UtrechtUniversity · lwesterhof · Nov 18, 2024 · Nov 1, 2024
diff --git a/.github/workflows/build-push-image-provider.yml b/.github/workflows/build-push-image-provider.yml
@@ -12,7 +12,6 @@ on:
       - 'docker/images/yoda_irods_icat/**'
       - 'roles/irods_completion/files/irods_completion.sh'
       - 'roles/pam_python/files/pam_python.so'
-      - 'roles/yoda_rulesets/files/run-intake-movetovault.sh'
 
 jobs:
   push-image:
@@ -55,4 +54,3 @@ jobs:
         tags: ghcr.io/utrechtuniversity/yoda-provider:${{ steps.extract_branch.outputs.branch }}
         build-args: |
           TAG=${{ steps.extract_branch.outputs.branch }}
-
diff --git a/docker/images/yoda_irods_icat/Dockerfile b/docker/images/yoda_irods_icat/Dockerfile
@@ -177,10 +177,7 @@ RUN for script in scheduled-copytovault.sh admin-remove-orphan-vault-if-empty.sh
     do install -m 0755 /etc/irods/yoda-ruleset/tools/${script} /var/lib/irods/msiExecCmd_bin/${script} ; \
     done && \
     /etc/irods/yoda-ruleset/tools/setup_tokens.sh /etc/irods/yoda-ruleset/accesstokens.db test
-COPY stage/run-intake-movetovault.sh /tmp/run-intake-movetovault.sh
 COPY job_movetovault.r /var/lib/irods/.irods/job_movetovault.r
-COPY job_clearintakelocks.r /var/lib/irods/.irods/job_clearintakelocks.r
-RUN install -o irods -g irods -m 0755 /tmp/run-intake-movetovault.sh /var/lib/irods/.irods/run-intake-movetovault.sh
 COPY cronjob-revision-cleanup.sh /tmp/cronjob-revision-cleanup.sh
 RUN install -o irods -g irods -m 0755 /tmp/cronjob-revision-cleanup.sh /var/lib/irods/.irods/cronjob-revision-cleanup.sh
 COPY service_account.config /tmp/service_account.config

diff --git a/docker/images/yoda_irods_icat/job_clearintakelocks.r b/docker/images/yoda_irods_icat/job_clearintakelocks.r
diff --git a/docker/images/yoda_irods_icat/job_movetovault.r b/docker/images/yoda_irods_icat/job_movetovault.r
diff --git a/docker/images/yoda_irods_icat/rules_uu.cfg b/docker/images/yoda_irods_icat/rules_uu.cfg
@@ -39,7 +39,6 @@ eus_api_tls_verify             = 'false'
 
 enable_deposit                 = 'true'
 enable_open_search             = 'false'
-enable_intake                  = 'true'
 enable_datarequest             = 'true'
 yoda_portal_fqdn               = 'portal.yoda'
 

diff --git a/docker/images/yoda_irods_icat/stage-uploads.sh b/docker/images/yoda_irods_icat/stage-uploads.sh
@@ -16,4 +16,3 @@ fi
 
 cp ../../../roles/pam_python/files/pam_python.so stage
 cp ../../../roles/irods_completion/files/irods_completion.sh stage
-cp ../../../roles/yoda_rulesets/files/run-intake-movetovault.sh stage
diff --git a/docker/images/yoda_portal/yoda_portal_init.sh b/docker/images/yoda_portal/yoda_portal_init.sh
@@ -92,8 +92,6 @@ YODA_COMMIT         = '$YODA_COMMIT'
 RESEARCH_ENABLED    = True
 OPEN_SEARCH_ENABLED = False
 DEPOSIT_ENABLED     = True
-INTAKE_ENABLED      = True
-INTAKE_EXT_TIMEOUT  = 1800
 DATAREQUEST_ENABLED = True
 TOKENS_ENABLED      = True
 TOKEN_LIFETIME      = 72

diff --git a/docker/run-cronjob.sh b/docker/run-cronjob.sh
@@ -25,10 +25,6 @@ case "$1" in
     docker exec "$EXEC_OPTIONS" provider.yoda sudo -iu irods /bin/bash /etc/irods/yoda-ruleset/tools/notification/notification-data-access-token-expiry.sh
     ;;
 
-  intakevault)
-    docker exec "$EXEC_OPTIONS" provider.yoda sudo -iu irods /var/lib/irods/.irods/run-intake-movetovault.sh
-    ;;
-
   publication)
     docker exec "$EXEC_OPTIONS" provider.yoda sudo -iu irods /bin/irule -r irods_rule_engine_plugin-irods_rule_language-instance -F /etc/irods/yoda-ruleset/tools/process-publication.r
     ;;

diff --git a/docs/administration/configuring-yoda.md b/docs/administration/configuring-yoda.md
@@ -282,14 +282,6 @@ Variable                     | Description
 -----------------------------|---------------------
 enable_deposit               | Enable deposit module
 
