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Trial Metadata Upload #5248

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Trial Metadata Upload #5248

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fb11da8
Trial Metadata: Upload UI
dwaring87 Dec 6, 2024
36ffd7c
Trial Metadata: update usage instructions
dwaring87 Dec 9, 2024
f69f968
Merge branch 'master' into topic/batch_update_trials
dwaring87 Dec 9, 2024
4433fa5
Trial Metadata: start of AJAX function to handle file upload
dwaring87 Dec 9, 2024
d77f88a
Trial Metadata: add upload plugin to verify & parse data
dwaring87 Dec 10, 2024
2918ff5
Trial Metadata: add update_metadata function to CXGN::Project
dwaring87 Dec 12, 2024
925b76d
Trial Metadata: update trials from file
dwaring87 Dec 12, 2024
9105394
Trial Tree Folders: add timeout to avoid race conditions with the wor…
dwaring87 Dec 12, 2024
005a8ed
Trial Metadata: refresh page when finished
dwaring87 Dec 12, 2024
f61188d
Trial Metadata: add validation check for new trial name
dwaring87 Dec 12, 2024
ef599fc
Trial Metadata: add design_type to update_metadata function
dwaring87 Dec 13, 2024
3a352a4
Tests: Add tests for updating trial metadata with files
dwaring87 Dec 13, 2024
452a1f2
Docs: Add section on updating trial metadata
dwaring87 Dec 13, 2024
e89e0ee
Tests: fix trial metadata test
dwaring87 Dec 13, 2024
a0807fb
update bookdown docs
invalid-email-address Dec 13, 2024
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5 changes: 3 additions & 2 deletions docs/404.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-07-22" />
<meta name="date" content="2024-12-13" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="10.2.10" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-tissue-sample-entries-to-your-trial"><i class="fa fa-check"></i><b>10.2.10</b> Adding Tissue Sample Entries To Your Trial</a></li>
<li class="chapter" data-level="10.2.11" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-gps-coordinates-for-plots"><i class="fa fa-check"></i><b>10.2.11</b> Uploading GPS Coordinates For Plots</a></li>
<li class="chapter" data-level="10.2.12" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-additional-files-to-trial"><i class="fa fa-check"></i><b>10.2.12</b> Uploading Additional Files To Trial</a></li>
<li class="chapter" data-level="10.2.13" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.2.13</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="managing-field-trials.html"><a href="managing-field-trials.html#updating-trial-data"><i class="fa fa-check"></i><b>10.3</b> Updating Trial Data</a></li>
<li class="chapter" data-level="10.4" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.4</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html"><i class="fa fa-check"></i><b>11</b> Managing Genotyping Plates</a>
<ul>
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43 changes: 41 additions & 2 deletions docs/BreedbaseManual.tex
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\title{User Manual of Breedbase}
\author{Breedbase team}
\date{2024-07-22}
\date{2024-12-13}

\begin{document}
\maketitle
Expand Down Expand Up @@ -1752,8 +1752,47 @@ \subsection{Uploading Additional Files To Trial}\label{uploading-additional-file

\begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_upload_additional_file_info} \end{center}

\hypertarget{updating-trial-data}{%
\section{Updating Trial Data}\label{updating-trial-data}}

To updated the trial-level metadata (such as the planting date, design type, description, etc) of one or more existing trials, click the ``Update Existing Trial(s)'' button from the Manage \textgreater{} Field Trials page. This upload can also be used to rename trials or move trials to a different breeding program. In order to update a trial, you must be a curator or a submitter (that is associated with the breeding program of the trials).

\begin{center}\includegraphics[width=0.95\linewidth]{assets/images/update_trial_metadata} \end{center}

Here you can upload a file that contains the new metadata for the existing trials in the database. The first column is labeled `trial\_name' and includes the name of the existing trial. Additional columns can be included for the metadata you want to update. Any columns not included in the file or values left blank will leave the existing metadata unchanged. The columns that can be included are:

\begin{itemize}
\tightlist
\item
new\_trial\_name: A new name for the trial, must not already exist in the database
\item
breeding\_program: The name of breeding program that managed the trial, must exist in the database.
\item
location: The name or abbreviation of the location where the trial was held, must exist in the database.
\item
year: The year the trial was held.
\item
transplanting\_date: The transplanting\_date of the trial was conducted. Date in YYYY-MM-DD format or `remove' to remove the date
\item
planting\_date: Date of Planting in YYYY-MM-DD format or `remove' to remove the date
\item
harvest\_date: Date of Harvest in YYYY-MM-DD format or `remove' to remove the date
\item
design\_type: The shorthand for the design type, must exist in the database. Possible values include CRD: Completely Randomized Design, RCBD: Randomized Complete Block Design, RRC: Resolvable Row-Column, DRRC: Doubly-Resolvable Row-Column, ARC: Augmented Row-Column, Alpha: Alpha Lattice Design, Lattice: Lattice Design, Augmented: Augmented Design, MAD: Modified Augmented Design, greenhouse: undesigned Nursery/Greenhouse, splitplot: Split Plot, p-rep: Partially Replicated, Westcott: Westcott Design
\item
description: Additional text with any other relevant information about the trial.
\item
trial\_type: The name of the trial type, must exist in the database. Possible values include Seedling Nursery, phenotyping\_trial, Advanced Yield Trial, Preliminary Yield Trial, Uniform Yield Trial, Variety Release Trial, Clonal Evaluation, genetic\_gain\_trial, storage\_trial, heterosis\_trial, health\_status\_trial, grafting\_trial, Screen House, Seed Multiplication, crossing\_block\_trial, Specialty Trial
\item
plot\_width: plot width in meters
\item
plot\_length: plot length in meters
\item
field\_size: field size in hectares
\end{itemize}

