From 541bcc88f4ffac4c8324a9e3091d7008edea8e37 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Wed, 9 Oct 2024 10:13:00 +1100 Subject: [PATCH 01/11] branch for tracking changes --- tools/aarnetfilesender/macros.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/aarnetfilesender/macros.xml b/tools/aarnetfilesender/macros.xml index 8e445cce..1110f95d 100644 --- a/tools/aarnetfilesender/macros.xml +++ b/tools/aarnetfilesender/macros.xml @@ -1,6 +1,6 @@ v3.0.0 - 1 + 2 22.05 From c0e6ceb5350e6780dbb75cf743bcb496d275a6ca Mon Sep 17 00:00:00 2001 From: "michael.dsilva" Date: Mon, 14 Oct 2024 09:56:40 +1100 Subject: [PATCH 02/11] change email from to be users email --- tools/aarnetfilesender/filesender.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml index 2b8c8c2d..1f0e56d4 100644 --- a/tools/aarnetfilesender/filesender.xml +++ b/tools/aarnetfilesender/filesender.xml @@ -34,7 +34,7 @@ mkdir filestosend && ln -s "$file" "filestosend/${file.element_identifier}" && #end for -filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f "galaxy-no-reply@usegalaxy.org.au" -r '$to' filestosend >$output 2>&1 +filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f '$__user_email__' -r '$to' filestosend >$output 2>&1 ]]> From e4794161540baab34d341ef02c3075ba22170ed8 Mon Sep 17 00:00:00 2001 From: "michael.dsilva" Date: Mon, 14 Oct 2024 10:12:24 +1100 Subject: [PATCH 03/11] more accurate description --- tools/aarnetfilesender/filesender.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml index 1f0e56d4..a1c164ed 100644 --- a/tools/aarnetfilesender/filesender.xml +++ b/tools/aarnetfilesender/filesender.xml @@ -1,5 +1,5 @@ - transfer files to AARNet's FileSender Service + transfer files with AARNet's FileSender Service macros.xml From ab259e1716203f0ed004dc737305fa3735133550 Mon Sep 17 00:00:00 2001 From: "michael.dsilva" Date: Mon, 14 Oct 2024 10:56:00 +1100 Subject: [PATCH 04/11] filesender: Set email subject to say it is from Galaxy --- tools/aarnetfilesender/filesender.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml index a1c164ed..bd57d1e2 100644 --- a/tools/aarnetfilesender/filesender.xml +++ b/tools/aarnetfilesender/filesender.xml @@ -34,7 +34,7 @@ mkdir filestosend && ln -s "$file" "filestosend/${file.element_identifier}" && #end for -filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f '$__user_email__' -r '$to' filestosend >$output 2>&1 +filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f '$__user_email__' -r '$to' -s 'Data sent from Galaxy Australia' filestosend >$output 2>&1 ]]> From f4948dfcea25ef73c99b9fac06cd0e4fc1747e0a Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Tue, 15 Oct 2024 09:00:49 +1100 Subject: [PATCH 05/11] @madsi1m just bc it's on the global toolshed --- .gitignore | 1 + tools/aarnetfilesender/filesender.xml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 2b65032a..87fbe02d 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ tools/alphafold/output venv tool_test_output.* +.Rproj.user diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml index bd57d1e2..10c5bce7 100644 --- a/tools/aarnetfilesender/filesender.xml +++ b/tools/aarnetfilesender/filesender.xml @@ -34,7 +34,7 @@ mkdir filestosend && ln -s "$file" "filestosend/${file.element_identifier}" && #end for -filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f '$__user_email__' -r '$to' -s 'Data sent from Galaxy Australia' filestosend >$output 2>&1 +filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f '$__user_email__' -r '$to' -s 'Data sent from Galaxy' filestosend >$output 2>&1 ]]> From 4876da002bc204ee4a16853eb719a911f065039f Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Tue, 15 Oct 2024 09:03:35 +1100 Subject: [PATCH 06/11] gitignore --- .gitignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitignore b/.gitignore index 87fbe02d..2b65032a 100644 --- a/.gitignore +++ b/.gitignore @@ -2,4 +2,3 @@ tools/alphafold/output venv tool_test_output.