From c5aa04652bcf9426a5c38f9b5c008b54a4ea224f Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 9 Feb 2025 00:35:35 +0100 Subject: [PATCH 1/2] cleanup, we should move users to user-based files sources --- .../config/user_preferences_extra_conf.yml | 150 +++++++++--------- .../galaxy/config/file_sources_conf.yml.j2 | 84 +++++----- 2 files changed, 117 insertions(+), 117 deletions(-) diff --git a/files/galaxy/config/user_preferences_extra_conf.yml b/files/galaxy/config/user_preferences_extra_conf.yml index da97548bf..723c77150 100644 --- a/files/galaxy/config/user_preferences_extra_conf.yml +++ b/files/galaxy/config/user_preferences_extra_conf.yml @@ -33,49 +33,49 @@ preferences: - [日本語, ja] # Used in file_sources_conf.yml - dropbox: - description: Your Dropbox account - inputs: - - name: access_token - label: Dropbox access token - type: password - required: False + #dropbox: + # description: Your Dropbox account + # inputs: + # - name: access_token + # label: Dropbox access token + # type: password + # required: False # Used in file_sources_conf.yml - nextcloud: - description: Your Personal Nextcloud / ownCloud account - inputs: - - name: url - label: Server Domain (e.g. https://myowncloud.org) - type: text - required: False - - name: root - label: Server Path (should end with /remote.php/webdav, e.g. /a/sub/path/remote.php/webdav) - type: text - required: False - - name: username - label: Username - type: text - required: False - - name: password - label: Password - type: password - # for storing the password in a vault (instead of plaintext in the DB) - # store: vault - required: False + #nextcloud: + # description: Your Personal Nextcloud / ownCloud account + # inputs: + # - name: url + # label: Server Domain (e.g. https://myowncloud.org) + # type: text + # required: False + # - name: root + # label: Server Path (should end with /remote.php/webdav, e.g. /a/sub/path/remote.php/webdav) + # type: text + # required: False + # - name: username + # label: Username + # type: text + # required: False + # - name: password + # label: Password + # type: password + # # for storing the password in a vault (instead of plaintext in the DB) + # # store: vault + # required: False - invenio: - description: Your Invenio RDM Integration Settings - inputs: - - name: token - label: Personal Token used to create draft records and to upload files - type: secret - store: vault # Requires setting up vault_config_file in your galaxy.yml - required: False - - name: public_name - label: Creator name to associate with new records (formatted as "Last name, First name"). If left blank "Anonymous Galaxy User" will be used. You can always change this by editing your record directly. - type: text - required: False + #invenio: + # description: Your Invenio RDM Integration Settings + # inputs: + # - name: token + # label: Personal Token used to create draft records and to upload files + # type: secret + # store: vault # Requires setting up vault_config_file in your galaxy.yml + # required: False + # - name: public_name + # label: Creator name to associate with new records (formatted as "Last name, First name"). If left blank "Anonymous Galaxy User" will be used. You can always change this by editing your record directly. + # type: text + # required: False zenodo: description: Your Zenodo Integration Settings @@ -104,22 +104,22 @@ preferences: required: False # Used in file_sources_conf.yml - onedata: - description: Your Onedata account - inputs: - - name: onezone_domain - label: Domain of the Onezone service (e.g. datahub.egi.eu). The minimal supported Onezone version is 21.02.4. - type: text - required: False - - name: access_token - label: Your access token, suitable for REST API access in a Oneprovider service - type: password - required: False - - name: disable_tls_certificate_validation - label: Allow connection to Onedata servers that do not present trusted SSL certificates. SHOULD NOT be used unless you really know what you are doing. - type: boolean - required: False - value: False + #onedata: + # description: Your Onedata account + # inputs: + # - name: onezone_domain + # label: Domain of the Onezone service (e.g. datahub.egi.eu). The minimal supported Onezone version is 21.02.4. + # type: text + # required: False + # - name: access_token + # label: Your access token, suitable for REST API access in a Oneprovider service + # type: password + # required: False + # - name: disable_tls_certificate_validation + # label: Allow connection to Onedata servers that do not present trusted SSL certificates. SHOULD NOT be used unless you really know what you are doing. + # type: boolean + # required: False + # value: False distributed_arc_compute: description: The URL to your ARC remote HPC compute resource. @@ -208,25 +208,25 @@ preferences: required: False value: https://auth.quantum-computing.ibm.com/api - generic_s3: - description: Your personal S3 account for data import - inputs: - - name: endpoint_url - label: Server Domain (e.g. byos.vm.fedcloud.eu) - type: text - required: False - - name: bucket - label: S3 Bucket (e.g. my-s3-bucket) - type: text - required: False - - name: secret - label: S3 secret (e.g. SuPerP4ssWord) - type: