From c9eeaa2dddc3266ce11b7ba629037eb00928d1f9 Mon Sep 17 00:00:00 2001
From: Oliver Stolpe <oliver.stolpe@bih-charite.de>
Date: Wed, 3 Apr 2024 16:38:08 +0200
Subject: [PATCH] fix: xlsx file export issues (#1504)

---
 Pipfile                                    |   1 +
 Pipfile.lock                               | 619 ++++++++++-----------
 utils/kickoff_orphaned_annotation_query.py |   2 +-
 utils/projectwide_query.py                 | 294 ++++++++++
 variants/file_export.py                    |   4 +-
 variants/serializers/__init__.py           |   2 +-
 variants/utils.py                          |  20 +-
 variants/views/api/__init__.py             |   6 +
 8 files changed, 610 insertions(+), 338 deletions(-)
 create mode 100644 utils/projectwide_query.py

diff --git a/Pipfile b/Pipfile
index 5b8e4a4c0..477d5e210 100644
--- a/Pipfile
+++ b/Pipfile
@@ -56,6 +56,7 @@ s3fs = "*"
 toml = "*"
 black = "*"
 drf-spectacular = {extras = ["sidecar"], version = "*"}
+rich = "*"
 
 [dev-packages]
 # packages for testing
diff --git a/Pipfile.lock b/Pipfile.lock
index 2683ad9df..a051eb961 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "0f57262f5d5253a53bfaae7e41e2be99552b0f9fb7c1deff7b0042dfb517d339"
+            "sha256": "0ba2c1456b9116c276a3fd7d6b349d7879c3020feba7eb241aeb0840ab798d1b"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -18,11 +18,11 @@
     "default": {
         "aiobotocore": {
             "hashes": [
-                "sha256:bc841cef234afcb781f2d600680c9e49d01b9a2e8169790a32579bb0df51777f",
-                "sha256:e121503dca049cf361dea19730e335aff2e7508f7f8b24db2e6a43a6fb70299e"
+                "sha256:41160f33cdada96815be7d180d1a2405fbf03f0364bac88c03d6ff1ad2cd83d7",
+                "sha256:eb595362cfa6cd70e2940766e3945b114e2522168b67096b0dbc3067f7fd60ad"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==2.12.0"
+            "version": "==2.12.2"
         },
         "aiohttp": {
             "hashes": [
@@ -136,7 +136,6 @@
                 "sha256:a739e2924bf7940daee3a17ccec99fd7175363a160d6e8c3329e61d6534a165e"
             ],
             "index": "pypi",
-            "markers": "python_version < '4.0' and python_full_version >= '3.6.1'",
             "version": "==2.6"
         },
         "altamisa": {
@@ -210,7 +209,7 @@
                 "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f",
                 "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"
             ],
-            "markers": "python_version >= '3.7'",
+            "markers": "python_full_version < '3.11.3'",
             "version": "==4.0.3"
         },
         "attrs": {
@@ -219,7 +218,6 @@
                 "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.7'",
             "version": "==23.2.0"
         },
         "awesome-slugify": {
@@ -242,7 +240,6 @@
                 "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"
             ],
             "index": "pypi",
-            "markers": "python_full_version >= '3.6.0'",
             "version": "==4.12.3"
         },
         "billiard": {
@@ -278,7 +275,6 @@
                 "sha256:e2af80566f43c85f5797365077fb64a393861a3730bd110971ab7a0c94e873e7"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
             "version": "==24.3.0"
         },
         "botocore": {
@@ -295,7 +291,6 @@
                 "sha256:a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
             "version": "==23.2.3"
         },
         "celery": {
@@ -478,11 +473,11 @@
         },
         "click-didyoumean": {
             "hashes": [
-                "sha256:a0713dc7a1de3f06bc0df5a9567ad19ead2d3d5689b434768a6145bff77c0667",
