From c1f16de433c76be6ffb3c52e90198e77959e250f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martynas=20Jusevi=C4=8Dius?= <martynas@atomgraph.com>
Date: Tue, 20 Jan 2026 10:01:13 +0100
Subject: [PATCH 1/7] [maven-release-plugin] prepare for next development
 iteration

---
 pom.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 32e9246e3..6f440bfff 100644
--- a/pom.xml
+++ b/pom.xml
@@ -3,7 +3,7 @@
 
     <groupId>com.atomgraph</groupId>
     <artifactId>linkeddatahub</artifactId>
-    <version>5.2.1</version>
+    <version>5.2.2-SNAPSHOT</version>
     <packaging>${packaging.type}</packaging>
 
     <name>AtomGraph LinkedDataHub</name>
@@ -46,7 +46,7 @@
         <url>https://github.com/AtomGraph/LinkedDataHub</url>
         <connection>scm:git:git://github.com/AtomGraph/LinkedDataHub.git</connection>
         <developerConnection>scm:git:git@github.com:AtomGraph/LinkedDataHub.git</developerConnection>
-        <tag>linkeddatahub-5.2.1</tag>
+        <tag>linkeddatahub-2.1.1</tag>
     </scm>
 
     <repositories>

From b2d3bce13403b345091753b6e4d3418efd85eee5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martynas=20Jusevi=C4=8Dius?= <martynas@atomgraph.com>
Date: Thu, 22 Jan 2026 12:55:59 +0100
Subject: [PATCH 2/7] Additional HTTP tests for file uploads

---
 http-tests/imports/PUT-file-format-browser.sh | 107 +++++++++++++++++
 .../imports/PUT-file-format-explicit.sh       | 113 ++++++++++++++++++
 2 files changed, 220 insertions(+)
 create mode 100755 http-tests/imports/PUT-file-format-browser.sh
 create mode 100755 http-tests/imports/PUT-file-format-explicit.sh

