com/qiita-spots/qiita/issues/3182), [3170](https://github.com/qiita-spots/qiita/issues/3170)
+
+
 Version 2021.11
 ---------------
 
diff --git a/qiita_core/__init__.py b/qiita_core/__init__.py
index eae6d2551..17d2f32f9 100644
--- a/qiita_core/__init__.py
+++ b/qiita_core/__init__.py
@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2021.11"
+__version__ = "2022.04"
diff --git a/qiita_db/__init__.py b/qiita_db/__init__.py
index f5b72f836..32be405fa 100644
--- a/qiita_db/__init__.py
+++ b/qiita_db/__init__.py
@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "2021.11"
+__version__ = "2022.04"
 
 __all__ = ["analysis", "artifact",  "archive", "base", "commands",
            "environment_manager", "exceptions", "investigation", "logger",
diff --git a/qiita_db/analysis.py b/qiita_db/analysis.py
index b21f10a1b..137bd78d9 100644
--- a/qiita_db/analysis.py
+++ b/qiita_db/analysis.py
@@ -1086,12 +1086,12 @@ def _build_mapping_file(self, samples, rename_dup_samples=False,
                 if si not in sample_infos:
                     si_df = si.to_dataframe()
                     if categories is not None:
-                        si_df = si_df[categories & set(si_df.columns)]
+                        si_df = si_df[set(categories) & set(si_df.columns)]
                     sample_infos[si] = si_df
                 pt = artifact.prep_templates[0]
                 pt_df = pt.to_dataframe()
                 if categories is not None:
-                    pt_df = pt_df[categories & set(pt_df.columns)]
+                    pt_df = pt_df[set(categories) & set(pt_df.columns)]
 
                 qm = pt_df.join(sample_infos[si], lsuffix="_prep")
 
diff --git a/qiita_pet/__init__.py b/qiita_pet/__init__.py
index eae6d2551..17d2f32f9 100644
--- a/qiita_pet/__init__.py
+++ b/qiita_pet/__init__.py
@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2021.11"
+__version__ = "2022.04"
diff --git a/qiita_pet/handlers/analysis_handlers/base_handlers.py b/qiita_pet/handlers/analysis_handlers/base_handlers.py
index 8000d3884..a063d64f8 100644
--- a/qiita_pet/handlers/analysis_handlers/base_handlers.py
+++ b/qiita_pet/handlers/analysis_handlers/base_handlers.py
@@ -27,6 +27,9 @@ def post(self):
         desc = self.get_argument('description')
         mdsi = self.get_argument('merge_duplicated_sample_ids', False)
         metadata = self.request.arguments.get('analysis-metadata', None)
+        # we need to change from bytes to strings
+        if metadata is not None:
+            metadata = [m.decode('utf-8') for m in metadata]
 
         if mdsi in (b'on', 'on'):
             mdsi = True
diff --git a/qiita_pet/handlers/api_proxy/__init__.py b/qiita_pet/handlers/api_proxy/__init__.py
index a00b812af..28c6acb66 100644
--- a/qiita_pet/handlers/api_proxy/__init__.py
+++ b/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__ = "2021.11"
+__version__ = "2022.04"
 
 __all__ = ['prep_template_summary_get_req', 'data_types_get_req',
            'study_get_req', 'sample_template_filepaths_get_req',
diff --git a/qiita_pet/templates/analysis_selected.html b/qiita_pet/templates/analysis_selected.html
index a5915a89f..9543a81b8 100644
--- a/qiita_pet/templates/analysis_selected.html
+++ b/qiita_pet/templates/analysis_selected.html
@@ -72,16 +72,20 @@
           if (is_sample) {
             if (jQuery.inArray(option.text, common_sample_fields) >= 0) {
               option.selected=true;
-              $('#analysis-metadata').append(
-                $('<option>', { value: option.value, text: option.text,
-                                selected: true}));
+              if (!$('#analysis-metadata').val().includes(option.text)) {
+                $('#analysis-metadata').append(
+                  $('<option>', { value: option.value, text: option.text,
+                                  selected: true}));
+              }
             }
           } else {
             if (jQuery.inArray(option.text, common_prep_fields) >= 0) {
               option.selected=true;
-              $('#analysis-metadata').append(
-                $('<option>', { value: option.value, text: option.text,
-                                selected: true}));
+              if (!$('#analysis-metadata').val().includes(option.text)) {
+                $('#analysis-metadata').append(
+                  $('<option>', { value: option.value, text: option.text,
+                                  selected: true}));
+              }
             }
           }
         });
@@ -102,7 +106,7 @@
         var toggle = key == 'selected';
         var selection = object[key];
 
