From 004ff1f35fe9e3b8e783c741a20e9e7441841f2a Mon Sep 17 00:00:00 2001
From: Leonidas Triantafyllou <leonidastri@users.noreply.github.com>
Date: Thu, 5 Sep 2024 16:24:37 +0200
Subject: [PATCH] YDA-5945: refactor update-publications.r to Python

---
 publication.py              | 32 ++++++++++++++++++++++++----
 tools/update-publications.r | 42 +------------------------------------
 2 files changed, 29 insertions(+), 45 deletions(-)

diff --git a/publication.py b/publication.py
index 31e98e3cf..47e7d3470 100644
--- a/publication.py
+++ b/publication.py
@@ -4,6 +4,7 @@
 __copyright__ = 'Copyright (c) 2019-2024, Utrecht University'
 __license__   = 'GPLv3, see LICENSE'
 
+import re
 from datetime import datetime
 
 import genquery
@@ -1314,7 +1315,7 @@ def process_republication(ctx, vault_package):
     return publication_state["status"]
 
 
-@rule.make(inputs=range(4), outputs=range(4, 6))
+@rule.make(inputs=range(4))
 def rule_update_publication(ctx, vault_package, update_datacite, update_landingpage, update_moai):
     """Rule interface for updating the publication of a vault package.
 
@@ -1323,10 +1324,33 @@ def rule_update_publication(ctx, vault_package, update_datacite, update_landingp
     :param update_datacite:    Flag that indicates updating DataCite
     :param update_landingpage: Flag that indicates updating landingpage
     :param update_moai:        Flag that indicates updating MOAI (OAI-PMH)
-
-    :returns: "OK" if all went ok
     """
-    return update_publication(ctx, vault_package, update_datacite == 'Yes', update_landingpage == 'Yes', update_moai == 'Yes')
+    if user.user_type(ctx) != 'rodsadmin':
+        log.write_stdout(ctx, "User is no rodsadmin")
+        return
+
+    log.write_stdout(ctx, "[UPDATE PUBLICATIONS] Start for {}".format(vault_package))
+    collections = genquery.row_iterator(
+        "COLL_NAME",
+        "COLL_NAME like '%%/home/vault-%%' "
+        "AND META_COLL_ATTR_NAME = '" + constants.UUORGMETADATAPREFIX + "vault_status' "
+        "AND META_COLL_ATTR_VALUE = '{}'".format(str(constants.vault_package_state.PUBLISHED)),
+        genquery.AS_LIST,
+        ctx
+    )
+
+    packages_found = False
+    for collection in collections:
+        coll_name = collection[0]
+        if ((vault_package == '*' and re.match(r'/[^/]+/home/vault-.*', coll_name)) or (vault_package != '*' and re.match(r'/[^/]+/home/vault-.*', coll_name) and coll_name == vault_package)):
+            packages_found = True
+            output = update_publication(ctx, coll_name, update_datacite == 'Yes', update_landingpage == 'Yes', update_moai == 'Yes')
+            log.write_stdout(ctx, coll_name + ': ' + output)
+
+    if not packages_found:
+        log.write_stdout(ctx, "[UPDATE PUBLICATIONS] No packages found for {}".format(vault_package))
+    else:
+        log.write_stdout(ctx, "[UPDATE PUBLICATIONS] Finished for {}".format(vault_package))
 
 
 def update_publication(ctx, vault_package, update_datacite=False, update_landingpage=False, update_moai=False):
diff --git a/tools/update-publications.r b/tools/update-publications.r
index e4ef73069..7e7f5c1ca 100644
--- a/tools/update-publications.r
+++ b/tools/update-publications.r
@@ -11,47 +11,7 @@
 # $ irule -r irods_rule_engine_plugin-irods_rule_language-instance -F /etc/irods/yoda-ruleset/tools/update-publications.r
 #
 updatePublications() {
-	writeLine("stdout", "[UPDATE PUBLICATIONS] Start for *package");
-	*packagesFound = 0;
-
-	# Scan for published vault packages.
-	*ContInxOld = 1;
-	msiAddSelectFieldToGenQuery("COLL_NAME", "", *GenQ2Inp);
-	msiAddConditionToGenQuery("COLL_NAME", "like", "%%/home/vault-%%", *GenQ2Inp);
-	msiAddConditionToGenQuery("META_COLL_ATTR_NAME", "=", UUORGMETADATAPREFIX ++ "vault_status", *GenQ2Inp);
-	msiAddConditionToGenQuery("META_COLL_ATTR_VALUE", "=", PUBLISHED, *GenQ2Inp);
-
-	msiExecGenQuery(*GenQ2Inp, *GenQ2Out);
-	msiGetContInxFromGenQueryOut(*GenQ2Out, *ContInxNew);
-
-	while(*ContInxOld > 0) {
-		foreach(*row in *GenQ2Out) {
-			*collName = *row.COLL_NAME;
-
-			# Check if this really is a vault package, or selected vault package
-			if ((*package == '*' && *collName like regex "/[^/]+/home/vault-.*") ||
-			    (*package != '*' && *collName like regex "/[^/]+/home/vault-.*" && *collName == *package ) ) {
-			    *packagesFound = 1;
-			    *status = ''
-			    *statusInfo = '';
-			    rule_update_publication(*collName, *updateDatacite, *updateLandingpage, *updateMOAI, *status, *statusInfo);
-			    writeLine("stdout", "*collName: *status *statusInfo");
-			}
-		}
-
-		*ContInxOld = *ContInxNew;
-		if(*ContInxOld > 0) {
-			msiGetMoreRows(*GenQ2Inp, *GenQ2Out, *ContInxNew);
-		}
-	}
-	msiCloseGenQuery(*GenQ2Inp, *GenQ2Out);
-
-	if (*packagesFound == 0) {
-		writeLine("stdout", "[UPDATE PUBLICATIONS] No packages found for *package")
-	}
-	else {
-		writeLine("stdout", "[UPDATE PUBLICATIONS] Finished for *package");
-	}
+	rule_update_publication(*package, *updateDatacite, *updateLandingpage, *updateMOAI);
 }
 
 input *updateDatacite="Yes", *updateLandingpage="Yes", *updateMOAI="Yes", *package='*'