diff --git a/http-tests/imports/PUT-file-format-browser.sh b/http-tests/imports/PUT-file-format-browser.sh
new file mode 100755
index 000000000..cf5a20616
--- /dev/null
+++ b/http-tests/imports/PUT-file-format-browser.sh
@@ -0,0 +1,107 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+initialize_dataset "$END_USER_BASE_URL" "$TMP_END_USER_DATASET" "$END_USER_ENDPOINT_URL"
+initialize_dataset "$ADMIN_BASE_URL" "$TMP_ADMIN_DATASET" "$ADMIN_ENDPOINT_URL"
+purge_cache "$END_USER_VARNISH_SERVICE"
+purge_cache "$ADMIN_VARNISH_SERVICE"
+purge_cache "$FRONTEND_VARNISH_SERVICE"
+
+pwd=$(realpath "$PWD")
+
+# add agent to the writers group
+
+add-agent-to-group.sh \
+  -f "$OWNER_CERT_FILE" \
+  -p "$OWNER_CERT_PWD" \
+  --agent "$AGENT_URI" \
+  "${ADMIN_BASE_URL}acl/groups/writers/"
+
+# create test file with sample content
+
+test_file=$(mktemp)
+echo "test,data,sample" > "$test_file"
+echo "1,2,3" >> "$test_file"
+echo "4,5,6" >> "$test_file"
+
+# upload file WITHOUT explicit media type (rely on browser detection via `file -b --mime-type`)
+
+file_doc=$(create-file.sh \
+-f "$AGENT_CERT_FILE" \
+-p "$AGENT_CERT_PWD" \
+-b "$END_USER_BASE_URL" \
+--title "Test File for Browser Media Type" \
+--file "$test_file")
+
+# get the file resource URI and initial dct:format
+
+file_doc_ntriples=$(get.sh \
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  --accept 'application/n-triples' \
+  "$file_doc")
+
+file_uri=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_doc//\//\\/}> <http:\/\/xmlns.com\/foaf\/0.1\/primaryTopic> <(.*)> \./\1/p")
+
+# get initial SHA1 hash
+initial_sha1=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <http:\/\/xmlns.com\/foaf\/0.1\/sha1> \"(.*)\" \./\1/p")
+
+# get initial dct:format (should be browser-detected)
+initial_format=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <http:\/\/purl.org\/dc\/terms\/format> <(.*)> \./\1/p")
+
+# re-upload the same file to the same document with explicit media type: text/csv
+# using PUT with RDF/POST multipart format
+# IMPORTANT: Include explicit dct:format in RDF to simulate user editing the format field in the form
+
+rdf_post=""
+rdf_post+="-F \"rdf=\"\n"
+rdf_post+="-F \"sb=file\"\n"
+rdf_post+="-F \"pu=http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName\"\n"
+rdf_post+="-F \"ol=@${test_file};type=text/csv\"\n"
+rdf_post+="-F \"pu=http://purl.org/dc/terms/title\"\n"
+rdf_post+="-F \"ol=Test File for Browser Media Type\"\n"
+rdf_post+="-F \"pu=http://www.w3.org/1999/02/22-rdf-syntax-ns#type\"\n"
+rdf_post+="-F \"ou=http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#FileDataObject\"\n"
+rdf_post+="-F \"pu=http://purl.org/dc/terms/format\"\n"
+rdf_post+="-F \"ou=http://www.sparontologies.net/mediatype/text/csv\"\n"
+rdf_post+="-F \"su=${file_doc}\"\n"
+rdf_post+="-F \"pu=http://purl.org/dc/terms/title\"\n"
+rdf_post+="-F \"ol=Test File for Browser Media Type\"\n"
+rdf_post+="-F \"pu=http://www.w3.org/1999/02/22-rdf-syntax-ns#type\"\n"
+rdf_post+="-F \"ou=https://www.w3.org/ns/ldt/document-hierarchy#Item\"\n"
+rdf_post+="-F \"pu=http://xmlns.com/foaf/0.1/primaryTopic\"\n"
+rdf_post+="-F \"ob=file\"\n"
+rdf_post+="-F \"pu=http://rdfs.org/sioc/ns#has_container\"\n"
+rdf_post+="-F \"ou=${END_USER_BASE_URL}files/\"\n"
+
+echo -e "$rdf_post" | curl -f -v -s -k -X PUT -H "Accept: text/turtle" -E "$AGENT_CERT_FILE":"$AGENT_CERT_PWD" -o /dev/null --config - "$file_doc"
+
+# get updated document
+
+updated_ntriples=$(get.sh \
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  --accept 'application/n-triples' \
+  "$file_doc")
+
+# get updated SHA1 hash (should be same as initial)
+updated_sha1=$(echo "$updated_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <http:\/\/xmlns.com\/foaf\/0.1\/sha1> \"(.*)\" \./\1/p")
+
+# get updated dct:format (should be text/csv)
+updated_format=$(echo "$updated_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <http:\/\/purl.org\/dc\/terms\/format> <(.*)> \./\1/p")
+
+# verify SHA1 is unchanged (same file content)
+if [ "$initial_sha1" != "$updated_sha1" ]; then
+    echo "ERROR: SHA1 hash changed! Initial: $initial_sha1, Updated: $updated_sha1"
+    exit 1
+fi
+
+# verify dct:format was updated to text/csv
+if [[ ! "$updated_format" =~ text/csv ]]; then
+    echo "ERROR: Format should have been updated to text/csv but got: $updated_format"
+    echo "Initial format was: $initial_format"
+    exit 1
+fi
+
+# cleanup
+rm -f "$test_file"
diff --git a/http-tests/imports/PUT-file-format-explicit.sh b/http-tests/imports/PUT-file-format-explicit.sh
new file mode 100755
index 000000000..eaa10401e
--- /dev/null
+++ b/http-tests/imports/PUT-file-format-explicit.sh
@@ -0,0 +1,113 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+initialize_dataset "$END_USER_BASE_URL" "$TMP_END_USER_DATASET" "$END_USER_ENDPOINT_URL"
+initialize_dataset "$ADMIN_BASE_URL" "$TMP_ADMIN_DATASET" "$ADMIN_ENDPOINT_URL"
+purge_cache "$END_USER_VARNISH_SERVICE"
+purge_cache "$ADMIN_VARNISH_SERVICE"
+purge_cache "$FRONTEND_VARNISH_SERVICE"
+
+pwd=$(realpath "$PWD")
+
+# add agent to the writers group
+
+add-agent-to-group.sh \
+  -f "$OWNER_CERT_FILE" \
+  -p "$OWNER_CERT_PWD" \
+  --agent "$AGENT_URI" \
+  "${ADMIN_BASE_URL}acl/groups/writers/"
+
+# create test file with sample content
+
+test_file=$(mktemp)
+echo "test,data,sample" > "$test_file"
+echo "1,2,3" >> "$test_file"
+echo "4,5,6" >> "$test_file"
+
+# upload file with explicit media type: text/plain
+
+file_doc=$(create-file.sh \
+-f "$AGENT_CERT_FILE" \
+-p "$AGENT_CERT_PWD" \
+-b "$END_USER_BASE_URL" \
+--title "Test File for Media Type Update" \
+--file "$test_file" \
+--file-content-type "text/plain")
+
+# get the file resource URI and initial dct:format
+
+file_doc_ntriples=$(get.sh \
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  --accept 'application/n-triples' \
+  "$file_doc")
+
+file_uri=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_doc//\//\\/}> <http:\/\/xmlns.com\/foaf\/0.1\/primaryTopic> <(.*)> \./\1/p")
+
+# get initial SHA1 hash
+initial_sha1=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <http:\/\/xmlns.com\/foaf\/0.1\/sha1> \"(.*)\" \./\1/p")
+
+# get initial dct:format
+initial_format=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <http:\/\/purl.org\/dc\/terms\/format> <(.*)> \./\1/p")
+
+# verify initial format is text/plain
+if [[ ! "$initial_format" =~ text/plain ]]; then
+    echo "ERROR: Initial format should contain text/plain but got: $initial_format"
+    exit 1
+fi
+
+# re-upload the same file to the same document with different explicit media type: text/csv
+# using PUT with RDF/POST multipart format
+# IMPORTANT: Include explicit dct:format in RDF to simulate user editing the format field in the form
+
+rdf_post=""
+rdf_post+="-F \"rdf=\"\n"
+rdf_post+="-F \"sb=file\"\n"
+rdf_post+="-F \"pu=http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName\"\n"
+rdf_post+="-F \"ol=@${test_file};type=text/csv\"\n"
+rdf_post+="-F \"pu=http://purl.org/dc/terms/title\"\n"
+rdf_post+="-F \"ol=Test File for Media Type Update\"\n"
+rdf_post+="-F \"pu=http://www.w3.org/1999/02/22-rdf-syntax-ns#type\"\n"
+rdf_post+="-F \"ou=http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#FileDataObject\"\n"
+rdf_post+="-F \"pu=http://purl.org/dc/terms/format\"\n"
+rdf_post+="-F \"ou=http://www.sparontologies.net/mediatype/text/csv\"\n"
+rdf_post+="-F \"su=${file_doc}\"\n"
+rdf_post+="-F \"pu=http://purl.org/dc/terms/title\"\n"
+rdf_post+="-F \"ol=Test File for Media Type Update\"\n"
+rdf_post+="-F \"pu=http://www.w3.org/1999/02/22-rdf-syntax-ns#type\"\n"
+rdf_post+="-F \"ou=https://www.w3.org/ns/ldt/document-hierarchy#Item\"\n"
+rdf_post+="-F \"pu=http://xmlns.com/foaf/0.1/primaryTopic\"\n"
+rdf_post+="-F \"ob=file\"\n"
+rdf_post+="-F \"pu=http://rdfs.org/sioc/ns#has_container\"\n"
+rdf_post+="-F \"ou=${END_USER_BASE_URL}files/\"\n"
+
+echo -e "$rdf_post" | curl -f -v -s -k -X PUT -H "Accept: text/turtle" -E "$AGENT_CERT_FILE":"$AGENT_CERT_PWD" -o /dev/null --config - "$file_doc"
+
+# get updated document
+
+updated_ntriples=$(get.sh \
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  --accept 'application/n-triples' \
+  "$file_doc")
+
+# get updated SHA1 hash (should be same as initial)
+updated_sha1=$(echo "$updated_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <http:\/\/xmlns.com\/foaf\/0.1\/sha1> \"(.*)\" \./\1/p")
+
+# get updated dct:format (should be text/csv)
+updated_format=$(echo "$updated_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <http:\/\/purl.org\/dc\/terms\/format> <(.*)> \./\1/p")
+
+# verify SHA1 is unchanged (same file content)
+if [ "$initial_sha1" != "$updated_sha1" ]; then
+    echo "ERROR: SHA1 hash changed! Initial: $initial_sha1, Updated: $updated_sha1"
+    exit 1
+fi
+
+# verify dct:format was updated to text/csv
+if [[ ! "$updated_format" =~ text/csv ]]; then
+    echo "ERROR: Format should have been updated to text/csv but got: $updated_format"
+    exit 1
+fi
+
+# cleanup
+rm -f "$test_file"