-                "sha256:f184f0d851d96b6d29297354ed981b7dd71df7ff500d82fa6d11f0856bee8035"
+                "sha256:4f82fdff0dbe64ef8ab2279bd6aa3f6a99c3b28c05aa09cbfc07c9d7fbb5a463",
+                "sha256:5c4bb6007cfea5f2fd6583a2fb6701a22a41eb98957e63d0fac41c10e7c3117c"
             ],
-            "markers": "python_full_version >= '3.6.2' and python_full_version < '4.0.0'",
-            "version": "==0.3.0"
+            "markers": "python_full_version >= '3.6.2'",
+            "version": "==0.3.1"
         },
         "click-plugins": {
             "hashes": [
@@ -567,7 +562,6 @@
                 "sha256:a52ea7fcf280b16f7b739cec38fa6d3f8953a5456986944c3ca97e79882b4e38"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.6'",
             "version": "==3.2.25"
         },
         "django-autocomplete-light": {
@@ -582,7 +576,6 @@
                 "sha256:ea2e5a770d01c62ecf66d0dd6e8df284e26321245b8abcc6d82d8740765b42d5"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.6'",
             "version": "==5.3.3"
         },
         "django-crispy-forms": {
@@ -612,7 +605,6 @@
                 "sha256:e09b7dcb8417b743234dfc57c95a7c1d1d87a88844abd13b4c5387f807b31bf6"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
             "version": "==4.3.0"
         },
         "django-dirtyfields": {
@@ -644,7 +636,6 @@
                 "sha256:9600b7562f79a92cbf1fde6403c04fee314608fefbb595502e34383ae8203401"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.6'",
             "version": "==3.2.3"
         },
         "django-iconify": {
@@ -694,12 +685,11 @@
         },
         "django-pydantic-field": {
             "hashes": [
-                "sha256:1db00a937b3c5f70ae2698a68c96aefa82ac7318dbfbbb5fb78699edbf4f9941",
-                "sha256:dde9df9ad22b00fb246b3010b271f4db34ab4369f6a17e26d00eab0de04150ed"
+                "sha256:0c40b2017c237916320be3e7154e49dc1e9d3f251d7748a5081757cf860fb74e",
+                "sha256:4c9f700dfcc3f868c3fb9b49572c6a2cd438c08be125a9030b8074583eab0323"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.7'",
-            "version": "==0.3.3"
+            "version": "==0.3.7"
         },
         "django-rest-knox": {
             "hashes": [
@@ -721,7 +711,6 @@
                 "sha256:55b6c73c4c0384d33c2a8cb2fae369475baa551aee924af20f05a07027201762"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
             "version": "==0.13.4"
         },
         "django-su": {
@@ -774,26 +763,26 @@
                 "sidecar"
             ],
             "hashes": [
-                "sha256:0a4cada4b7136a0bf17233476c066c511a048bc6a485ae2140326ac7ba4003b2",
-                "sha256:452e0cff3c12ee057b897508a077562967b9e62717992eeec10e62dbbc7b5a33"
+                "sha256:a199492f2163c4101055075ebdbb037d59c6e0030692fc83a1a8c0fc65929981",
+                "sha256:b1c04bf8b2fbbeaf6f59414b4ea448c8787aba4d32f76055c3b13335cf7ec37b"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==0.27.1"
+            "index": "pypi",
+            "version": "==0.27.2"
         },
         "drf-spectacular-sidecar": {
             "hashes": [
-                "sha256:db95a38971c9be09986356f82041fac60183d28ebdf60c0c51eb8c1f86da3937",
-                "sha256:dc819ef7a35448c18b2bf4273b38fe1468e14daea5fc8675afb5d0f9e6d9a0ba"
+                "sha256:68532dd094714f79c1775c00848f22c10f004826abc856442ff30c3bc9c40bb4",
+                "sha256:8359befe69a8953fea86be01c1ff37038854a62546225551de16c47c07dccd4e"
             ],
-            "version": "==2024.2.1"
+            "version": "==2024.4.1"
         },
         "elementpath": {
             "hashes": [
-                "sha256:8d25db9150f5a6aa978c9f58e607fcd5ab6e6e3017140563439a9884ab1eb304",
