Merge pull request #3195 from antgonza/2022.04

fixes for 2022.04

Author: charles-cowart

.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
 

CHANGELOG.md

@@ -1,5 +1,21 @@
 # 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).
+* 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).
+
+
 Version 2021.11
 ---------------
 

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"

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",

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")
 

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"

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

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',

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}));

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"

setup.py

@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "2021.11"
+__version__ = "2022.04"
 
 
 classes = """