From 85262f0d3305a2ff8fd8ede2bbaf95c7cec97733 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martynas=20Jusevi=C4=8Dius?= <martynas@atomgraph.com>
Date: Thu, 22 Jan 2026 14:29:06 +0100
Subject: [PATCH 3/7] Test fix

---
 http-tests/imports/PUT-file-format-browser.sh | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/http-tests/imports/PUT-file-format-browser.sh b/http-tests/imports/PUT-file-format-browser.sh
index cf5a20616..dbc20e42c 100755
--- a/http-tests/imports/PUT-file-format-browser.sh
+++ b/http-tests/imports/PUT-file-format-browser.sh
@@ -51,7 +51,7 @@ initial_format=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <h
 
 # re-upload the same file to the same document with explicit media type: text/csv
 # using PUT with RDF/POST multipart format
-# IMPORTANT: Include explicit dct:format in RDF to simulate user editing the format field in the form
+# IMPORTANT: Do NOT include explicit dct:format in RDF - test fallback to bodyPart.getMediaType()
 
 rdf_post=""
 rdf_post+="-F \"rdf=\"\n"
@@ -62,8 +62,6 @@ rdf_post+="-F \"pu=http://purl.org/dc/terms/title\"\n"
 rdf_post+="-F \"ol=Test File for Browser Media Type\"\n"
 rdf_post+="-F \"pu=http://www.w3.org/1999/02/22-rdf-syntax-ns#type\"\n"
 rdf_post+="-F \"ou=http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#FileDataObject\"\n"
-rdf_post+="-F \"pu=http://purl.org/dc/terms/format\"\n"
-rdf_post+="-F \"ou=http://www.sparontologies.net/mediatype/text/csv\"\n"
 rdf_post+="-F \"su=${file_doc}\"\n"
 rdf_post+="-F \"pu=http://purl.org/dc/terms/title\"\n"
 rdf_post+="-F \"ol=Test File for Browser Media Type\"\n"