\hypertarget{deleting-trial-data}{%
\subsection{Deleting Trial Data}\label{deleting-trial-data}}
\section{Deleting Trial Data}\label{deleting-trial-data}}

To delete a trial data, click on the ``Delete trial data'' section. There are links to delete traits, layout and trial entry data.

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5 changes: 3 additions & 2 deletions docs/basic-website-usage.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-07-22" />
<meta name="date" content="2024-12-13" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="10.2.10" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-tissue-sample-entries-to-your-trial"><i class="fa fa-check"></i><b>10.2.10</b> Adding Tissue Sample Entries To Your Trial</a></li>
<li class="chapter" data-level="10.2.11" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-gps-coordinates-for-plots"><i class="fa fa-check"></i><b>10.2.11</b> Uploading GPS Coordinates For Plots</a></li>
<li class="chapter" data-level="10.2.12" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-additional-files-to-trial"><i class="fa fa-check"></i><b>10.2.12</b> Uploading Additional Files To Trial</a></li>
<li class="chapter" data-level="10.2.13" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.2.13</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="managing-field-trials.html"><a href="managing-field-trials.html#updating-trial-data"><i class="fa fa-check"></i><b>10.3</b> Updating Trial Data</a></li>
<li class="chapter" data-level="10.4" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.4</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html"><i class="fa fa-check"></i><b>11</b> Managing Genotyping Plates</a>
<ul>
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5 changes: 3 additions & 2 deletions docs/data-analysis-tools.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-07-22" />
<meta name="date" content="2024-12-13" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
Expand Down Expand Up @@ -185,8 +185,9 @@
<li class="chapter" data-level="10.2.10" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-tissue-sample-entries-to-your-trial"><i class="fa fa-check"></i><b>10.2.10</b> Adding Tissue Sample Entries To Your Trial</a></li>
<li class="chapter" data-level="10.2.11" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-gps-coordinates-for-plots"><i class="fa fa-check"></i><b>10.2.11</b> Uploading GPS Coordinates For Plots</a></li>
<li class="chapter" data-level="10.2.12" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-additional-files-to-trial"><i class="fa fa-check"></i><b>10.2.12</b> Uploading Additional Files To Trial</a></li>
<li class="chapter" data-level="10.2.13" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.2.13</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="managing-field-trials.html"><a href="managing-field-trials.html#updating-trial-data"><i class="fa fa-check"></i><b>10.3</b> Updating Trial Data</a></li>
<li class="chapter" data-level="10.4" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.4</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html"><i class="fa fa-check"></i><b>11</b> Managing Genotyping Plates</a>
<ul>
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7 changes: 4 additions & 3 deletions docs/index.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-07-22" />
<meta name="date" content="2024-12-13" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
Expand Down Expand Up @@ -185,8 +185,9 @@
<li class="chapter" data-level="10.2.10" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-tissue-sample-entries-to-your-trial"><i class="fa fa-check"></i><b>10.2.10</b> Adding Tissue Sample Entries To Your Trial</a></li>
<li class="chapter" data-level="10.2.11" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-gps-coordinates-for-plots"><i class="fa fa-check"></i><b>10.2.11</b> Uploading GPS Coordinates For Plots</a></li>
<li class="chapter" data-level="10.2.12" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-additional-files-to-trial"><i class="fa fa-check"></i><b>10.2.12</b> Uploading Additional Files To Trial</a></li>
<li class="chapter" data-level="10.2.13" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.2.13</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="managing-field-trials.html"><a href="managing-field-trials.html#updating-trial-data"><i class="fa fa-check"></i><b>10.3</b> Updating Trial Data</a></li>
<li class="chapter" data-level="10.4" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.4</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html"><i class="fa fa-check"></i><b>11</b> Managing Genotyping Plates</a>
<ul>
Expand Down Expand Up @@ -357,7 +358,7 @@ <h1>
<div id="header">
<h1 class="title">User Manual of Breedbase</h1>
<p class="author"><em>Breedbase team</em></p>
<p class="date"><em>2024-07-22</em></p>
<p class="date"><em>2024-12-13</em></p>
</div>
<div id="introduction" class="section level1 unnumbered hasAnchor">
<h1>Introduction<a href="index.html#introduction" class="anchor-section" aria-label="Anchor link to header"></a></h1>
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-07-22" />
<meta name="date" content="2024-12-13" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="10.2.10" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-tissue-sample-entries-to-your-trial"><i class="fa fa-check"></i><b>10.2.10</b> Adding Tissue Sample Entries To Your Trial</a></li>
