enasequence · corneliusroemer · Oct 7, 2023 · Oct 7, 2023 · Oct 7, 2023 · Oct 7, 2023
diff --git a/conf.py b/conf.py
@@ -63,7 +63,8 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+# 2023-10-08 explicitly set to address warning
+language = 'en_GB'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -106,7 +107,8 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# 2023-10-08: Results in warning if not commented out `WARNING: html_static_path entry '_static' does not exist`
+# html_static_path = ['_static']
 
 
 # -- Options for HTMLHelp output ------------------------------------------
@@ -178,3 +180,4 @@
     '.md': 'markdown',
 }
 
+myst_heading_anchors = 2
diff --git a/faq/archive-generated-analysis-files.rst b/faq/archive-generated-analysis-files.rst
@@ -1,6 +1,6 @@
-=============================
+================================
 Archive Generated Analysis Files
-=============================
+================================
 
 Archive generated analysis files are generated for primary and binned metagenome assemblies. These submissions
 will not have a GCA (assembly accession) or sequence accessions but only ERZ accessions.

diff --git a/faq/archive-generated-files.rst b/faq/archive-generated-files.rst
@@ -1,6 +1,6 @@
-=============================
+===========================
 Archive Generated Run Files
-=============================
+===========================
 
 Whenever possible, ENA provides access to two types of file for each run we
 present: the submitted file(s) and archive-generated file(s). Both are visible

diff --git a/faq/pathogen-subs-guide.rst b/faq/pathogen-subs-guide.rst
@@ -1,5 +1,5 @@
 General Pathogens Submissions Guide
-==================================
+===================================
 
 .. image:: images/pathogens_logo_1.png
  :width: 400

diff --git a/faq/runs.rst b/faq/runs.rst
@@ -260,7 +260,7 @@ To do this:
 7. Remove the 'checksum' value for the errored file(s) and enter the correct value. The checksum is shown in the pink
    box:
 
-.. images:: images/run_errors_md5_edit.png
+.. image:: images/run_errors_md5_edit.png
 
 8. When editing the checksum value, change only the 32-digit string: do not remove the quotation marks, the word
    'checksum', or any other parts of the XML

diff --git a/index.rst b/index.rst
@@ -53,7 +53,7 @@ bottom of the page.
    faq/taxonomy
    faq/taxonomy_requests
    faq/metagenomes
-   faq/missing-values
+   submit/samples/missing-values
    faq/locus_tags
    faq/archive-generated-files
    faq/third_party_tools

diff --git a/retrieval/file-download.rst b/retrieval/file-download.rst
@@ -297,6 +297,7 @@ For private files, configure like this (and then use '-Pmypriv'):
 ::
 
     ascli conf preset update mypriv --url=ssh://fasp.sra.ebi.ac.uk:33001 --username=dcc_name --password=dcc_pass --ts=@json:'{"target_rate_kbps":300000}'
+
 Common Issues
 -------------
 Downloading a large number of records

diff --git a/retrieval/programmatic-access/cram-reference-cache.rst b/retrieval/programmatic-access/cram-reference-cache.rst
@@ -100,6 +100,7 @@ If you wish SAMTools to cache retrieved sequences in addition to caching them in
 **REF_PATH** and **REF_CACHE** environment variables:
 
 .. code-block:: bash
+
    export REF_PATH=<dir>/%2s/%2s/%s:http://<hostname>:<port>/ena/cram/md5/%s
    export REF_CACHE=/<dir>/%2s/%2s/%s
 
@@ -122,13 +123,15 @@ CRAMTools can be instructed to use the Squid cache by defining the following Jav
 .. code-block:: bash
 
    java -DREF_URL_TEMPLATE=http://<hostname>:<port>/ena/cram/md5/%s
+
 where **<hostname>** and **<port>** are the ones used by the Squid server.
 
 8. Testing Squid.
 
 Execute the following command to test the cache:
 
 .. code-block:: bash
+
    curl -v http://<hostname>:<port>/ena/cram/md5/9aff30af7b14df874594c8ed07b279ba | md5
 
 The computed md5 checksum should match the requested entry.  The cache status of the request can be determined by
@@ -143,7 +146,7 @@ and can be one of the following:
 +-----------------+---------------------------------------------------------------------+
 | TCP_HIT/200     | | The requested object is available in the Squid disk cache.        |
 +-----------------+---------------------------------------------------------------------+
-| TCP_MEM_HIT/200 |	The requested object is available in the Squid memory cache.        |
+| TCP_MEM_HIT/200 | | The requested object is available in the Squid memory cache.      |
 +-----------------+---------------------------------------------------------------------+
 