From 279e4aa945ee2eba8e6e2978812d5a4ed64699e5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martynas=20Jusevi=C4=8Dius?= <martynas@atomgraph.com>
Date: Thu, 22 Jan 2026 15:23:08 +0100
Subject: [PATCH 4/7] HTTP test updates

---
 .../imports/PUT-file-format-explicit.sh       | 55 ++++++++-----------
 ...e-format-browser.sh => PUT-file-format.sh} | 51 ++++++++---------
 2 files changed, 45 insertions(+), 61 deletions(-)
 rename http-tests/imports/{PUT-file-format-browser.sh => PUT-file-format.sh} (62%)

diff --git a/http-tests/imports/PUT-file-format-explicit.sh b/http-tests/imports/PUT-file-format-explicit.sh
index eaa10401e..3c9dffd8b 100755
--- a/http-tests/imports/PUT-file-format-explicit.sh
+++ b/http-tests/imports/PUT-file-format-explicit.sh
@@ -24,15 +24,20 @@ echo "test,data,sample" > "$test_file"
 echo "1,2,3" >> "$test_file"
 echo "4,5,6" >> "$test_file"
 
+# generate slug for the file document
+
+slug=$(uuidgen | tr '[:upper:]' '[:lower:]')
+
 # upload file with explicit media type: text/plain
 
 file_doc=$(create-file.sh \
--f "$AGENT_CERT_FILE" \
--p "$AGENT_CERT_PWD" \
--b "$END_USER_BASE_URL" \
---title "Test File for Media Type Update" \
---file "$test_file" \
---file-content-type "text/plain")
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  -b "$END_USER_BASE_URL" \
+  --title "Test File for Media Type Update" \
+  --slug "$slug" \
+  --file "$test_file" \
+  --file-content-type "text/plain")
 
 # get the file resource URI and initial dct:format
 
@@ -56,32 +61,18 @@ if [[ ! "$initial_format" =~ text/plain ]]; then
     exit 1
 fi
 
-# re-upload the same file to the same document with different explicit media type: text/csv
-# using PUT with RDF/POST multipart format
-# IMPORTANT: Include explicit dct:format in RDF to simulate user editing the format field in the form
-
-rdf_post=""
-rdf_post+="-F \"rdf=\"\n"
-rdf_post+="-F \"sb=file\"\n"
-rdf_post+="-F \"pu=http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName\"\n"
-rdf_post+="-F \"ol=@${test_file};type=text/csv\"\n"
-rdf_post+="-F \"pu=http://purl.org/dc/terms/title\"\n"
-rdf_post+="-F \"ol=Test File for Media Type Update\"\n"
-rdf_post+="-F \"pu=http://www.w3.org/1999/02/22-rdf-syntax-ns#type\"\n"
-rdf_post+="-F \"ou=http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#FileDataObject\"\n"
-rdf_post+="-F \"pu=http://purl.org/dc/terms/format\"\n"
-rdf_post+="-F \"ou=http://www.sparontologies.net/mediatype/text/csv\"\n"
-rdf_post+="-F \"su=${file_doc}\"\n"
-rdf_post+="-F \"pu=http://purl.org/dc/terms/title\"\n"
-rdf_post+="-F \"ol=Test File for Media Type Update\"\n"
-rdf_post+="-F \"pu=http://www.w3.org/1999/02/22-rdf-syntax-ns#type\"\n"
-rdf_post+="-F \"ou=https://www.w3.org/ns/ldt/document-hierarchy#Item\"\n"
-rdf_post+="-F \"pu=http://xmlns.com/foaf/0.1/primaryTopic\"\n"
-rdf_post+="-F \"ob=file\"\n"
-rdf_post+="-F \"pu=http://rdfs.org/sioc/ns#has_container\"\n"
-rdf_post+="-F \"ou=${END_USER_BASE_URL}files/\"\n"
-
-echo -e "$rdf_post" | curl -f -v -s -k -X PUT -H "Accept: text/turtle" -E "$AGENT_CERT_FILE":"$AGENT_CERT_PWD" -o /dev/null --config - "$file_doc"
+# re-upload the same file with same slug but different explicit media type: text/csv
+# this simulates editing the file document through the UI and uploading a new file
+
+create-file.sh \
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  -b "$END_USER_BASE_URL" \
+  --title "Test File for Media Type Update" \
+  --slug "$slug" \
+  --file "$test_file" \
+  --file-content-type "text/csv" \
+  > /dev/null
 
 # get updated document
 
diff --git a/http-tests/imports/PUT-file-format-browser.sh b/http-tests/imports/PUT-file-format.sh
similarity index 62%
rename from http-tests/imports/PUT-file-format-browser.sh
rename to http-tests/imports/PUT-file-format.sh
index dbc20e42c..4a30ad9d6 100755
--- a/http-tests/imports/PUT-file-format-browser.sh
+++ b/http-tests/imports/PUT-file-format.sh
@@ -24,14 +24,19 @@ echo "test,data,sample" > "$test_file"
 echo "1,2,3" >> "$test_file"
 echo "4,5,6" >> "$test_file"
 
