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Versioned resources copyedits #178

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4 changes: 4 additions & 0 deletions redirects.yml
Original file line number Diff line number Diff line change
Expand Up @@ -190,3 +190,7 @@
- type: page
from_url: /reference/style.html
to_url: /reference/documentation-style-guide.html

- type: page
from_url: /guides/versions.html
to_url: /guides/snapshots.html
24 changes: 12 additions & 12 deletions src/guides/versions.rst → src/guides/snapshots.rst
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
=================================
Viewing previous versions of data
=================================
=========================
Viewing previous analyses
=========================


.. contents:: Sections in this document
Expand Down Expand Up @@ -36,19 +36,19 @@ will load the dataset that was the latest available at that particular date.
Tanglegrams to compare changes
------------------------------

Using tanglegrams allows us to easily view two different versions of the same
Using tanglegrams allows us to easily view two different snapshots of the same
dataset side-by-side. Using the above examples we can view the latest dataset
against the one from the middle of 2023 via the URL
`flu/seasonal/h3n2/ha/6y:flu/seasonal/h3n2/ha/6y@2023-07-01
<https://nextstrain.org/flu/seasonal/h3n2/ha/6y:flu/seasonal/h3n2/ha/6y@2023-07-01>`__.
Here's a screenshot of this taken in early January 2024, allowing us to see the
expansion of clade 2a.3a.1 over the past 6 months:

.. image:: ../images/versions-tanglegram-h3n2.jpg
.. image:: ../images/snapshots-tanglegram-h3n2.jpg
:alt: Tanglegram of flu/seasonal/h3n2/ha/6y:flu/seasonal/h3n2/ha/6y@2023-07-01

Over time, the data shown by this URL link will start to change as we update the
latest version, but by versioning both datasets we can preserve this exact view
latest snapshot, but by dating both datasets we can preserve this exact view
into the data:
`flu/seasonal/h3n2/ha/6y@2024-01-03:flu/seasonal/h3n2/ha/6y@2023-07-01
<https://nextstrain.org/flu/seasonal/h3n2/ha/6y@2024-01-03:flu/seasonal/h3n2/ha/6y@2023-07-01>`__.
Expand All @@ -57,7 +57,7 @@ into the data:
SARS-CoV-2 datestamped datasets
-------------------------------

Prior to the functionality described here we exposed dated versions of some of
Prior to the functionality described here we exposed dated snapshots of some of
our datasets by including the YYYY-MM-DD in the URL without the ``@`` character,
i.e. the date string was part of the dataset name. This functionality is now
superseded by the new URL syntax described here, and we may stop producing these
Expand Down Expand Up @@ -100,24 +100,24 @@ able to provide this functionality. When files are "deleted" from a versioned
bucket, the normal behaviour is to preserve the file but add a `delete marker
<https://docs.aws.amazon.com/AmazonS3/latest/userguide/DeleteMarker.html>`__.
When looking back at versions over time, we interpret the intended behaviour of
a delete marker as removing the then-latest file from history, so it wont be
a delete marker as removing the then-latest file from history, so it won't be
available via any ``@YYYY-MM-DD`` value.

.. image:: ../images/delete-markers.png
.. image:: ../images/snapshots-delete-markers.png


What about if the URL changed over time?
----------------------------------------

We've often changed the URL which (core) datasets appear at, for instance we
recently changed the URL for `/dengue/denv1
recently changed the URL for `dengue/denv1
<https://nextstrain.org/dengue/denv1>`__ to `dengue/denv1/genome
<https://nextstrain.org/dengue/denv1/genome>`__, with the former now redirecting
to the latter. The result of this is that the earliest available
``dengue/denv1/genome`` dataset is from 2024-01-03, despite DENV1 datasets being
available since January 2019.

We have plans to expose these versions - see `this issue
We have plans to expose these snapshots - see `this issue
<https://github.com/nextstrain/nextstrain.org/issues/777>`__ for progress here.


Expand All @@ -139,6 +139,6 @@ meta+tree JSONs in the case of v1 datasets).
How far back does this go?
--------------------------

The oldest versioned dataset `is a H3N2 dataset from August 2018
The oldest dataset snapshot `is a H3N2 dataset from August 2018
<https://nextstrain.org/flu/seasonal/h3n2/ha/3y@2018-08-01>`__. While Nextstrain
datasets existed before then, we didn't have versioning enabled.
2 changes: 1 addition & 1 deletion src/index.rst
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Expand Up @@ -68,9 +68,9 @@ team and other Nextstrain users provide assistance. For private inquiries,
Bioinformatics <guides/bioinformatics/index>
Sharing analyses <guides/share/index>
Communicating scientific insights <guides/communicate/index>
Viewing previous analyses <guides/snapshots>
Managing an installation <guides/manage-installation>
Contributing <guides/contribute/index>
Viewing previous versions <guides/versions>

.. toctree::
:maxdepth: 1
Expand Down
6 changes: 3 additions & 3 deletions src/learn/about.rst
Original file line number Diff line number Diff line change
Expand Up @@ -25,9 +25,9 @@ snapshots of evolving pathogen populations such as `SARS-CoV-2
We use interactive visualizations to enable exploration of curated datasets and
analyses which are continually updated when new genomes are available. This
offers a powerful pathogen surveillance tool to virologists, epidemiologists,
public health officials, and community scientists. In many cases old versions of
these analyses are able to be easily accessed, see :doc:`viewing previous versions
</guides/versions>` for more.
public health officials, and community scientists. In many cases old snapshots of
these analyses are able to be easily accessed, see :doc:`viewing previous analyses
</guides/snapshots>` for more.

.. rubric:: Open-source software

Expand Down