-                "sha256:ecc885f2bb5bd5322fd68ace071f134a8fabf05f0019d77c638b906b844f6593"
+                "sha256:cda092281afe508ece1bf65373905b30196c9426f3730cfea46059e103a131bd",
+                "sha256:dfc4b8ca3d87966dcb0df40b5b6d04a98f053683271930fad9e7fa000924dfb2"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==4.3.0"
+            "version": "==4.4.0"
         },
         "exceptiongroup": {
             "hashes": [
@@ -888,11 +877,11 @@
         },
         "fsspec": {
             "hashes": [
-                "sha256:817f969556fa5916bc682e02ca2045f96ff7f586d45110fcb76022063ad2c7d8",
-                "sha256:b6ad1a679f760dda52b1168c859d01b7b80648ea6f7f7c7f5a8a91dc3f3ecb84"
+                "sha256:918d18d41bf73f0e2b261824baeb1b124bcf771767e3a26425cd7dec3332f512",
+                "sha256:f39780e282d7d117ffb42bb96992f8a90795e4d0fb0f661a70ca39fe9c43ded9"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==2024.2.0"
+            "version": "==2024.3.1"
         },
         "greenlet": {
             "hashes": [
@@ -1008,6 +997,7 @@
             "hashes": [
                 "sha256:32c28f9a4b1526c9e1b4cb23c65a85428fde5ba117eac7fc8394ec5d0a9b411f"
             ],
+            "index": "pypi",
             "version": "==0.4"
         },
         "jinja2": {
@@ -1040,7 +1030,6 @@
                 "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
             "version": "==4.21.1"
         },
         "jsonschema-specifications": {
@@ -1053,11 +1042,11 @@
         },
         "kombu": {
             "hashes": [
-                "sha256:0eac1bbb464afe6fb0924b21bf79460416d25d8abc52546d4f16cad94f789488",
-                "sha256:30e470f1a6b49c70dc6f6d13c3e4cc4e178aa6c469ceb6bcd55645385fc84b93"
+                "sha256:49f1e62b12369045de2662f62cc584e7df83481a513db83b01f87b5b9785e378",
+                "sha256:f3da5b570a147a5da8280180aa80b03807283d63ea5081fcdb510d18242431d9"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==5.3.5"
+            "version": "==5.3.6"
         },
         "lxml": {
             "hashes": [
@@ -1156,7 +1145,6 @@
                 "sha256:fdb325b7fba1e2c40b9b1db407f85642e32404131c08480dd652110fc908561b"
             ],
             "index": "pypi",
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
             "version": "==4.9.4"
         },
         "markdown": {
@@ -1167,6 +1155,14 @@
             "markers": "python_version >= '3.7'",
             "version": "==3.4.1"
         },
+        "markdown-it-py": {
+            "hashes": [
+                "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1",
+                "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==3.0.0"
+        },
         "markupsafe": {
             "hashes": [
                 "sha256:00e046b6dd71aa03a41079792f8473dc494d564611a8f89bbbd7cb93295ebdcf",
@@ -1233,6 +1229,14 @@
             "markers": "python_version >= '3.7'",
             "version": "==2.1.5"
         },
+        "mdurl": {
+            "hashes": [
+                "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8",
+                "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==0.1.2"
+        },
         "mistune": {
             "hashes": [
                 "sha256:0246113cb2492db875c6be56974a7c893333bf26cd92891c85f63151cee09d34",
@@ -1384,7 +1388,6 @@
                 "sha256:ffa75af20b44f8dba823498024771d5ac50620e6915abac414251bd971b4529f"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.9'",
             "version": "==1.26.4"
         },
         "packaging": {
@@ -1428,7 +1431,6 @@
                 "sha256:f9d3558d263073ed95e46f4650becff0c5e1ffe0fc3a015de3c79283dfbdb3df"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.9'",