+# generate slug for the file document
+
+slug=$(uuidgen | tr '[:upper:]' '[:lower:]')
+
 # upload file WITHOUT explicit media type (rely on browser detection via `file -b --mime-type`)
 
 file_doc=$(create-file.sh \
--f "$AGENT_CERT_FILE" \
--p "$AGENT_CERT_PWD" \
--b "$END_USER_BASE_URL" \
---title "Test File for Browser Media Type" \
---file "$test_file")
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  -b "$END_USER_BASE_URL" \
+  --title "Test File for Browser Media Type" \
+  --slug "$slug" \
+  --file "$test_file")
 
 # get the file resource URI and initial dct:format
 
@@ -49,30 +54,18 @@ initial_sha1=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <htt
 # get initial dct:format (should be browser-detected)
 initial_format=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_uri//\//\\/}> <http:\/\/purl.org\/dc\/terms\/format> <(.*)> \./\1/p")
 
-# re-upload the same file to the same document with explicit media type: text/csv
-# using PUT with RDF/POST multipart format
-# IMPORTANT: Do NOT include explicit dct:format in RDF - test fallback to bodyPart.getMediaType()
-
-rdf_post=""
-rdf_post+="-F \"rdf=\"\n"
-rdf_post+="-F \"sb=file\"\n"
-rdf_post+="-F \"pu=http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName\"\n"
-rdf_post+="-F \"ol=@${test_file};type=text/csv\"\n"
-rdf_post+="-F \"pu=http://purl.org/dc/terms/title\"\n"
-rdf_post+="-F \"ol=Test File for Browser Media Type\"\n"
-rdf_post+="-F \"pu=http://www.w3.org/1999/02/22-rdf-syntax-ns#type\"\n"
-rdf_post+="-F \"ou=http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#FileDataObject\"\n"
-rdf_post+="-F \"su=${file_doc}\"\n"
-rdf_post+="-F \"pu=http://purl.org/dc/terms/title\"\n"
-rdf_post+="-F \"ol=Test File for Browser Media Type\"\n"
-rdf_post+="-F \"pu=http://www.w3.org/1999/02/22-rdf-syntax-ns#type\"\n"
-rdf_post+="-F \"ou=https://www.w3.org/ns/ldt/document-hierarchy#Item\"\n"
-rdf_post+="-F \"pu=http://xmlns.com/foaf/0.1/primaryTopic\"\n"
-rdf_post+="-F \"ob=file\"\n"
-rdf_post+="-F \"pu=http://rdfs.org/sioc/ns#has_container\"\n"
-rdf_post+="-F \"ou=${END_USER_BASE_URL}files/\"\n"
-
-echo -e "$rdf_post" | curl -f -v -s -k -X PUT -H "Accept: text/turtle" -E "$AGENT_CERT_FILE":"$AGENT_CERT_PWD" -o /dev/null --config - "$file_doc"
+# re-upload the same file with same slug but WITH explicit media type: text/csv
+# this simulates editing and uploading with a corrected format after browser auto-detection was wrong
+
+create-file.sh \
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  -b "$END_USER_BASE_URL" \
+  --title "Test File for Browser Media Type" \
+  --slug "$slug" \
+  --file "$test_file" \
+  --file-content-type "text/csv" \
+  > /dev/null
 
 # get updated document
 

From 31d433a2d87a5d4421f20c71786f87a49b89d53d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martynas=20Jusevi=C4=8Dius?= <martynas@atomgraph.com>
Date: Fri, 23 Jan 2026 11:16:58 +0100
Subject: [PATCH 5/7] Added missing class constant

---
 src/main/java/com/atomgraph/linkeddatahub/vocabulary/ACL.java | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/main/java/com/atomgraph/linkeddatahub/vocabulary/ACL.java b/src/main/java/com/atomgraph/linkeddatahub/vocabulary/ACL.java
index 1a528e187..259d34a0e 100644
--- a/src/main/java/com/atomgraph/linkeddatahub/vocabulary/ACL.java
+++ b/src/main/java/com/atomgraph/linkeddatahub/vocabulary/ACL.java
@@ -60,6 +60,9 @@ public static String getURI()
     /** <code>acl:Append</code> access mode */
     public static final OntClass Append = m_model.createClass( NS + "Append" );
 
+    /** <code>acl:Control</code> access mode */
+    public static final OntClass Control = m_model.createClass( NS + "Control" );
+
     /** <code>acl:AuthenticatedAgent</code> class */
     public static final OntClass AuthenticatedAgent = m_model.createClass( NS + "AuthenticatedAgent" );
 

From 20fe469e307d27e3baf837e3f0858b5502b725c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martynas=20Jusevi=C4=8Dius?= <martynas@atomgraph.com>
Date: Sat, 24 Jan 2026 11:46:39 +0100
Subject: [PATCH 6/7] Ontology from upload deadlock test