<li class="chapter" data-level="10.2.11" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-gps-coordinates-for-plots"><i class="fa fa-check"></i><b>10.2.11</b> Uploading GPS Coordinates For Plots</a></li>
<li class="chapter" data-level="10.2.12" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-additional-files-to-trial"><i class="fa fa-check"></i><b>10.2.12</b> Uploading Additional Files To Trial</a></li>
<li class="chapter" data-level="10.2.13" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.2.13</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="managing-field-trials.html"><a href="managing-field-trials.html#updating-trial-data"><i class="fa fa-check"></i><b>10.3</b> Updating Trial Data</a></li>
<li class="chapter" data-level="10.4" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.4</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html"><i class="fa fa-check"></i><b>11</b> Managing Genotyping Plates</a>
<ul>
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-07-22" />
<meta name="date" content="2024-12-13" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="10.2.10" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-tissue-sample-entries-to-your-trial"><i class="fa fa-check"></i><b>10.2.10</b> Adding Tissue Sample Entries To Your Trial</a></li>
<li class="chapter" data-level="10.2.11" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-gps-coordinates-for-plots"><i class="fa fa-check"></i><b>10.2.11</b> Uploading GPS Coordinates For Plots</a></li>
<li class="chapter" data-level="10.2.12" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-additional-files-to-trial"><i class="fa fa-check"></i><b>10.2.12</b> Uploading Additional Files To Trial</a></li>
<li class="chapter" data-level="10.2.13" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.2.13</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="managing-field-trials.html"><a href="managing-field-trials.html#updating-trial-data"><i class="fa fa-check"></i><b>10.3</b> Updating Trial Data</a></li>
<li class="chapter" data-level="10.4" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.4</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html"><i class="fa fa-check"></i><b>11</b> Managing Genotyping Plates</a>
<ul>
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5 changes: 3 additions & 2 deletions docs/managing-breeding-programs.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-07-22" />
<meta name="date" content="2024-12-13" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="10.2.10" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-tissue-sample-entries-to-your-trial"><i class="fa fa-check"></i><b>10.2.10</b> Adding Tissue Sample Entries To Your Trial</a></li>
<li class="chapter" data-level="10.2.11" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-gps-coordinates-for-plots"><i class="fa fa-check"></i><b>10.2.11</b> Uploading GPS Coordinates For Plots</a></li>
<li class="chapter" data-level="10.2.12" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-additional-files-to-trial"><i class="fa fa-check"></i><b>10.2.12</b> Uploading Additional Files To Trial</a></li>
<li class="chapter" data-level="10.2.13" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.2.13</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="managing-field-trials.html"><a href="managing-field-trials.html#updating-trial-data"><i class="fa fa-check"></i><b>10.3</b> Updating Trial Data</a></li>
<li class="chapter" data-level="10.4" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.4</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html"><i class="fa fa-check"></i><b>11</b> Managing Genotyping Plates</a>
<ul>
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-07-22" />
<meta name="date" content="2024-12-13" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="10.2.10" data-path="managing-field-trials.html"><a href="managing-field-trials.html#adding-tissue-sample-entries-to-your-trial"><i class="fa fa-check"></i><b>10.2.10</b> Adding Tissue Sample Entries To Your Trial</a></li>
<li class="chapter" data-level="10.2.11" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-gps-coordinates-for-plots"><i class="fa fa-check"></i><b>10.2.11</b> Uploading GPS Coordinates For Plots</a></li>
<li class="chapter" data-level="10.2.12" data-path="managing-field-trials.html"><a href="managing-field-trials.html#uploading-additional-files-to-trial"><i class="fa fa-check"></i><b>10.2.12</b> Uploading Additional Files To Trial</a></li>
<li class="chapter" data-level="10.2.13" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.2.13</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="managing-field-trials.html"><a href="managing-field-trials.html#updating-trial-data"><i class="fa fa-check"></i><b>10.3</b> Updating Trial Data</a></li>
<li class="chapter" data-level="10.4" data-path="managing-field-trials.html"><a href="managing-field-trials.html#deleting-trial-data"><i class="fa fa-check"></i><b>10.4</b> Deleting Trial Data</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="managing-genotyping-plates.html"><a href="managing-genotyping-plates.html"><i class="fa fa-check"></i><b>11</b> Managing Genotyping Plates</a>
<ul>
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