             "version": "==2.2.1"
         },
         "pathspec": {
@@ -1449,77 +1451,78 @@
         },
         "pillow": {
             "hashes": [
-                "sha256:0304004f8067386b477d20a518b50f3fa658a28d44e4116970abfcd94fac34a8",
-                "sha256:0689b5a8c5288bc0504d9fcee48f61a6a586b9b98514d7d29b840143d6734f39",
-                "sha256:0eae2073305f451d8ecacb5474997c08569fb4eb4ac231ffa4ad7d342fdc25ac",
-                "sha256:0fb3e7fc88a14eacd303e90481ad983fd5b69c761e9e6ef94c983f91025da869",
-                "sha256:11fa2e5984b949b0dd6d7a94d967743d87c577ff0b83392f17cb3990d0d2fd6e",
-                "sha256:127cee571038f252a552760076407f9cff79761c3d436a12af6000cd182a9d04",
-                "sha256:154e939c5f0053a383de4fd3d3da48d9427a7e985f58af8e94d0b3c9fcfcf4f9",
-                "sha256:15587643b9e5eb26c48e49a7b33659790d28f190fc514a322d55da2fb5c2950e",
-                "sha256:170aeb00224ab3dc54230c797f8404507240dd868cf52066f66a41b33169bdbe",
-                "sha256:1b5e1b74d1bd1b78bc3477528919414874748dd363e6272efd5abf7654e68bef",
-                "sha256:1da3b2703afd040cf65ec97efea81cfba59cdbed9c11d8efc5ab09df9509fc56",
-                "sha256:1e23412b5c41e58cec602f1135c57dfcf15482013ce6e5f093a86db69646a5aa",
-                "sha256:2247178effb34a77c11c0e8ac355c7a741ceca0a732b27bf11e747bbc950722f",
-                "sha256:257d8788df5ca62c980314053197f4d46eefedf4e6175bc9412f14412ec4ea2f",
-                "sha256:3031709084b6e7852d00479fd1d310b07d0ba82765f973b543c8af5061cf990e",
-                "sha256:322209c642aabdd6207517e9739c704dc9f9db943015535783239022002f054a",
-                "sha256:322bdf3c9b556e9ffb18f93462e5f749d3444ce081290352c6070d014c93feb2",
-                "sha256:33870dc4653c5017bf4c8873e5488d8f8d5f8935e2f1fb9a2208c47cdd66efd2",
-                "sha256:35bb52c37f256f662abdfa49d2dfa6ce5d93281d323a9af377a120e89a9eafb5",
-                "sha256:3c31822339516fb3c82d03f30e22b1d038da87ef27b6a78c9549888f8ceda39a",
-                "sha256:3eedd52442c0a5ff4f887fab0c1c0bb164d8635b32c894bc1faf4c618dd89df2",
-                "sha256:3ff074fc97dd4e80543a3e91f69d58889baf2002b6be64347ea8cf5533188213",
-                "sha256:47c0995fc4e7f79b5cfcab1fc437ff2890b770440f7696a3ba065ee0fd496563",
-                "sha256:49d9ba1ed0ef3e061088cd1e7538a0759aab559e2e0a80a36f9fd9d8c0c21591",
-                "sha256:51f1a1bffc50e2e9492e87d8e09a17c5eea8409cda8d3f277eb6edc82813c17c",
-                "sha256:52a50aa3fb3acb9cf7213573ef55d31d6eca37f5709c69e6858fe3bc04a5c2a2",
-                "sha256:54f1852cd531aa981bc0965b7d609f5f6cc8ce8c41b1139f6ed6b3c54ab82bfb",
-                "sha256:609448742444d9290fd687940ac0b57fb35e6fd92bdb65386e08e99af60bf757",
-                "sha256:69ffdd6120a4737710a9eee73e1d2e37db89b620f702754b8f6e62594471dee0",
-                "sha256:6fad5ff2f13d69b7e74ce5b4ecd12cc0ec530fcee76356cac6742785ff71c452",
-                "sha256:7049e301399273a0136ff39b84c3678e314f2158f50f517bc50285fb5ec847ad",
-                "sha256:70c61d4c475835a19b3a5aa42492409878bbca7438554a1f89d20d58a7c75c01",
-                "sha256:716d30ed977be8b37d3ef185fecb9e5a1d62d110dfbdcd1e2a122ab46fddb03f",
-                "sha256:753cd8f2086b2b80180d9b3010dd4ed147efc167c90d3bf593fe2af21265e5a5",
-                "sha256:773efe0603db30c281521a7c0214cad7836c03b8ccff897beae9b47c0b657d61",
-                "sha256:7823bdd049099efa16e4246bdf15e5a13dbb18a51b68fa06d6c1d4d8b99a796e",
-                "sha256:7c8f97e8e7a9009bcacbe3766a36175056c12f9a44e6e6f2d5caad06dcfbf03b",
-                "sha256:823ef7a27cf86df6597fa0671066c1b596f69eba53efa3d1e1cb8b30f3533068",
