diff --git a/conf.py b/conf.py index a906ce0e..47ea485c 100755 --- 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 index b525643f..6fb6476f 100644 --- 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 index 06caae14..f79b9dc7 100644 --- 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 index 31418d08..2acb0679 100644 --- 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 index 98125a56..e0f25b2d 100644 --- 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 index 82182627..d280fd83 100755 --- 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 index 7cfeea9a..e0f3b0d3 100644 --- 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 index 6e4e4958..3504aa1e 100644 --- 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=/%2s/%2s/%s:http://:/ena/cram/md5/%s export REF_CACHE=//%2s/%2s/%s @@ -122,6 +123,7 @@ CRAMTools can be instructed to use the Squid cache by defining the following Jav .. code-block:: bash java -DREF_URL_TEMPLATE=http://:/ena/cram/md5/%s + where **** and **** are the ones used by the Squid server. 8. Testing Squid. @@ -129,6 +131,7 @@ where **** and **** are the ones used by the Squid server. Execute the following command to test the cache: .. code-block:: bash + curl -v http://:/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 index e7983e2f..cc87bbde 100644 --- 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 index 37d298f0..37c22b45 100644 --- 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:
+ | 1. `Download the Webin File Uploader diff --git a/submit/general-guide/interactive.rst b/submit/general-guide/interactive.rst index d8eac26b..438d127c 100644 --- 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 index 883e53ad..5abd1ebf 100644 --- 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 index 59218f66..34bbdc8f 100644 --- 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 index 6fb8b362..01d7f3e1 100644 --- 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 index 5ac8d2ec..ac207db7 100644 --- 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 `///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 `///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 index af718cf8..3fdb10b2 100644 --- 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 index d6a9900e..065405ef 100644 --- 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 `_ 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 `_ and select the 'Analyses Report' button to be diff --git a/update/metadata/programmatic-read.md b/update/metadata/programmatic-read.md index da0231fb..57049bd7 100644 --- 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 index b64f3740..3d3fa0b5 100644 --- 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 index 57677a37..a585a664 100644 --- 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).