From df5b9a6755299cf222c6dab45ef4a1bbd2c89330 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 3 Jun 2024 10:41:13 +0200 Subject: [PATCH 1/5] Import onedata blogpost --- news/_posts/2024-06-03-onedata.md | 78 +++++++++++++++++++++++++++++ news/images/galaxy-data-upload.png | Bin 0 -> 40878 bytes 2 files changed, 78 insertions(+) create mode 100644 news/_posts/2024-06-03-onedata.md create mode 100644 news/images/galaxy-data-upload.png diff --git a/news/_posts/2024-06-03-onedata.md b/news/_posts/2024-06-03-onedata.md new file mode 100644 index 0000000000000..23f0503d54a03 --- /dev/null +++ b/news/_posts/2024-06-03-onedata.md @@ -0,0 +1,78 @@ +--- +title: All GTN training data in one basket +contributions: + authorship: + - plushz + funding: + - eurosciencegateway +tags: [esg-wp4, esg] +cover: news/images/galaxy-data-upload.png +coveralt: screenshot of galaxy data upload interface showing a folder named GTN Training Data +layout: news +--- + +As part of the [EuroScienceGateway](https://eurosciencegateway.eu/) and in cooperation with [Onedata](https://onedata.org) and [EGI](https://www.egi.eu/) we are providing all [GTN](https://training.galaxyproject.org/) training data on a publicly accessible [cloud storage](https://datahub.egi.eu/share/2697e33bd34f1870b0961414b8c77753chf583). +Those training datasets are curated, small but meaningful for educational purposes and contain 1530 files with a total size of 170Gb. +An invaluable set of resources for everyone dealing with data science and training. +Please thank the more than [350 contributors to GTN]({% link hall-of-fame.md %}). + +## Accessing GTN Data in the Cloud + +GTN training data is always accessible, annotated and linked for every tutorial. Usually, it's stored in Zenodo, referenced via a DOI. +You can access all GTN training data using several methods: + +1. **Onedata Share** — access without authentication: + + a. Visit the [public share link](https://datahub.egi.eu/share/2697e33bd34f1870b0961414b8c77753chf583) + to browse and download the data via the Onedata Web UI. + + b. Use the public [REST API](https://onedata.org/#/home/api/stable/onezone?anchor=operation/get_shared_data) + to access the data; on the share page (see above) you will find ready-to-use `curl` examples by right-clicking on a file/directory and choosing the **Information** context menu. + +2. **Galaxy Server integration**: access the data on the [European Galaxy server](https://usegalaxy.eu/). Go to the "Upload data" button, select "Choose remote files," and navigate to the GTN repository. + +3. **Configure your own Galaxy server**: to include the GTN data in your Galaxy server, use the following configuration: + + ```yaml + - type: onedata + id: gtn_public_onedata + label: GTN training data + doc: Training data from the Galaxy Training Network (powered by Onedata) + # The following token is a public, read-only token that can be shared. + accessToken: "MDAxY2xvY2F00aW9uIGRhdGFodWIuZWdpLmV1CjAwNmJpZGVudGlmaWVyIDIvbm1kL3Vzci00yNmI4ZTZiMDlkNDdjNGFkN2E3NTU00YzgzOGE3MjgyY2NoNTNhNS9hY3QvMGJiZmY1NWU4NDRiMWJjZGEwNmFlODViM2JmYmRhNjRjaDU00YjYKMDAxNmNpZCBkYXRhLnJlYWRvbmx5CjAwNDljaWQgZGF00YS5wYXRoID00gTHpaa1pUTTROMkl4WmpjMllXVmpOMlU00WWpreU5XWmtNV00ZpT1RKbU1ETXlZMmhoWTJReAowMDJmc2lnbmF00dXJlIIQvnXp01Oey02LnaNwEkFJAyArzhHN8SlXSYFsBbSkqdqCg" + onezoneDomain: "datahub.egi.eu" + ``` + +4. **Onedata