-                "sha256:8373c6c251f7ef8bda6675dd6d2b3a0fcc31edf1201266b5cf608b62a37407f9",
-                "sha256:83b2021f2ade7d1ed556bc50a399127d7fb245e725aa0113ebd05cfe88aaf588",
-                "sha256:870ea1ada0899fd0b79643990809323b389d4d1d46c192f97342eeb6ee0b8483",
-                "sha256:8d12251f02d69d8310b046e82572ed486685c38f02176bd08baf216746eb947f",
-                "sha256:9c23f307202661071d94b5e384e1e1dc7dfb972a28a2310e4ee16103e66ddb67",
-                "sha256:9d189550615b4948f45252d7f005e53c2040cea1af5b60d6f79491a6e147eef7",
-                "sha256:a086c2af425c5f62a65e12fbf385f7c9fcb8f107d0849dba5839461a129cf311",
-                "sha256:a2b56ba36e05f973d450582fb015594aaa78834fefe8dfb8fcd79b93e64ba4c6",
-                "sha256:aebb6044806f2e16ecc07b2a2637ee1ef67a11840a66752751714a0d924adf72",
-                "sha256:b1b3020d90c2d8e1dae29cf3ce54f8094f7938460fb5ce8bc5c01450b01fbaf6",
-                "sha256:b4b6b1e20608493548b1f32bce8cca185bf0480983890403d3b8753e44077129",
-                "sha256:b6f491cdf80ae540738859d9766783e3b3c8e5bd37f5dfa0b76abdecc5081f13",
-                "sha256:b792a349405fbc0163190fde0dc7b3fef3c9268292586cf5645598b48e63dc67",
-                "sha256:b7c2286c23cd350b80d2fc9d424fc797575fb16f854b831d16fd47ceec078f2c",
-                "sha256:babf5acfede515f176833ed6028754cbcd0d206f7f614ea3447d67c33be12516",
-                "sha256:c365fd1703040de1ec284b176d6af5abe21b427cb3a5ff68e0759e1e313a5e7e",
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@@ -1535,7 +1538,6 @@
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@@ -1572,7 +1574,6 @@
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@@ -1595,7 +1596,6 @@
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@@ -1697,10 +1697,11 @@
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-            "version": "==2.21"
+            "markers": "python_version >= '3.8'",
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@@ -1746,7 +1747,6 @@
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@@ -1844,11 +1844,11 @@
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@@ -1881,7 +1881,6 @@
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@@ -1898,7 +1897,6 @@
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@@ -1907,7 +1905,6 @@
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@@ -1972,25 +1969,23 @@
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-            "markers": "python_version >= '3.7'",
-            "version": "==5.0.2"
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@@ -2097,8 +2092,7 @@
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@@ -2108,6 +2102,14 @@
             "index": "pypi",
             "version": "==0.2.0"
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@@ -2222,20 +2224,19 @@
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@@ -2347,7 +2348,6 @@
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@@ -2461,56 +2461,55 @@
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@@ -2518,7 +2517,6 @@
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@@ -2527,7 +2525,6 @@
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@@ -2544,7 +2541,6 @@
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@@ -2552,7 +2548,7 @@
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@@ -2572,12 +2568,11 @@
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@@ -2707,7 +2702,6 @@
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@@ -2716,7 +2710,6 @@
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@@ -2838,37 +2831,35 @@
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@@ -3044,7 +3035,6 @@
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@@ -3069,7 +3059,6 @@