---
 .../ontology-import-upload-no-deadlock.sh     | 154 ++++++++++++++++++
 .../admin/model/test-ontology-import.ttl      |  17 ++
 2 files changed, 171 insertions(+)
 create mode 100755 http-tests/admin/model/ontology-import-upload-no-deadlock.sh
 create mode 100644 http-tests/admin/model/test-ontology-import.ttl

diff --git a/http-tests/admin/model/ontology-import-upload-no-deadlock.sh b/http-tests/admin/model/ontology-import-upload-no-deadlock.sh
new file mode 100755
index 000000000..af69d213f
--- /dev/null
+++ b/http-tests/admin/model/ontology-import-upload-no-deadlock.sh
@@ -0,0 +1,154 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Test that ontology imports of uploaded files do not cause deadlock
+# This verifies the fix for circular dependency when:
+# 1. Request arrives for /uploads/xyz
+# 2. OntologyFilter intercepts it and loads ontology
+# 3. Ontology has owl:imports for /uploads/xyz
+# 4. Jena FileManager makes HTTP request to /uploads/xyz
+# 5. Would cause infinite loop/deadlock without the fix
+
+initialize_dataset "$END_USER_BASE_URL" "$TMP_END_USER_DATASET" "$END_USER_ENDPOINT_URL"
+initialize_dataset "$ADMIN_BASE_URL" "$TMP_ADMIN_DATASET" "$ADMIN_ENDPOINT_URL"
+purge_cache "$END_USER_VARNISH_SERVICE"
+purge_cache "$ADMIN_VARNISH_SERVICE"
+purge_cache "$FRONTEND_VARNISH_SERVICE"
+
+pwd=$(realpath "$PWD")
+
+# add agent to the writers group so they can upload files
+
+add-agent-to-group.sh \
+  -f "$OWNER_CERT_FILE" \
+  -p "$OWNER_CERT_PWD" \
+  --agent "$AGENT_URI" \
+  "${ADMIN_BASE_URL}acl/groups/writers/"
+
+# Step 1: Upload an RDF file
+
+file_content_type="text/turtle"
+
+file_doc=$(create-file.sh \
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  -b "$END_USER_BASE_URL" \
+  --title "Test ontology for upload import" \
+  --file "$pwd/test-ontology-import.ttl" \
+  --file-content-type "${file_content_type}")
+
+# Step 2: Extract the uploaded file URI (content-addressed)
+
+file_doc_ntriples=$(get.sh \
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  --accept 'application/n-triples' \
+  "$file_doc")
+
+upload_uri=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_doc//\//\\/}> <http:\/\/xmlns.com\/foaf\/0.1\/primaryTopic> <(.*)> \./\1/p")
+
+echo "Uploaded file URI: $upload_uri"
+
+# Verify the uploaded file is accessible before we add it as an import
+curl -k -f -s \
+  -E "$AGENT_CERT_FILE":"$AGENT_CERT_PWD" \
+  -H "Accept: ${file_content_type}" \
+  "$upload_uri" > /dev/null
+
+echo "Upload file is accessible"
+
+# Step 3: Add the uploaded file as an owl:import to the namespace ontology
+
+namespace_doc="${END_USER_BASE_URL}ns"
+namespace="${namespace_doc}#"
+ontology_doc="${ADMIN_BASE_URL}ontologies/namespace/"
+
+add-ontology-import.sh \
+  -f "$OWNER_CERT_FILE" \
+  -p "$OWNER_CERT_PWD" \
+  --import "$upload_uri" \
+  "$ontology_doc"
+
+echo "Added owl:import of uploaded file to namespace ontology"
+
+# Step 4: Clear the namespace ontology from memory to force reload on next request
+
+clear-ontology.sh \
+  -f "$OWNER_CERT_FILE" \
+  -p "$OWNER_CERT_PWD" \
+  -b "$ADMIN_BASE_URL" \
+  --ontology "$namespace"
+
+echo "Cleared ontology cache to force reload"
+
+# Step 5: Make a request that triggers ontology loading
+# This would cause a deadlock without the OntologyFilter fix
+# Use portable timeout implementation (works on both macOS and Linux)
+
+echo "Making request to trigger ontology loading (testing for deadlock)..."
+
+# Portable timeout function - works on both macOS and Linux
+request_pid=""
+(
+  curl -k -f -s \
+    -E "$OWNER_CERT_FILE":"$OWNER_CERT_PWD" \
+    -H "Accept: application/n-triples" \
+    "$namespace_doc" > /dev/null
+) &
+request_pid=$!
+
+# Wait up to 30 seconds for the request to complete
+timeout_seconds=30
+elapsed=0
+while kill -0 "$request_pid" 2>/dev/null; do
+  if [ $elapsed -ge $timeout_seconds ]; then
+    kill -9 "$request_pid" 2>/dev/null || true
+    echo "ERROR: Request timed out after ${timeout_seconds} seconds - deadlock detected!"
+    exit 1
+  fi
+  sleep 1
+  ((elapsed++))
+done
+
+# Check if curl succeeded
+wait "$request_pid"
+curl_exit_code=$?
+if [ $curl_exit_code -ne 0 ]; then
+  echo "ERROR: Request failed with exit code $curl_exit_code"
+  exit 1
+fi
+
+echo "Request completed successfully in ${elapsed}s (no deadlock)"
+
+# Step 6: Verify the import is present in the loaded ontology
+
+curl -k -f -s \
+  -H "Accept: application/n-triples" \
+  "$namespace_doc" \
+| grep "<${namespace}> <http://www.w3.org/2002/07/owl#imports> <${upload_uri}>" > /dev/null
+
+echo "Verified owl:import is present in namespace ontology"
+
+# Step 7: Verify the uploaded file is still accessible after ontology loading
+
+curl -k -f -s \
+  -E "$AGENT_CERT_FILE":"$AGENT_CERT_PWD" \
+  -H "Accept: ${file_content_type}" \
+  "$upload_uri" > /dev/null
+
+echo "Uploaded file is still accessible after ontology import"
+
+# Step 8: Verify that the imported ontology content is accessible via the namespace document
+# This confirms the import was actually loaded (not just skipped)
+
+curl -k -f -s \
+  -G \
+  -E "$OWNER_CERT_FILE":"$OWNER_CERT_PWD" \
+  -H 'Accept: application/sparql-results+xml' \
+  --data-urlencode "query=SELECT * { <https://example.org/test#TestClass> ?p ?o }" \
+  "$namespace_doc" \
+| grep '<literal>Test Class</literal>' > /dev/null
+
+echo "Verified imported ontology content is accessible via SPARQL"
+
+echo "✓ All tests passed - no deadlock detected when importing uploaded files in ontology"
diff --git a/http-tests/admin/model/test-ontology-import.ttl b/http-tests/admin/model/test-ontology-import.ttl
new file mode 100644
index 000000000..24361b035
--- /dev/null
+++ b/http-tests/admin/model/test-ontology-import.ttl
@@ -0,0 +1,17 @@
+@prefix : <https://example.org/test#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+: a owl:Ontology ;
+    rdfs:label "Test ontology for upload import" ;
+    rdfs:comment "This ontology is uploaded to test that ontology imports of uploaded files do not cause deadlock" .
+
+:TestClass a owl:Class ;
+    rdfs:label "Test Class" ;
+    rdfs:comment "A test class to verify ontology was loaded" .
+
+:testProperty a owl:DatatypeProperty ;
+    rdfs:label "Test Property" ;
+    rdfs:domain :TestClass ;
+    rdfs:range xsd:string .