clients** — access the data using the public read-only access token and + [Oneclient](https://www.onedata.org/#/home/documentation/21.02/user-guide/oneclient.html) (local POSIX mount) + or [OnedataFS](https://onedata.org/#/home/documentation/21.02/user-guide/onedatafs.html) + ([PyFilesystem](https://www.pyfilesystem.org/) interface), e.g.: + + ```bash + mkdir ~/oneclient + oneclient \ + -H plg-cyfronet-01.datahub.egi.eu \ + -t MDAxY2xvY2F00aW9uIGRhdGFodWIuZWdpLmV1CjAwNmJpZGVudGlmaWVyIDIvbm1kL3Vzci00yNmI4ZTZiMDlkNDdjNGFkN2E3NTU00YzgzOGE3MjgyY2NoNTNhNS9hY3QvMGJiZmY1NWU4NDRiMWJjZGEwNmFlODViM2JmYmRhNjRjaDU00YjYKMDAxNmNpZCBkYXRhLnJlYWRvbmx5CjAwNDljaWQgZGF00YS5wYXRoID00gTHpaa1pUTTROMkl4WmpjMllXVmpOMlU00WWpreU5XWmtNV00ZpT1RKbU1ETXlZMmhoWTJReAowMDJmc2lnbmF00dXJlIIQvnXp01Oey02LnaNwEkFJAyArzhHN8SlXSYFsBbSkqdqCg \ + ~/oneclient + ls ~/oneclient/GTN\ data + ``` + +## What is the GTN Downloader? + +[GTN-Downloader](https://github.com/usegalaxy-eu/gtn-downloader) makes it easier for users to access and organize data from the [Galaxy Training Network (GTN)](https://training.galaxyproject.org/). +The GTN Downloader is a Python script that automates the download of data from GTN tutorials. It goes through the tutorials in the GTN repository, finds `data-library.yaml` files, +and creates a structured directory based on the tutorial names and file contents. + +### Key Features: +- **Automated Data Download**: The script finds `data-library.yaml` files in the GTN repository and downloads the associated data files. +- **Structured Organization**: It creates directories based on the tutorial names and the information in the `data-library.yaml` files, so the files are organized. +- **Download Summary**: It generates a `download-summary.tsv` file, which includes metadata about the downloaded files, a download report (error, success, already downloaded), and the overall size of the files. + +## Seamless Integration with Onedata + +In addition to local downloads, the GTN Downloader can upload data to [Onedata](https://onedata.org), a distributed data management platform. 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zS@F^SCsC!Q9_!m=t!TTXqPVyN8U9;xgs0Hhp@?oN1X71_qGRT>%9-Db5Fq{@e6Q?n zb0uk@JjjAQBJhm%D}1$KCDzaHSKxKQ zSYO?hz%u^SfOea8s8#7gw5q@G?n-Z9#=q;DDK!|opT`;k>r27hBC*+YY_+-scpyI8 z+kHk(S}SSOjT*4j}8 zRjbQ19S=d08m2sz9^PkGtVhhwovI%d2{kbwxpPgAeAhy;E>g8lUy_GpAw$3Vwsbqe zUkDgS#Ifgw-|KPrx`b)G3C!4Ejs0&nGBF!90F?gE|8Z4<{&Iuzx1s*3{ED5bgk|13 zTe$mg1_o)!WhEK*24tbU&0t_YLCe7j#qc@6`oIemR-;&j_^l7*!LMQP(NS6UmYAL3 Pior=A^ofS!7qb2bXUPoA literal 0 HcmV?d00001 From b4843a3f9995ad37f1eabe01f061cde86ab09166 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 3 Jun 2024 10:41:52 +0200 Subject: [PATCH 2/5] own blurb --- news/_posts/2024-06-03-onedata.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/news/_posts/2024-06-03-onedata.md b/news/_posts/2024-06-03-onedata.md index 23f0503d54a03..6d080fbd09507 100644 --- a/news/_posts/2024-06-03-onedata.md +++ b/news/_posts/2024-06-03-onedata.md @@ -1,5 +1,5 @@ --- -title: All GTN training data in one basket +title: All GTN training data are now automatically mirrored via Onedata contributions: authorship: - plushz From 0b150e3a0b2031977c89ea85a686d0c84d0d069e Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 3 Jun 2024 10:48:10 +0200 Subject: [PATCH 3/5] gtn specific section --- news/_posts/2024-06-03-onedata.