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@@ -3108,16 +3097,15 @@
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@@ -3132,7 +3120,6 @@
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@@ -3148,7 +3135,6 @@
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@@ -3157,7 +3143,6 @@
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@@ -3190,16 +3175,15 @@
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         "ipython": {
             "hashes": [
-                "sha256:39c6f9efc079fb19bfb0f17eee903978fe9a290b1b82d68196c641cecb76ea22",
-                "sha256:869335e8cded62ffb6fac8928e5287a05433d6462e3ebaac25f4216474dd6bc4"
+                "sha256:07232af52a5ba146dc3372c7bf52a0f890a23edf38d77caef8d53f9cdc2584c1",
+                "sha256:7468edaf4f6de3e1b912e57f66c241e6fd3c7099f2ec2136e239e142e800274d"
             ],
             "markers": "python_version < '3.11' and python_version >= '3.7'",
-            "version": "==8.22.1"
+            "version": "==8.23.0"
         },
         "isort": {
             "hashes": [
@@ -3207,7 +3191,6 @@
                 "sha256:8ca5e72a8d85860d5a3fa69b8745237f2939afe12dbf656afbcb47fe72d947a6"
             ],
             "index": "pypi",
-            "markers": "python_full_version >= '3.8.0'",
             "version": "==5.13.2"
         },
         "jedi": {
@@ -3216,7 +3199,6 @@
                 "sha256:e983c654fe5c02867aef4cdfce5a2fbb4a50adc0af145f70504238f18ef5e7e0"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.6'",
             "version": "==0.19.1"
         },
         "jsonmatch": {
@@ -3322,7 +3304,6 @@
                 "sha256:f91456ead12ab3c6c2e9491cf33ba6d08357d802192379bb482f1033ade496f5"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.6'",
             "version": "==3.1.2"
         },
         "outcome": {
@@ -3347,7 +3328,6 @@
                 "sha256:7fc905272cefa4f364c1a3429cbbe9c0f98b793988efb5bf90aac80f08db09b1"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.7'",
             "version": "==0.9.0"
         },
         "parso": {
@@ -3438,12 +3418,11 @@
         },
         "python-dateutil": {
             "hashes": [
-                "sha256:78e73e19c63f5b20ffa567001531680d939dc042bf7850431877645523c66709",
-                "sha256:cbf2f1da5e6083ac2fbfd4da39a25f34312230110440f424a14c7558bb85d82e"
+                "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3",
+                "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"
             ],
             "index": "pypi",
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==2.9.0"
+            "version": "==2.9.0.post0"
         },
         "requests": {
             "hashes": [
@@ -3451,25 +3430,23 @@
                 "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.7'",
-            "version": "==2.31.0"
+            "version": "==2.31"
         },
         "requests-mock": {
             "hashes": [
-                "sha256:ef10b572b489a5f28e09b708697208c4a3b2b89ef80a9f01584340ea357ec3c4",
-                "sha256:f7fae383f228633f6bececebdab236c478ace2284d6292c6e7e2867b9ab74d15"
+                "sha256:b1e37054004cdd5e56c84454cc7df12b25f90f382159087f4b6915aaeef39563",
+                "sha256:e9e12e333b525156e82a3c852f22016b9158220d2f47454de9cae8a77d371401"
             ],
             "index": "pypi",
-            "version": "==1.11.0"
+            "version": "==1.12.1"
         },
         "selenium": {
             "hashes": [
-                "sha256:a11f67afa8bfac6b77e148c987b33f6b14eb1cae4d352722a75de1f26e3f0ae2",
-                "sha256:b24a3cdd2d47c29832e81345bfcde0c12bb608738013e53c781b211b418df241"
