fix: fixes CaSe InSenSiTiVe duplicates

clusters/ammunitions.json

@@ -3569,16 +3569,6 @@
       "uuid": "9aa0a1b7-c9ff-422c-9ef1-431459e1e1b9",
       "value": "PMC Bronze 44 Magnum Ammo - 500 Rounds of 180 Grain JHP Ammunition"
     },
-    {
-      "meta": {
-        "caliber": "X",
-        "description": "Tac 7.62x51mm Ammo",
-        "manufacturer": "PMC",
-        "name": "PMC X"
-      },
-      "uuid": "0dd1db3c-8d5d-4296-b780-ae5ac7a92fed",
-      "value": "PMC X - Tac 7.62x51mm Ammo"
-    },
     {
       "meta": {
         "caliber": "Bronze 308 Win Ammo",
@@ -4110,5 +4100,5 @@
       "value": "NobelSport High Brass Field 12 Gauge Ammo - 250 Rounds of 1"
     }
   ],
-  "version": 1
+  "version": 2
 }

clusters/malpedia.json

@@ -3660,25 +3660,6 @@
       "uuid": "6cb47609-b03e-43d9-a4c7-8342f1011f3b",
       "value": "ANGRYREBEL"
     },
-    {
-      "description": "",
-      "meta": {
-        "refs": [
-          "https://malpedia.caad.fkie.fraunhofer.de/details/elf.avoslocker",
-          "https://blogs.blackberry.com/en/2022/04/threat-thursday-avoslocker-prompts-advisory-from-fbi-and-fincen",
-          "https://blog.qualys.com/vulnerabilities-threat-research/2022/03/06/avoslocker-ransomware-behavior-examined-on-windows-linux",
-          "https://blog.cyble.com/2022/01/17/avoslocker-ransomware-linux-version-targets-vmware-esxi-servers/",
-          "https://blog.lexfo.fr/Avoslocker.html",
-          "https://www.ic3.gov/Media/News/2022/220318.pdf",
-          "https://blogs.vmware.com/security/2022/09/esxi-targeting-ransomware-the-threats-that-are-after-your-virtual-machines-part-1.html",
-          "https://blogs.vmware.com/security/2022/02/avoslocker-modern-linux-ransomware-threats.html"
-        ],
-        "synonyms": [],
-        "type": []
-      },
-      "uuid": "465b6a74-87ca-4459-b4be-3f8b272f4485",
-      "value": "Avoslocker"
-    },
     {
       "description": "AVrecon is a Linux-based Remote Access Trojan (RAT) targeting small-office/home-office (SOHO) routers and other ARM-embedded devices. The malware is distributed via exploitation of unpatched vulnerabilities or common misconfiguration of the targeted devices. Once deployed, AVreckon will collect some information about the infected device, open a session to pre-configured C&C server, and spawn a remote shell for command execution. It might also download additional arbitrary files and run them. The malware has recently been used in campaigns aimed at ad-fraud activities, password spraying and data exfiltration.",
       "meta": {
@@ -15170,7 +15151,10 @@
           "https://news.sophos.com/en-us/2021/12/22/avos-locker-remotely-accesses-boxes-even-running-in-safe-mode/",
           "https://news.sophos.com/en-us/2022/03/17/the-ransomware-threat-intelligence-center/",
           "https://unit42.paloaltonetworks.com/emerging-ransomware-groups/",
-          "https://blog.qualys.com/vulnerabilities-threat-research/2022/03/06/avoslocker-ransomware-behavior-examined-on-windows-linux"
+          "https://blog.qualys.com/vulnerabilities-threat-research/2022/03/06/avoslocker-ransomware-behavior-examined-on-windows-linux",
+          "https://blog.lexfo.fr/Avoslocker.html",
+          "https://blogs.vmware.com/security/2022/09/esxi-targeting-ransomware-the-threats-that-are-after-your-virtual-machines-part-1.html",
+          "https://blogs.vmware.com/security/2022/02/avoslocker-modern-linux-ransomware-threats.html"
         ],
         "synonyms": [],
         "type": []
@@ -56457,5 +56441,5 @@
       "value": "Zyklon"
     }
   ],
-  "version": 19803
+  "version": 19804
 }

clusters/ransomware.json

@@ -24250,11 +24250,6 @@
       "uuid": "90c6daf8-8212-4ea8-9b59-af49b290b3b9",
       "value": "TurkStatik"
     },
-    {
-      "description": "ransomware",
-      "uuid": "93277946-177a-4f92-833d-30db9d432656",
-      "value": "Tyrant"
-    },
     {
       "description": "ransomware",
       "uuid": "0407e98d-cd3e-42e1-8daf-3c51d2e4906a",
@@ -29200,5 +29195,5 @@
       "value": "apos"
     }
   ],
-  "version": 122
+  "version": 123
 }

clusters/rat.json

@@ -1770,7 +1770,7 @@
         "date": "1998"
       },
       "uuid": "2a47361d-584b-493f-80a4-37c74c30cf1b",
-      "value": "Vortex"
+      "value": "VorteX"
     },
     {
       "meta": {
@@ -2140,13 +2140,6 @@
       "uuid": "c42394f8-5f35-4797-9393-8289ab8ad3ad",
       "value": "SharpEye"
     },
-    {
-      "meta": {
-        "date": "2010"
-      },
-      "uuid": "58e2e2ee-5c25-4a13-abfc-2a6c85d978fa",
-      "value": "VorteX"
-    },
     {
       "meta": {
         "date": "2010",
@@ -3648,5 +3641,5 @@
       "value": "COATHANGER"
     }
   ],
-  "version": 45
+  "version": 46
 }

tools/gen_ukhsa_culture_collections.py

@@ -19,10 +19,10 @@
 #    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 
-import os
 import json
 import requests
 import uuid
+from pymispgalaxies import Cluster, Galaxy
 