From 7f4b8f419d3d31cc482d60a07cd788c84312e149 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martynas=20Jusevi=C4=8Dius?= <martynas@atomgraph.com>
Date: Sun, 25 Jan 2026 14:58:47 +0100
Subject: [PATCH 7/7] Ignored paths in `OntologyFilter` (#269)

* Ignored paths in `OntologyFilter`

* Debug test

* Debug test

* Debug test

* Removed debug output

* Debug test

* Debug test

* Removed debug output
---
 .../ontology-import-upload-no-deadlock.sh     | 62 ++-----------------
 .../server/filter/request/OntologyFilter.java | 31 ++++++++++
 2 files changed, 35 insertions(+), 58 deletions(-)

diff --git a/http-tests/admin/model/ontology-import-upload-no-deadlock.sh b/http-tests/admin/model/ontology-import-upload-no-deadlock.sh
index af69d213f..939da9687 100755
--- a/http-tests/admin/model/ontology-import-upload-no-deadlock.sh
+++ b/http-tests/admin/model/ontology-import-upload-no-deadlock.sh
@@ -47,16 +47,12 @@ file_doc_ntriples=$(get.sh \
 
 upload_uri=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_doc//\//\\/}> <http:\/\/xmlns.com\/foaf\/0.1\/primaryTopic> <(.*)> \./\1/p")
 
-echo "Uploaded file URI: $upload_uri"
-
 # Verify the uploaded file is accessible before we add it as an import
 curl -k -f -s \
   -E "$AGENT_CERT_FILE":"$AGENT_CERT_PWD" \
   -H "Accept: ${file_content_type}" \
   "$upload_uri" > /dev/null
 
-echo "Upload file is accessible"
-
 # Step 3: Add the uploaded file as an owl:import to the namespace ontology
 
 namespace_doc="${END_USER_BASE_URL}ns"
@@ -69,8 +65,6 @@ add-ontology-import.sh \
   --import "$upload_uri" \
   "$ontology_doc"
 
-echo "Added owl:import of uploaded file to namespace ontology"
-
 # Step 4: Clear the namespace ontology from memory to force reload on next request
 
 clear-ontology.sh \
@@ -79,66 +73,22 @@ clear-ontology.sh \
   -b "$ADMIN_BASE_URL" \
   --ontology "$namespace"
 