-        if (toggle) {
+        if (toggle && !$('#analysis-metadata').val().includes(selection)) {
           $('#analysis-metadata').append(
             $('<option>', { value: selection, text: selection,
                             selected: true}));
diff --git a/qiita_ware/__init__.py b/qiita_ware/__init__.py
index eae6d2551..17d2f32f9 100644
--- a/qiita_ware/__init__.py
+++ b/qiita_ware/__init__.py
@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2021.11"
+__version__ = "2022.04"
diff --git a/setup.py b/setup.py
index a54a277f8..37100736c 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "2021.11"
+__version__ = "2022.04"
 
 
 classes = """

From 0238908f4867bba786e94a0349bf5651e8b4b96b Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Thu, 7 Apr 2022 15:01:05 -0600
Subject: [PATCH 2/6] improve CHANGELOG.md

---
 CHANGELOG.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index de4d9e070..adec95654 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,8 +8,11 @@ Version 2022.04
 * Updated all available JavaScript libraries, [details here](https://github.com/qiita-spots/qiita/pull/3177).
 * User can select which metadata to use when creating a new analysis, by default only overlapping metadata in all studies is selected.
 * Now we can fully delete users in the backend.
+* Updated documentation to reflect the new EMPO version 2.
 * Fixed outstanding issues to add default workflow to a preparation, [details here](https://github.com/qiita-spots/qiita/issues/3158).
-* Fixed the following issues: [3183](https://github.com/qiita-spots/qiita/issues/3183), [3182](https://github.com/qiita-spots/qiita/issues/3182), [3170](https://github.com/qiita-spots/qiita/issues/3170)
+* Fixed the following issues: [3183](https://github.com/qiita-spots/qiita/issues/3183), [3182](https://github.com/qiita-spots/qiita/issues/3182), [3170](https://github.com/qiita-spots/qiita/issues/3170), [3193](https://github.com/qiita-spots/qiita/pull/3193).
+* We deprecated the use of specimen_id from Qiita; this is no longer required in the backend or the GUI.
+* Fixed the following issues [qp-knight-lab-processing #15](https://github.com/qiita-spots/qp-knight-lab-processing/issues/15), [qp-knight-lab-processing #16](https://github.com/qiita-spots/qp-knight-lab-processing/issues/16), [qp-knight-lab-processing #17](https://github.com/qiita-spots/qp-knight-lab-processing/issues/17), [qp-knight-lab-processing #19](https://github.com/qiita-spots/qp-knight-lab-processing/issues/19), [mg-scripts #60](https://github.com/biocore/mg-scripts/issues/60), [mg-scripts #62](https://github.com/biocore/mg-scripts/issues/62) from the [Knight Lab Sequence Processing Pipeline](https://github.com/qiita-spots/qp-knight-lab-processing).
 
 
 Version 2021.11

From b65b99d88fd4762094b94028cad0df58a6679139 Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Thu, 7 Apr 2022 15:34:19 -0600
Subject: [PATCH 3/6] add future to setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 37100736c..508cf2781 100644
--- a/setup.py
+++ b/setup.py
@@ -102,7 +102,7 @@
       scripts=glob('scripts/*'),
       # making sure that numpy is installed before biom
       setup_requires=['numpy', 'cython'],
-      install_requires=['psycopg2', 'click', 'bcrypt', 'pandas',
+      install_requires=['psycopg2', 'click', 'bcrypt', 'pandas', 'future',
                         'biom-format', 'tornado<6.0', 'toredis', 'redis',
                         'scp', 'pyparsing', 'h5py',  'natsort', 'nose', 'pep8',
                         'networkx', 'humanize', 'wtforms<3.0.0', 'nltk',

From 49cd1815efccccefb39f21744aef3f9c1fde51bf Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Fri, 8 Apr 2022 11:24:24 -0600
Subject: [PATCH 4/6] install biom-format from conda