-### Intake module configuration
-
-Variable                     | Description
------------------------------|---------------------
-enable_intake                | Enable intake module
-intake_groups                | List of intake groups (without the "grp-intake-" prefix)
-intake_extended_timeout      | If the intake module is enabled, portal iRODS session timeouts and portal VHost timeouts will be changed to this value (in seconds), in order to be able to handle long synchronous operations, such as intake scans (default: 1800)
-
 ### Datarequest module configuration
 
 Variable                       | Description

diff --git a/docs/design/api/index.md b/docs/design/api/index.md
@@ -11,5 +11,4 @@ has_toc: false
 - [Core API documentation](https://petstore.swagger.io/?url=https://utrechtuniversity.github.io/yoda-ruleset/api_core.json)
 
 ### Module API
-- [Intake API documentation](https://petstore.swagger.io/?url=https://utrechtuniversity.github.io/yoda-ruleset/api_intake.json)
 - [Datarequest API documentation](https://petstore.swagger.io/?url=https://utrechtuniversity.github.io/yoda-ruleset/api_datarequest.json)
diff --git a/docs/design/overview/index.md b/docs/design/overview/index.md
@@ -39,11 +39,6 @@ The user module provides settings and notifications.
 
 ## Additional modules
 
-### Intake
-This module processes uploaded YOUth programme experiment data, and facilitate its archival in the vault by a data manager.
-
-[Technical design](intake.md){: .btn }
-
 ### Datarequest
 Module adding support for the submission, review and approval of requests to obtain research data stored in Yoda.
 

diff --git a/docs/design/overview/intake.md b/docs/design/overview/intake.md
diff --git a/docs/design/processes/asynchronous-processes.md b/docs/design/processes/asynchronous-processes.md
@@ -19,7 +19,6 @@ This page contains an overview of asynchronous processes in Yoda.
 * [Statistics job](#statistics-job)
 * [Archiving](#archiving)
 * [Archiving - retry-copy-to-vault job](#archiving-retry-copy-job)
-* [Archiving - intake to vault job](#archiving-intake-to-vault-job)
 * [Archiving - publication job](#archiving-publication-job)
 
 <a name="metadata"/>
@@ -141,7 +140,7 @@ and communities.
 
 ## Archiving and publication
 
-Asynchronous jobs are also used to copy data packages from a research or intake folder to the vault,
+Asynchronous jobs are also used to copy data packages from a research folder to the vault,
 as well as to process publications.
 
 <a name="archiving-retry-copy-job"/>
@@ -158,17 +157,6 @@ as well as to process publications.
 By default, groups that are to be copied to the vault are marked with a metadata attribute named
 `cronjob_copy_to_vault`.
 
-<a name="archiving-intake-to-vault-job"/>
-
-### Intake copy to vault job
-
-|   |   |
-|---|---|
-| Script               | /var/lib/irods/.irods/job_movetovault.r                                     |
-| Purpose              | copy data packages from intake groups to the vault                          |
-| Lock file            | uses lock attribute on the vault folder                                     |
-| Typically started by | cronjob, runs every five minutes                                            |
-
 <a name="archiving-publication-job"/>
 
 ### Process publication job

diff --git a/environments/development/allinone/group_vars/allinone.yml b/environments/development/allinone/group_vars/allinone.yml
@@ -35,9 +35,6 @@ opensearch_server: combined.yoda.test
 # Deposit module configuration
 enable_deposit: true                               # Enable deposit module
 
-# Intake module configuration
-enable_intake: true                                # Enable intake module
-
 # Datarequest module configuration
 enable_datarequest: true                           # Enable datarequest module
 datarequest_help_contact_name: PLACEHOLDER         # Help contact name

diff --git a/environments/development/el8-database/group_vars/el8.yml b/environments/development/el8-database/group_vars/el8.yml
@@ -30,9 +30,6 @@ opensearch_server: combined.yoda.test
 # Deposit module configuration
 enable_deposit: true                               # Enable deposit module
 
-# Intake module configuration
-enable_intake: true                                # Enable intake module
-
 # Datarequest module configuration
 enable_datarequest: true                           # Enable datarequest module
 datarequest_help_contact_name: PLACEHOLDER         # Help contact name

diff --git a/environments/development/full/group_vars/full.yml b/environments/development/full/group_vars/full.yml
@@ -32,9 +32,6 @@ opensearch_server: portal.yoda.test
 # Deposit module configuration
 enable_deposit: true                               # Enable deposit module
 
-# Intake module configuration
-enable_intake: true                                # Enable intake module
-
 # Datarequest module configuration
 enable_datarequest: true                           # Enable datarequest module
 datarequest_help_contact_name: PLACEHOLDER         # Help contact name

diff --git a/environments/development/single_fqdn/group_vars/single_fqdn.yml b/environments/development/single_fqdn/group_vars/single_fqdn.yml
@@ -37,9 +37,6 @@ opensearch_server: combined.yoda.test
 # Deposit module configuration
 enable_deposit: true                               # Enable deposit module
 
-# Intake module configuration
-enable_intake: true                                # Enable intake module
-
 # Datarequest module configuration
 enable_datarequest: true                           # Enable datarequest module
 datarequest_help_contact_name: PLACEHOLDER         # Help contact name