password - required: False - - name: key - label: S3 access key (e.g. project01) - type: password - required: False + #generic_s3: + # description: Your personal S3 account for data import + # inputs: + # - name: endpoint_url + # label: Server Domain (e.g. byos.vm.fedcloud.eu) + # type: text + # required: False + # - name: bucket + # label: S3 Bucket (e.g. my-s3-bucket) + # type: text + # required: False + # - name: secret + # label: S3 secret (e.g. SuPerP4ssWord) + # type: password + # required: False + # - name: key + # label: S3 access key (e.g. project01) + # type: password + # required: False # Require to attach pulsar endpoint to the Pulsar Network byoc_pulsar: diff --git a/templates/galaxy/config/file_sources_conf.yml.j2 b/templates/galaxy/config/file_sources_conf.yml.j2 index 92f7bf762..2e77150c1 100644 --- a/templates/galaxy/config/file_sources_conf.yml.j2 +++ b/templates/galaxy/config/file_sources_conf.yml.j2 @@ -1,30 +1,30 @@ -- type: dropbox - id: dropbox - label: Your Dropbox Files - doc: Your Dropbox files - configure an access token via the user preferences - accessToken: ${user.preferences['dropbox|access_token']} - -- type: webdav - id: b2drop - doc: B2Drop WebDAV server - url: https://b2drop.eudat.eu - root: /remote.php/dav/files/${user.preferences['b2drop|username']}/ - use_temp_files: true - temp_path: /data/jwd04/tmp - login: ${user.preferences['b2drop|username']} - password: ${user.preferences['b2drop|password']} - -- type: webdav - id: generic_nextcloud - label: Nextcloud/ownCloud - doc: You personal Cloud files - writable: true - url: ${user.preferences['nextcloud|url']} - root: ${user.preferences['nextcloud|root']} - use_temp_files: true - temp_path: /data/jwd04/tmp - login: ${user.preferences['nextcloud|username']} - password: ${user.preferences['nextcloud|password']} +#- type: dropbox +# id: dropbox +# label: Your Dropbox Files +# doc: Your Dropbox files - configure an access token via the user preferences +# accessToken: ${user.preferences['dropbox|access_token']} + +#- type: webdav +# id: b2drop +# doc: B2Drop WebDAV server +# url: https://b2drop.eudat.eu +# root: /remote.php/dav/files/${user.preferences['b2drop|username']}/ +# use_temp_files: true +# temp_path: /data/jwd04/tmp +# login: ${user.preferences['b2drop|username']} +# password: ${user.preferences['b2drop|password']} + +#- type: webdav +# id: generic_nextcloud +# label: Nextcloud/ownCloud +# doc: You personal Cloud files +# writable: true +# url: ${user.preferences['nextcloud|url']} +# root: ${user.preferences['nextcloud|root']} +# use_temp_files: true +# temp_path: /data/jwd04/tmp +# login: ${user.preferences['nextcloud|username']} +# password: ${user.preferences['nextcloud|password']} - type: webdav id: erga_nextcloud @@ -111,15 +111,15 @@ config_path: "" port: 2222 -- type: s3fs - label: Generic S3 instance - id: generic_s3 - doc: Access to a generic S3 endpoint. - endpoint_url: ${user.preferences['generic_s3|endpoint_url']} - bucket: ${user.preferences['generic_s3|bucket']} - writable: true - secret: ${user.preferences['generic_s3|secret']} - key: ${user.preferences['generic_s3|key']} +#- type: s3fs +# label: Generic S3 instance +# id: generic_s3 +# doc: Access to a generic S3 endpoint. +# endpoint_url: ${user.preferences['generic_s3|endpoint_url']} +# bucket: ${user.preferences['generic_s3|bucket']} +# writable: true +# secret: ${user.preferences['generic_s3|secret']} +# key: ${user.preferences['generic_s3|key']} - type: s3fs label: Genome Ark @@ -288,12 +288,12 @@ public_name: ${user.preferences['zenodo_sandbox|public_name']} writable: true -- type: onedata - id: onedata1 - label: Onedata - doc: Your Onedata files - configure an access token via user preferences - accessToken: ${user.preferences['onedata|access_token']} - onezoneDomain: ${user.preferences['onedata|onezone_domain']} +#- type: onedata +# id: onedata1 +# label: Onedata +# doc: Your Onedata files - configure an access token via user preferences +# accessToken: ${user.preferences['onedata|access_token']} +# onezoneDomain: ${user.preferences['onedata|onezone_domain']} - type: onedata id: gtn_public_onedata From 9583e32706312f67d8a3d9be02a7ae9a5799e33e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 17 Feb 2025 20:26:49 +0100 Subject: [PATCH 2/2] Update file_sources_conf.yml.j2 --- templates/galaxy/config/file_sources_conf.yml.j2 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/galaxy/config/file_sources_conf.yml.j2 b/templates/galaxy/config/file_sources_conf.yml.j2 index 2e77150c1..c5eaa9b0a 100644 --- a/templates/galaxy/config/file_sources_conf.yml.j2 +++ b/templates/galaxy/config/file_sources_conf.yml.j2 @@ -271,7 +271,7 @@ - type: inveniordm id: zenodo doc: Zenodo is an open-access digital repository created by CERN (the European Organization for Nuclear Research) to enable researchers to share, preserve, and cite research outputs across various disciplines. - label: Zenodo + label: Zenodo (public) url: https://zenodo.org token: ${user.user_vault.read_secret('preferences/zenodo/token')} # token: ${user.preferences['zenodo|token']} # Alternatively use this for retrieving the token from user preferences instead of the Vault