+                "sha256:5b4f49240d61e687a73f7968ae2517d403882aae3550eae2a229c745e619f1d9",
+                "sha256:d9dfd6d0b021d71d0a48b865fe7746490ba82b81e9c87b212360006629eb1853"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
-            "version": "==4.18.1"
+            "version": "==4.19.0"
         },
         "setuptools": {
             "hashes": [
@@ -3523,7 +3500,6 @@
                 "sha256:93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
             "version": "==3.0.0"
         },
         "termcolor": {
@@ -3544,19 +3520,19 @@
         },
         "traitlets": {
             "hashes": [
-                "sha256:2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74",
-                "sha256:8585105b371a04b8316a43d5ce29c098575c2e477850b62b848b964f1444527e"
+                "sha256:8cdd83c040dab7d1dee822678e5f5d100b514f7b72b01615b26fc5718916fdf9",
+                "sha256:fcdf85684a772ddeba87db2f398ce00b40ff550d1528c03c14dbf6a02003cd80"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==5.14.1"
+            "version": "==5.14.2"
         },
         "trio": {
             "hashes": [
-                "sha256:c3bd3a4e3e3025cd9a2241eae75637c43fe0b9e88b4c97b9161a55b9e54cd72c",
-                "sha256:ffa09a74a6bf81b84f8613909fb0beaee84757450183a7a2e0b47b455c0cac5d"
+                "sha256:9b41f5993ad2c0e5f62d0acca320ec657fdb6b2a2c22b8c7aed6caf154475c4e",
+                "sha256:e6458efe29cc543e557a91e614e2b51710eba2961669329ce9c862d50c6e8e81"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==0.24.0"
+            "version": "==0.25.0"
         },
         "trio-websocket": {
             "hashes": [
@@ -3653,7 +3629,6 @@
                 "sha256:f9b2fdca47dc855516b2d66eef3c39f2672cbf7e7a42e7e67ad2cbfcd6ba107d"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
             "version": "==4.0.0"
         },
         "wcwidth": {
@@ -3665,12 +3640,11 @@
         },
         "werkzeug": {
             "hashes": [
-                "sha256:507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc",
-                "sha256:90a285dc0e42ad56b34e696398b8122ee4c681833fb35b8334a095d82c56da10"
+                "sha256:3aac3f5da756f93030740bc235d3e09449efcf65f2f55e3602e1d851b8f48795",
+                "sha256:e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
-            "version": "==3.0.1"
+            "version": "==3.0.2"
         },
         "wsproto": {
             "hashes": [
@@ -3684,61 +3658,64 @@
     "ldap-packages": {
         "asgiref": {
             "hashes": [
-                "sha256:89b2ef2247e3b562a16eef663bc0e2e703ec6468e2fa8a5cd61cd449786d4f6e",
-                "sha256:9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed"
+                "sha256:3e1e3ecc849832fe52ccf2cb6686b7a55f82bb1d6aee72a58826471390335e47",
+                "sha256:c343bd80a0bec947a9860adb4c432ffa7db769836c64238fc34bdc3fec84d590"
             ],
-            "markers": "python_version >= '3.7'",
-            "version": "==3.7.2"
+            "markers": "python_version >= '3.8'",
+            "version": "==3.8.1"
         },
         "django": {
             "hashes": [
-                "sha256:5dd5b787c3ba39637610fe700f54bf158e33560ea0dba600c19921e7ff926ec5",
-                "sha256:aaee9fb0fb4ebd4311520887ad2e33313d368846607f82a9a0ed461cd4c35b18"
+                "sha256:7ca38a78654aee72378594d63e51636c04b8e28574f5505dff630895b5472777",
+                "sha256:a52ea7fcf280b16f7b739cec38fa6d3f8953a5456986944c3ca97e79882b4e38"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.6'",
-            "version": "==3.2.24"
+            "version": "==3.2.25"
         },
         "django-auth-ldap": {