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/news/_posts/2024-06-03-onedata.md b/news/_posts/2024-06-03-onedata.md index 6d080fbd09507..02cdab3ced05c 100644 --- a/news/_posts/2024-06-03-onedata.md +++ b/news/_posts/2024-06-03-onedata.md @@ -11,11 +11,19 @@ coveralt: screenshot of galaxy data upload interface showing a folder named GTN layout: news --- + + As part of the [EuroScienceGateway](https://eurosciencegateway.eu/) and in cooperation with [Onedata](https://onedata.org) and [EGI](https://www.egi.eu/) we are providing all [GTN](https://training.galaxyproject.org/) training data on a publicly accessible [cloud storage](https://datahub.egi.eu/share/2697e33bd34f1870b0961414b8c77753chf583). Those training datasets are curated, small but meaningful for educational purposes and contain 1530 files with a total size of 170Gb. An invaluable set of resources for everyone dealing with data science and training. Please thank the more than [350 contributors to GTN]({% link hall-of-fame.md %}). +## What does this mean for you? + +- Teachers: if you're a teacher contributing to the GTN, you can now be sure that the datasets you use in your materials are even more accessible and easier to use. +- GTN Users: When following training materials, it'll now be easier to access those same datasets in new locations. +- Galaxy Admins: If you're running a Galaxy server, you can now more easily integrate the GTN data into your server without taking up unnecessary storage space, and still making it available to all your users. + ## Accessing GTN Data in the Cloud GTN training data is always accessible, annotated and linked for every tutorial. Usually, it's stored in Zenodo, referenced via a DOI. From ed1bd34578d9f49254fa476bf802054051df0cae Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 3 Jun 2024 13:02:26 +0200 Subject: [PATCH 4/5] add egi --- ORGANISATIONS.yaml | 6 ++++++ news/_posts/2024-06-03-onedata.md | 1 + 2 files changed, 7 insertions(+) diff --git a/ORGANISATIONS.yaml b/ORGANISATIONS.yaml index 5ed4af5d31b8d..0dec878fd2be7 100644 --- a/ORGANISATIONS.yaml +++ b/ORGANISATIONS.yaml @@ -112,3 +112,9 @@ jetstream2: url: https://jetstream-cloud.org/ avatar: https://jetstream-cloud.org/images/home/jetstream-2.png github: false + +egi: + name: EGI + url: https://www.egi.eu/ + avatar: https://cdn.egi.eu/app/uploads/2021/11/egi-logo.svg + github: false diff --git a/news/_posts/2024-06-03-onedata.md b/news/_posts/2024-06-03-onedata.md index 02cdab3ced05c..6afca01812971 100644 --- a/news/_posts/2024-06-03-onedata.md +++ b/news/_posts/2024-06-03-onedata.md @@ -5,6 +5,7 @@ contributions: - plushz funding: - eurosciencegateway + - egi tags: [esg-wp4, esg] cover: news/images/galaxy-data-upload.png coveralt: screenshot of galaxy data upload interface showing a folder named GTN Training Data From 78739a7d08456c39dd7d3ce601c9a7f3b52be82f Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 3 Jun 2024 13:12:54 +0200 Subject: [PATCH 5/5] fix lint --- CONTRIBUTORS.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 46cf9ce427f90..b057220c866f1 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -120,6 +120,13 @@ almahmoud: name: Alex Mahmoud joined: 2019-06 +andreacabibbe: + name: Andrea Cabibbe + affiliations: + - irccs + github: false + joined: 2024-06 + andreasrichter: name: Andreas Richter github: false