 9. Shut down Squid.

diff --git a/submit/fileprep/reads.md b/submit/fileprep/reads.md
@@ -18,8 +18,8 @@ Multi-fastq data submissions can be made using the programmatic route or
 Webin-CLI. This is done by entering multiple file names and their 
 respective read_type qualifiers. For more information please see:
 
-- [Multi-fastq using Webin-CLI](../reads/webin-cli.html)
-- [Multi-fastq using the programmatic route](../reads/programmatic.html)
+- [Multi-fastq using Webin-CLI](../reads/webin-cli.md)
+- [Multi-fastq using the programmatic route](../reads/programmatic.rst)
 
 ## Other read data
 

diff --git a/submit/fileprep/upload.rst b/submit/fileprep/upload.rst
@@ -64,6 +64,7 @@ To use this program, follow the below instructions in video or text format:
     <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden; max-width: 100%; height: auto;">
         <iframe src="https://www.youtube.com/embed/LjYmhWWGnhM" frameborder="0" allowfullscreen style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"></iframe>
     </div>
+
 |
 
 1.  `Download the Webin File Uploader

diff --git a/submit/general-guide/interactive.rst b/submit/general-guide/interactive.rst
@@ -28,7 +28,7 @@ service.
 
 
 What Can Be Submitted Through Webin Portal?
-==================================
+===========================================
 
 
 Some submissions can be done entirely through Webin Portal, for example you could submit a study comprising only read data

diff --git a/submit/general-guide/programmatic-v2.rst b/submit/general-guide/programmatic-v2.rst
@@ -164,9 +164,9 @@ For example, a submission with one sample object could be submitted like this:
     ]
     }
 
-===========
+============
 Receipt JSON
-===========
+============
 
 The ``success`` attribute in the receipt is ``true`` if the submission was successful and ``false`` if the submission was not successful.
 

diff --git a/submit/general-guide/programmatic.md b/submit/general-guide/programmatic.md
@@ -30,7 +30,7 @@ establising an automated submission pipeline.
 
 ## Webin Rest V2 API
 
-Programmatic submissions can also be made using the new Webin Rest V2 service. This has been developed to address issues such as timeout errors during submissions. The V2 API has been designed to accept submissions at 2 different endpoints, 1 synchronous and 1 asynchronous, depending on the scale of the submission. Please refer to the [Webin Rest V2 documentation](./programmatic-v2.html) to find out more.  
+Programmatic submissions can also be made using the new Webin Rest V2 service. This has been developed to address issues such as timeout errors during submissions. The V2 API has been designed to accept submissions at 2 different endpoints, 1 synchronous and 1 asynchronous, depending on the scale of the submission. Please refer to the [Webin Rest V2 documentation](./programmatic-v2.rst) to find out more.  
 
 ## Upload data files
 

diff --git a/submit/general-guide/webin-cli.md b/submit/general-guide/webin-cli.md
@@ -34,12 +34,12 @@ Webin-CLI has been tested against openjdk version 1.8.0_212. You are recommended
 
 Download openapi JDKs from the below links:
 
-[https://adoptopenjdk.net/?variant=openjdk8&jvmVariant=hotspot](https://adoptopenjdk.net/?variant=openjdk8&jvmVariant=hotspot)
+[https://adoptium.net/en-GB/marketplace/?version=8&arch=any&os=any](https://adoptium.net/en-GB/marketplace/?version=8&arch=any&os=any)
 
 Download Oracle JREs from the below links:
 
-- [ **Latest JRE Version** ](https://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html)
-- [ Older JRE Versions ](https://www.oracle.com/technetwork/java/javase/downloads/java-archive-javase8-2177648.html)
+- [ **Latest JRE Version** ](https://www.oracle.com/java/technologies/downloads/#java8)
+- [ Older JRE Versions ](https://www.oracle.com/java/technologies/javase/javase8-archive-downloads.html)
 
 ## Run the program as a Java jar file
 

diff --git a/submit/reads/webin-cli.md b/submit/reads/webin-cli.md
@@ -352,5 +352,5 @@ variables as in [samtools](http://www.htslib.org/doc/samtools.html).
 