* -.Rproj.user From b7f8f542c891079b0bdaef253374c20cf7f2657f Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Mon, 21 Oct 2024 16:11:26 +1100 Subject: [PATCH 07/11] initial help text --- tools/aarnetfilesender/filesender.xml | 32 ++++++++++++++++++++++----- 1 file changed, 26 insertions(+), 6 deletions(-) diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml index 10c5bce7..acc8a82a 100644 --- a/tools/aarnetfilesender/filesender.xml +++ b/tools/aarnetfilesender/filesender.xml @@ -37,7 +37,7 @@ mkdir filestosend && filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f '$__user_email__' -r '$to' -s 'Data sent from Galaxy' filestosend >$output 2>&1 ]]> - + @@ -62,12 +62,32 @@ filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/res -**What it does** - Send dataset(s) from Galaxy to anyone via AARNet's FileSender service. + **What it does** -**Remarks** - This tool leverages AARNet's FileSender (https://filesender.aarnet.edu.au) - to send files out of Galaxy. + Uses `AARNet’s FileSender service`_ to send dataset(s) from Galaxy. The + recipient will receive an email with a link to download the files. + + **Who can use it** + + AARNet FileSender is available to all institutions affiliated with the + `Australian Access Federation (AAF)`_. You can use your institution + login details to access and use FileSender. + + **How to connect your Galaxy account to FileSender** + + To send files from Galaxy you will need to connect your Galaxy account + to FileSender. This is done by entering you FileSender API key into your + Galaxy user profile. + + 1. Copy your API key from the “API Secret” section on the FileSender “My + Profile” page. See the `AARNet Knowledge Base`_ for more information. + 2. In Galaxy, add your API key to the “AARNet FileSender API Key” field + in User > Preferences > Manage Information. Your AARNet FileSender + Username is the email address you used to log in to FileSender. + + .. _AARNet’s FileSender service: https://filesender.aarnet.edu.au + .. _Australian Access Federation (AAF): https://aaf.edu.au/subscribers/ + .. _AARNet Knowledge Base: https://support.aarnet.edu.au/hc/en-us/articles/235972948-FileSender-API From ca1c769a0fe611036c2e300544824c5521416770 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Mon, 21 Oct 2024 16:15:39 +1100 Subject: [PATCH 08/11] readme --- tools/aarnetfilesender/filesender.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml index acc8a82a..8cbb8953 100644 --- a/tools/aarnetfilesender/filesender.xml +++ b/tools/aarnetfilesender/filesender.xml @@ -76,8 +76,8 @@ filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/res **How to connect your Galaxy account to FileSender** To send files from Galaxy you will need to connect your Galaxy account - to FileSender. This is done by entering you FileSender API key into your - Galaxy user profile. + to FileSender. This is done by entering your FileSender API key into your + Galaxy user preferences. 1. Copy your API key from the “API Secret” section on the FileSender “My Profile” page. See the `AARNet Knowledge Base`_ for more information. From 13d27035ea2d43cd9f02c091b6c205fd80493cd9 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Mon, 21 Oct 2024 16:17:56 +1100 Subject: [PATCH 09/11] readme --- tools/aarnetfilesender/filesender.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnetfilesender/filesender.xml index 8cbb8953..e220c648 100644 --- a/tools/aarnetfilesender/filesender.xml +++ b/tools/aarnetfilesender/filesender.xml @@ -79,7 +79,7 @@ filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/res to FileSender. This is done by entering your FileSender API key into your Galaxy user preferences. - 1. Copy your API key from the “API Secret” section on the FileSender “My + 1. Log in to FileSender, and copy your API key from the “API Secret” section on the FileSender “My Profile” page. See the `AARNet Knowledge Base`_ for more information. 