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Merge pull request #3121 from antgonza/2021.07
2021.07
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‎CHANGELOG.md

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# Qiita changelog
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Version 2021.07
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---------------
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* Added a new "Add Default Workflow" button to the preparation tab so we automatically add all the "recommended" steps in a preparation based on our workflows.
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* New Preparation Listing GUI + searching within preparation types, thank you @AmandaBirmingham!
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* We limit the parameters displayed to the user per command based on which have already been run successfully; for example if a preparation has already a "Trim 100" job, this option will not be shown.
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* Re-added Coveralls to Qiita and removed codecov.
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* We are limiting the number of samples in a [preparation file to 800](https://qiita.ucsd.edu/static/doc/html/faq.html#how-should-i-split-my-samples-within-preparations).
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* Added User.update_email which allows to update a Users email.
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* Fixed the following issues: [#3113](https://github.com/qiita-spots/qiita/issues/3113), and [#3079](https://github.com/qiita-spots/qiita/issues/3079).
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Version 2021.05
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---------------
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‎README.rst

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.. |Build Status| image:: https://github.com/qiita-spots/qiita/actions/workflows/qiita-ci.yml/badge.svg
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:target: https://github.com/qiita-spots/qiita/actions/workflows/qiita-ci.yml
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.. |Coverage Status| image:: https://coveralls.io/repos/github/qiita-spots/qiita/badge.svg?branch=master
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.. |Coverage Status| image:: https://coveralls.io/repos/github/qiita-spots/qiita/badge.svg?branch=dev
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:target: https://coveralls.io/github/qiita-spots/qiita?branch=master

‎qiita_core/__init__.py

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# The full license is in the file LICENSE, distributed with this software.
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# -----------------------------------------------------------------------------
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__version__ = "2021.05"
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__version__ = "2021.07"

‎qiita_db/__init__.py

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from . import user
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from . import processing_job
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__version__ = "2021.05"
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__version__ = "2021.07"
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__all__ = ["analysis", "artifact", "archive", "base", "commands",
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"environment_manager", "exceptions", "investigation", "logger",

‎qiita_pet/__init__.py

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# The full license is in the file LICENSE, distributed with this software.
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# -----------------------------------------------------------------------------
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__version__ = "2021.05"
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__version__ = "2021.07"

‎qiita_pet/handlers/api_proxy/__init__.py

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from .user import (user_jobs_get_req)
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from .util import check_access, check_fp
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__version__ = "2021.05"
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__version__ = "2021.07"
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__all__ = ['prep_template_summary_get_req', 'data_types_get_req',
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'study_get_req', 'sample_template_filepaths_get_req',

‎qiita_pet/static/js/networkVue.js

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'<td><small>Job status (circles):</small></td>' +
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'<td>' + circle_statuses.join('') + '</td>' +
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'<td rowspan="2" width="20px">&nbsp;</td>' +
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'<td rowspan="2">' +
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'<td rowspan="2">&nbsp;&nbsp;&nbsp;</td>' +
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'<td rowspan="2" align="center">' +
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'<a class="btn btn-success form-control" id="add-default-workflow"><span class="glyphicon glyphicon-flash"></span> Add Default Workflow</a>' +
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"<br/><br/><a href='https://qiita.ucsd.edu/workflows/' target='_blank'> "+
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'<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-exclamation-triangle" viewBox="0 0 16 16">' +
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'<path d="M7.938 2.016A.13.13 0 0 1 8.002 2a.13.13 0 0 1 .063.016.146.146 0 0 1 .054.057l6.857 11.667c.036.06.035.124.002.183a.163.163 0 0 1-.054.06.116.116 0 0 ' +
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'1-.066.017H1.146a.115.115 0 0 1-.066-.017.163.163 0 0 1-.054-.06.176.176 0 0 1 .002-.183L7.884 2.073a.147.147 0 0 1 .054-.057zm1.044-.45a1.13 1.13 0 0 0-1.96 0L.165 ' +
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'13.233c-.457.778.091 1.767.98 1.767h13.713c.889 0 1.438-.99.98-1.767L8.982 1.566z"></path>' +
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'<path d="M7.002 12a1 1 0 1 1 2 0 1 1 0 0 1-2 0zM7.1 5.995a.905.905 0 1 1 1.8 0l-.35 3.507a.552.552 0 0 1-1.1 0L7.1 5.995z"></path>' +
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'</svg>' +
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" Important note about Default Workflow</a>" +
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'</td>' +
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'</tr>' +
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'<tr>' +

‎qiita_pet/templates/workflows.html

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{% block content %}
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{% if workflows %}
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<h3>Recommended Workflows</h3>
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<h3>Recommended Default Workflows</h3>
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<div class="row">
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<div class="col-sm-10">
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In this page you will find our recommendations on how to processes each data type available in Qiita and the minimum processing requirements to make your data public.
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<br/><br/>
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For convenience, there is an "Add Default Workflow" button for each preparation that will add the recommended workflow steps for your raw data which then you can process.
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It is important to note however that some steps in this default workflow will not work with all raw data; for example, for target gene the workflow is based on the
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default Earth Microbiome Project protocol and so assumes the uploaded data are multiplexed sequences with the reversed barcodes in your mapping file and index sequence
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file (<a href="https://earthmicrobiome.org/protocols-and-standards/" target="_blank">see here</a> for more details). Thus, if the protocol does not apply to your data
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you can still use the Default Workflow, however, you should first manually process your data using the appropriate steps until you have a defined step; in our example,
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demultiplexed your reads. After demultiplexing the Default Workflow is safe to use with any protocol.
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<br/><br/>
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If you have already manually performed one of the processing steps in the Defaul Workflow pipeline, the "Add Default Workflow" button will not re-select those steps but
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instead will only select any remaining steps that have not been completed. You can also add additional workflows on top of the recommended Default Workflow at any time.
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<br/><br/>
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Note that this is not a full inclusive list of data types accepted by Qiita but only those that have a defined workflow.
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</div>
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</div>
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<h5>Hover on the spheres to get more information</h5>
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{% for i, w in enumerate(workflows) %}
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<div class="row">
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<div class="col-sm-7" style="background-color: #DCDCDC; height: 650px" id="workflow_{{i}}"></div>

‎qiita_ware/__init__.py

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# The full license is in the file LICENSE, distributed with this software.
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# -----------------------------------------------------------------------------
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__version__ = "2021.05"
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__version__ = "2021.07"

‎setup.py

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from setuptools import setup
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from glob import glob
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__version__ = "2021.07"
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classes = """

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