---
 .github/workflows/qiita-ci.yml | 1 +
 setup.py                       | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml
index 7da130fbd..181970579 100644
--- a/.github/workflows/qiita-ci.yml
+++ b/.github/workflows/qiita-ci.yml
@@ -96,6 +96,7 @@ jobs:
           export REDBIOM_HOST="http://localhost:7379"
 
           pip install . --no-binary redbiom
+          conda install -c conda-forge --yes biom-format
           pwd
           mkdir ~/.qiita_plugins
 
diff --git a/setup.py b/setup.py
index 508cf2781..37100736c 100644
--- a/setup.py
+++ b/setup.py
@@ -102,7 +102,7 @@
       scripts=glob('scripts/*'),
       # making sure that numpy is installed before biom
       setup_requires=['numpy', 'cython'],
-      install_requires=['psycopg2', 'click', 'bcrypt', 'pandas', 'future',
+      install_requires=['psycopg2', 'click', 'bcrypt', 'pandas',
                         'biom-format', 'tornado<6.0', 'toredis', 'redis',
                         'scp', 'pyparsing', 'h5py',  'natsort', 'nose', 'pep8',
                         'networkx', 'humanize', 'wtforms<3.0.0', 'nltk',

From ce6d87bd0110b30d50b3834aa8184340a7b0dec8 Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Fri, 8 Apr 2022 12:57:44 -0600
Subject: [PATCH 5/6] improve CHANGELOG.md [skip ci]

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index adec95654..92d25a7ff 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,12 +6,13 @@ Version 2022.04
 * Moved from Python 3.6 to 3.9.
 * Added support for Pandas 1.4.0, [details here](https://github.com/qiita-spots/qiita/pull/3174).
 * Updated all available JavaScript libraries, [details here](https://github.com/qiita-spots/qiita/pull/3177).
-* User can select which metadata to use when creating a new analysis, by default only overlapping metadata in all studies is selected.
+* Users can select which metadata to use when creating a new analysis, by default only overlapping metadata in all studies is selected.
 * Now we can fully delete users in the backend.
 * Updated documentation to reflect the new EMPO version 2.
 * Fixed outstanding issues to add default workflow to a preparation, [details here](https://github.com/qiita-spots/qiita/issues/3158).
 * Fixed the following issues: [3183](https://github.com/qiita-spots/qiita/issues/3183), [3182](https://github.com/qiita-spots/qiita/issues/3182), [3170](https://github.com/qiita-spots/qiita/issues/3170), [3193](https://github.com/qiita-spots/qiita/pull/3193).
 * We deprecated the use of specimen_id from Qiita; this is no longer required in the backend or the GUI.
+* Moved [qp-fastp-minimap2](https://github.com/qiita-spots/qp-fastp-minimap2/) to per sample parallelization. Now an iSeq processing takes ~20min, while before it took close to 2hrs.
 * Fixed the following issues [qp-knight-lab-processing #15](https://github.com/qiita-spots/qp-knight-lab-processing/issues/15), [qp-knight-lab-processing #16](https://github.com/qiita-spots/qp-knight-lab-processing/issues/16), [qp-knight-lab-processing #17](https://github.com/qiita-spots/qp-knight-lab-processing/issues/17), [qp-knight-lab-processing #19](https://github.com/qiita-spots/qp-knight-lab-processing/issues/19), [mg-scripts #60](https://github.com/biocore/mg-scripts/issues/60), [mg-scripts #62](https://github.com/biocore/mg-scripts/issues/62) from the [Knight Lab Sequence Processing Pipeline](https://github.com/qiita-spots/qp-knight-lab-processing).
 
 

From 1451ed88a4f47125bd9e42d37e3cd3c322baa7e3 Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Fri, 8 Apr 2022 13:13:25 -0600
Subject: [PATCH 6/6] addressing @charles-cowart comment

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 92d25a7ff..e228af36a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,7 @@ Version 2022.04
 * Moved from Python 3.6 to 3.9.
 * Added support for Pandas 1.4.0, [details here](https://github.com/qiita-spots/qiita/pull/3174).
 * Updated all available JavaScript libraries, [details here](https://github.com/qiita-spots/qiita/pull/3177).
-* Users can select which metadata to use when creating a new analysis, by default only overlapping metadata in all studies is selected.
+* Users can select which metadata to use when creating a new analysis. By default only overlapping metadata in all studies is selected.
 * Now we can fully delete users in the backend.
 * Updated documentation to reflect the new EMPO version 2.
 * Fixed outstanding issues to add default workflow to a preparation, [details here](https://github.com/qiita-spots/qiita/issues/3158).