2. In Galaxy, add your API key to the “AARNet FileSender API Key” field in User > Preferences > Manage Information. Your AARNet FileSender From 2ef95bdceff4da9efe2bb4791d0d4c233e9f0a83 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Tue, 22 Oct 2024 10:00:14 +1100 Subject: [PATCH 10/11] match filenames to tool id --- tools/{aarnetfilesender => aarnet_filesender}/.shed.yml | 4 ++-- tools/{aarnetfilesender => aarnet_filesender}/README.rst | 0 .../aarnet_filesender.xml} | 0 tools/{aarnetfilesender => aarnet_filesender}/macros.xml | 0 .../test-data/output.log | 0 .../test-data/summary_statistics.txt | 0 6 files changed, 2 insertions(+), 2 deletions(-) rename tools/{aarnetfilesender => aarnet_filesender}/.shed.yml (85%) rename tools/{aarnetfilesender => aarnet_filesender}/README.rst (100%) rename tools/{aarnetfilesender/filesender.xml => aarnet_filesender/aarnet_filesender.xml} (100%) rename tools/{aarnetfilesender => aarnet_filesender}/macros.xml (100%) rename tools/{aarnetfilesender => aarnet_filesender}/test-data/output.log (100%) rename tools/{aarnetfilesender => aarnet_filesender}/test-data/summary_statistics.txt (100%) diff --git a/tools/aarnetfilesender/.shed.yml b/tools/aarnet_filesender/.shed.yml similarity index 85% rename from tools/aarnetfilesender/.shed.yml rename to tools/aarnet_filesender/.shed.yml index b83091c8..7f1a5fd0 100644 --- a/tools/aarnetfilesender/.shed.yml +++ b/tools/aarnet_filesender/.shed.yml @@ -1,13 +1,13 @@ name: aarnet_filesender owner: galaxy-australia homepage_url: https://filesender.aarnet.edu.au -remote_repository_url: https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnetfilesender +remote_repository_url: https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender categories: - Data Export type: unrestricted description: Transfer files to AARNet's FileSender Service long_description: Transfer files to AARNet's FileSender Service include: - - filesender.xml + - aarnet_filesender.xml - macros.xml - test-data diff --git a/tools/aarnetfilesender/README.rst b/tools/aarnet_filesender/README.rst similarity index 100% rename from tools/aarnetfilesender/README.rst rename to tools/aarnet_filesender/README.rst diff --git a/tools/aarnetfilesender/filesender.xml b/tools/aarnet_filesender/aarnet_filesender.xml similarity index 100% rename from tools/aarnetfilesender/filesender.xml rename to tools/aarnet_filesender/aarnet_filesender.xml diff --git a/tools/aarnetfilesender/macros.xml b/tools/aarnet_filesender/macros.xml similarity index 100% rename from tools/aarnetfilesender/macros.xml rename to tools/aarnet_filesender/macros.xml diff --git a/tools/aarnetfilesender/test-data/output.log b/tools/aarnet_filesender/test-data/output.log similarity index 100% rename from tools/aarnetfilesender/test-data/output.log rename to tools/aarnet_filesender/test-data/output.log diff --git a/tools/aarnetfilesender/test-data/summary_statistics.txt b/tools/aarnet_filesender/test-data/summary_statistics.txt similarity index 100% rename from tools/aarnetfilesender/test-data/summary_statistics.txt rename to tools/aarnet_filesender/test-data/summary_statistics.txt From 656581874729dccf1e91c876fc8657fbb5eb17eb Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Tue, 22 Oct 2024 10:10:57 +1100 Subject: [PATCH 11/11] shed file --- tools/aarnet_filesender/.shed.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/tools/aarnet_filesender/.shed.yml b/tools/aarnet_filesender/.shed.yml index 7f1a5fd0..18cec93b 100644 --- a/tools/aarnet_filesender/.shed.yml +++ b/tools/aarnet_filesender/.shed.yml @@ -7,7 +7,6 @@ categories: type: unrestricted description: Transfer files to AARNet's FileSender Service long_description: Transfer files to AARNet's FileSender Service -include: - - aarnet_filesender.xml - - macros.xml - - test-data +exclude: + - tool_test_output.html + - tool_test_output.json \ No newline at end of file