 ## Webin-CLI Validation
 
-When submitting data using the Webin command line interface, your files will be validated and uploaded to your private Webin file upload area in webin.ebi.ac.uk. Any validation error reports are written into the `<outputDir>/<context>/<name>/validate` directory. Read more about validation reports on the [Webin-CLI Submissions](../general-guide/webin-cli.html) section.
+When submitting data using the Webin command line interface, your files will be validated and uploaded to your private Webin file upload area in webin.ebi.ac.uk. Any validation error reports are written into the `<outputDir>/<context>/<name>/validate` directory. Read more about validation reports on the [Webin-CLI Submissions](../general-guide/webin-cli.md) section.
 
diff --git a/submit/study/interactive.rst b/submit/study/interactive.rst
@@ -27,8 +27,6 @@ Once registration is complete, you will be assigned accession numbers.
 You may return to the dashboard and select the 'Studies Report' button to review registered studies.
 
 
-.. _Locus Tag Prefixes
-
 Locus Tag Prefixes
 ==================
 

diff --git a/update/metadata/interactive.rst b/update/metadata/interactive.rst
@@ -1,6 +1,6 @@
-=============================================================
+=======================================================================
 Updating Studies, Samples, Experiments, Runs and Analyses Interactively
-=============================================================
+=======================================================================
 
 
 The `Webin Portal <https://www.ebi.ac.uk/ena/submit/webin/>`_ allows you to edit some of your
@@ -128,7 +128,7 @@ If the submitted file has failed validation, it must be replaced with an identic
 
 
 Analysis Edits
-============
+==============
 
 
 1. Log in to `Webin Portal <https://www.ebi.ac.uk/ena/submit/webin/login>`_ and select the 'Analyses Report' button to be

diff --git a/update/metadata/programmatic-read.md b/update/metadata/programmatic-read.md
@@ -18,9 +18,9 @@ assigned accession number for the correct object to be updated.
 
 Detailed advice on how to programmatically update XMLs
 including instructions for retrieving previously submitted XMLs can be
-found in [Programmatic Submission Options](../../submit/general-guide/programmatic.html).
+found in [Programmatic Submission Options](../../submit/general-guide/programmatic.md).
 Experiment and run XMLs can also be manually edited using the
-[Webin Portal](../../submit/general-guide/submissions-portal.html).
+[Webin Portal](../../submit/general-guide/submissions-portal.rst).
 
 ## Reasons for Updating Experiment XML
 

diff --git a/update/metadata/programmatic-sample.md b/update/metadata/programmatic-sample.md
@@ -18,6 +18,6 @@ assigned accession number for the correct sample to be updated.
 
 Detailed advice on how to programmatically update samples using XML 
 including instructions for retrieving previously submitted Sample XMLs can be 
-found in [Programmatic Submission Options](../../submit/general-guide/programmatic.html).
+found in [Programmatic Submission Options](../../submit/general-guide/programmatic.md).
 Sample XMLs can also be manually edited using the 
-[Webin Portal](../../submit/general-guide/submissions-portal.html).
+[Webin Portal](../../submit/general-guide/submissions-portal.rst).
diff --git a/update/metadata/programmatic-study.md b/update/metadata/programmatic-study.md
@@ -18,6 +18,6 @@ assigned accession number for the correct study to be updated.
 
 Detailed advice on how to programmatically update studies using XML 
 including instructions for retrieving previously submitted Study XMLs can be 
-found in [Programmatic Submission Options](../../submit/general-guide/programmatic.html).
+found in [Programmatic Submission Options](../../submit/general-guide/programmatic.md).
 Study XMLs can also be manually edited using the 
-[Webin Portal](../../submit/general-guide/submissions-portal.html).
+[Webin Portal](../../submit/general-guide/submissions-portal.rst).
-Original file line number
+Diff line change
@@ Expand Up @@
     ::
         ascli conf preset update mypriv --url=ssh://fasp.sra.ebi.ac.uk:33001 --username=dcc_name --password=dcc_pass --ts=@json:'{"target_rate_kbps":300000}'
     Common Issues
     -------------
     Downloading a large number of records
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -352,5 +352,5 @@ variables as in [samtools](http://www.htslib.org/doc/samtools.html).

		## Webin-CLI Validation

		When submitting data using the Webin command line interface, your files will be validated and uploaded to your private Webin file upload area in webin.ebi.ac.uk. Any validation error reports are written into the `<outputDir>/<context>/<name>/validate` directory. Read more about validation reports on the [Webin-CLI Submissions](../general-guide/webin-cli.html) section.
		When submitting data using the Webin command line interface, your files will be validated and uploaded to your private Webin file upload area in webin.ebi.ac.uk. Any validation error reports are written into the `<outputDir>/<context>/<name>/validate` directory. Read more about validation reports on the [Webin-CLI Submissions](../general-guide/webin-cli.md) section.