-echo "Cleared ontology cache to force reload"
-
-# Step 5: Make a request that triggers ontology loading
-# This would cause a deadlock without the OntologyFilter fix
-# Use portable timeout implementation (works on both macOS and Linux)
-
-echo "Making request to trigger ontology loading (testing for deadlock)..."
-
-# Portable timeout function - works on both macOS and Linux
-request_pid=""
-(
-  curl -k -f -s \
-    -E "$OWNER_CERT_FILE":"$OWNER_CERT_PWD" \
-    -H "Accept: application/n-triples" \
-    "$namespace_doc" > /dev/null
-) &
-request_pid=$!
-
-# Wait up to 30 seconds for the request to complete
-timeout_seconds=30
-elapsed=0
-while kill -0 "$request_pid" 2>/dev/null; do
-  if [ $elapsed -ge $timeout_seconds ]; then
-    kill -9 "$request_pid" 2>/dev/null || true
-    echo "ERROR: Request timed out after ${timeout_seconds} seconds - deadlock detected!"
-    exit 1
-  fi
-  sleep 1
-  ((elapsed++))
-done
-
-# Check if curl succeeded
-wait "$request_pid"
-curl_exit_code=$?
-if [ $curl_exit_code -ne 0 ]; then
-  echo "ERROR: Request failed with exit code $curl_exit_code"
-  exit 1
-fi
-
-echo "Request completed successfully in ${elapsed}s (no deadlock)"
-
-# Step 6: Verify the import is present in the loaded ontology
+# Step 5: Verify the import is present in the loaded ontology
+# This request also triggers ontology loading and would detect deadlock
 
 curl -k -f -s \
   -H "Accept: application/n-triples" \
   "$namespace_doc" \
 | grep "<${namespace}> <http://www.w3.org/2002/07/owl#imports> <${upload_uri}>" > /dev/null
 
-echo "Verified owl:import is present in namespace ontology"
-
-# Step 7: Verify the uploaded file is still accessible after ontology loading
+# Step 6: Verify the uploaded file is still accessible after ontology loading
 
 curl -k -f -s \
   -E "$AGENT_CERT_FILE":"$AGENT_CERT_PWD" \
   -H "Accept: ${file_content_type}" \
   "$upload_uri" > /dev/null
 
-echo "Uploaded file is still accessible after ontology import"
-
-# Step 8: Verify that the imported ontology content is accessible via the namespace document
+# Step 7: Verify that the imported ontology content is accessible via the namespace document
 # This confirms the import was actually loaded (not just skipped)
 
 curl -k -f -s \
@@ -148,7 +98,3 @@ curl -k -f -s \
   --data-urlencode "query=SELECT * { <https://example.org/test#TestClass> ?p ?o }" \
   "$namespace_doc" \
 | grep '<literal>Test Class</literal>' > /dev/null
-
-echo "Verified imported ontology content is accessible via SPARQL"
-
-echo "✓ All tests passed - no deadlock detected when importing uploaded files in ontology"
diff --git a/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/OntologyFilter.java b/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/OntologyFilter.java
index c996d5214..0390a989b 100644
--- a/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/OntologyFilter.java
+++ b/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/OntologyFilter.java
@@ -54,12 +54,43 @@ public class OntologyFilter implements ContainerRequestFilter
     
     private static final Logger log = LoggerFactory.getLogger(OntologyFilter.class);
 
+    /**
+     * Paths that should not trigger ontology loading to avoid circular dependencies.
+     *
+     * When an ontology contains owl:imports pointing to URIs within these paths,
+     * loading the ontology would trigger HTTP requests to those URIs. If those requests
+     * are intercepted by this filter, it creates a circular dependency:
+     *
+     * 1. Request arrives for /uploads/xyz
+     * 2. OntologyFilter intercepts it and loads ontology
+     * 3. Ontology has owl:imports for /uploads/xyz
+     * 4. Jena FileManager makes HTTP request to /uploads/xyz
+     * 5. OntologyFilter intercepts it again → infinite loop/deadlock
+     *
+     * Additionally, uploaded files are binary/RDF content that don't require
+     * ontology context for their serving logic.
+     */
+    private static final java.util.Set<String> IGNORED_PATH_PREFIXES = java.util.Set.of(
+        "uploads/"
+    );
+
     @Inject com.atomgraph.linkeddatahub.Application system;
 
     
     @Override
     public void filter(ContainerRequestContext crc) throws IOException
     {
+        String path = crc.getUriInfo().getPath();
+
+        // Skip ontology loading for paths that may be referenced in owl:imports
+        // to prevent circular dependency deadlocks during ontology resolution
+        if (IGNORED_PATH_PREFIXES.stream().anyMatch(path::startsWith))
+        {
+            if (log.isTraceEnabled()) log.trace("Skipping ontology loading for path: {}", path);
+            crc.setProperty(OWL.Ontology.getURI(), Optional.empty());
+            return;
+        }
+
         crc.setProperty(OWL.Ontology.getURI(), getOntology(crc));
     }