 '''
 From https://www.culturecollections.org.uk/search/?searchScope=Product&pageNumber=1&filter.collectionGroup=0&filter.collection=0&filter.sorting=DateCreated
@@ -42,6 +42,7 @@ cell culture characteristics. Passage numbers where given act only as a guide an
 the passage number stated will be the passage number received by the customer.
 '''
 
+
 def download_items():
     data = {'items': [],
             'collections': {},
@@ -75,11 +76,13 @@ def save_items(d):
         json.dump(d, f, indent=2, sort_keys=True)
     return True
 
+
 def load_saved_items():
     with open('items.json', 'r') as f:
         d = json.load(f)
     return d
 
+
 data = download_items()
 # save_items(data)
 # data = load_saved_items()
@@ -110,12 +113,19 @@ for item in data['items']:
         clusters_dict[cluster['value']] = cluster
 
 # transform dict to list
-clusters = []
+cluster = Cluster('ukhsa-culture-collections', skip_duplicates=True)
+cluster.cluster_values = {}
 for item in clusters_dict.values():
-    clusters.append(item)
+    cluster.append(item, skip_duplicates=True)
+cluster.save('ukhsa-culture-collections')
 
+for cluster, duplicate in cluster.duplicates:
+    print(f"WARNING: Skipped duplicate: {duplicate} in cluster {cluster}")
 
-json_galaxy = {
+try:
+    galaxy = Galaxy('ukhsa-culture-collections')
+except KeyError:
+    galaxy = Galaxy({
         'icon': "virus",
         'name': "UKHSA Culture Collections",
         'description': "UK Health Security Agency Culture Collections represent deposits of cultures that consist of expertly preserved, authenticated cell lines and microbial strains of known provenance.",
@@ -123,20 +133,7 @@ json_galaxy = {
         'type': "ukhsa-culture-collections",
         'uuid': "bbe11c06-1d6a-477e-88f1-cdda2d71de56",
         'version': 1
-}
-
-with open(os.path.join('..', 'clusters', 'ukhsa-culture-collections.json'), 'r') as f:
-    json_cluster = json.load(f)
-json_cluster['values'] = clusters
-json_cluster['version'] += 1
-
-# save the Galaxy and Cluster file
-with open(os.path.join('..', 'galaxies', 'ukhsa-culture-collections.json'), 'w') as f:
-    json.dump(json_galaxy, f, indent=2, sort_keys=True, ensure_ascii=False)
-    f.write('\n')  # only needed for the beauty and to be compliant with jq_all_the_things
-
-with open(os.path.join('..', 'clusters', 'ukhsa-culture-collections.json'), 'w') as f:
-    json.dump(json_cluster, f, indent=2, sort_keys=True, ensure_ascii=False)
-    f.write('\n')  # only needed for the beauty and to be compliant with jq_all_the_things
+    })
+galaxy.save('ukhsa-culture-collections')
 
 print("All done, please don't forget to ./jq_all_the_things.sh, commit, and then ./validate_all.sh.")

tools/tidal-api/models/cluster.py

@@ -132,7 +132,8 @@ class Cluster:
 
     def save_to_file(self, path):
         with open(path, "w") as file:
-            file.write(json.dumps(self.__dict__(), indent=4))
+            file.write(json.dumps(self.__dict__(), indent=2))
+            file.write('\n')
 
     def __str__(self) -> str:
         return f"Cluster: {self.name} - {self.type} - {self.uuid}"
@@ -367,6 +368,7 @@ class SoftwareCluster(Cluster):
                         uuid=associated_software.get("associated_software_id"),
                         value=associated_software.get("name") + " - Associated Software",
                     )
+
                     self.values.append(value.return_value())
                     related.append(
                         {
@@ -384,6 +386,12 @@ class SoftwareCluster(Cluster):
                 uuid=entry.get("id"),
                 value=entry.get("name"),
             )
+            # duplicates, manually handled
+            if value.uuid == '6af0eac2-c35f-4569-ae09-47f1ca846961':
+                value.value = f"{value.value} - Duplicate"
+            if value.uuid == '39d81c48-8f7c-54cb-8fac-485598e31a55':
+                value.value = f"{value.value} - Duplicate"
+
             self.values.append(value.return_value())
 
 
@@ -585,6 +593,17 @@ class ReferencesCluster(Cluster):
                 uuid=entry.get("id"),
                 value=entry.get("name"),
             )
+
+            # handle duplicates manually
+            if value.uuid == 'eea178f4-80bd-49d1-84b1-f80671e9a3e4':
+                value.value = f"{value.value} - Duplicate"
+            if value.uuid == '9bb5c330-56bd-47e7-8414-729d8e6cb3b3':
+                value.value = f"{value.value} - Duplicate"
+            if value.uuid == '8b4bdce9-da19-443f-88d2-11466e126c09':
+                value.value = f"{value.value} - Duplicate"
+            if value.uuid == 'b4727044-51bb-43b3-afdb-515bb4bb0f7e':
+                value.value = f"{value.value} - Duplicate"
+
             self.values.append(value.return_value())
 
 

tools/tidal-api/models/galaxy.py

@@ -14,4 +14,5 @@ class Galaxy:
 
     def save_to_file(self, path: str):
         with open(path, "w") as file:
-            file.write(json.dumps(asdict(self), indent=4))
+            file.write(json.dumps(asdict(self), indent=2))
+            file.write('\n')