             "hashes": [
-                "sha256:4e82ded9292dc6ac7a75784d81b95174b72ca5e650a76e11317e3b68008e56d8",
-                "sha256:9ae2bf87f9b6367b6cfd94a0451896cbc728e5400ed81cbfbd58ce743c0909a2"
+                "sha256:8dea65376b8b2fa1beee52348760e3082e642939a5038cbe881a5e6381b65b8a",
+                "sha256:de02c36e9f9025be9242cd40b5617403a886c72e3c5e0dd489b9b3db996dc875"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
-            "version": "==4.6.0"
+            "version": "==4.7.0"
         },
         "pyasn1": {
             "hashes": [
-                "sha256:4439847c58d40b1d0a573d07e3856e95333f1976294494c325775aeca506eb58",
-                "sha256:6d391a96e59b23130a5cfa74d6fd7f388dbbe26cc8f1edf39fdddf08d9d6676c"
+                "sha256:3a35ab2c4b5ef98e17dfdec8ab074046fbda76e281c5a706ccd82328cfc8f64c",
+                "sha256:cca4bb0f2df5504f02f6f8a775b6e416ff9b0b3b16f7ee80b5a3153d9b804473"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
-            "version": "==0.5.1"
+            "markers": "python_version >= '3.8'",
+            "version": "==0.6.0"
         },
         "pyasn1-modules": {
             "hashes": [
-                "sha256:5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c",
-                "sha256:d3ccd6ed470d9ffbc716be08bd90efbd44d0734bc9303818f7336070984a162d"
+                "sha256:831dbcea1b177b28c9baddf4c6d1013c24c3accd14a1873fffaa6a2e905f17b6",
+                "sha256:be04f15b66c206eed667e0bb5ab27e2b1855ea54a842e5037738099e8ca4ae0b"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
-            "version": "==0.3.0"
+            "markers": "python_version >= '3.8'",
+            "version": "==0.4.0"
         },
         "python-ldap": {
             "hashes": [
                 "sha256:7edb0accec4e037797705f3a05cbf36a9fde50d08c8f67f2aef99a2628fab828"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.6'",
             "version": "==3.4.4"
         },
+        "pytz": {
+            "hashes": [
+                "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812",
+                "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"
+            ],
+            "version": "==2024.1"
+        },
         "sqlparse": {
             "hashes": [
                 "sha256:5430a4fe2ac7d0f93e66f1efc6e1338a41884b7ddf2a350cedd20ccc4d9d28f3",
                 "sha256:d446183e84b8349fa3061f0fe7f06ca94ba65b426946ffebe6e3e8295332420c"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.5'",
             "version": "==0.4.4"
         },
         "typing-extensions": {
@@ -3753,28 +3730,27 @@
     "prod-packages": {
         "asgiref": {
             "hashes": [
-                "sha256:89b2ef2247e3b562a16eef663bc0e2e703ec6468e2fa8a5cd61cd449786d4f6e",
-                "sha256:9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed"
+                "sha256:3e1e3ecc849832fe52ccf2cb6686b7a55f82bb1d6aee72a58826471390335e47",
+                "sha256:c343bd80a0bec947a9860adb4c432ffa7db769836c64238fc34bdc3fec84d590"
             ],
-            "markers": "python_version >= '3.7'",
-            "version": "==3.7.2"
+            "markers": "python_version >= '3.8'",
+            "version": "==3.8.1"
         },
         "async-timeout": {
             "hashes": [
                 "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f",
                 "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"
             ],
-            "markers": "python_version >= '3.7'",
+            "markers": "python_full_version < '3.11.3'",
             "version": "==4.0.3"
         },
         "boto3": {
             "hashes": [
-                "sha256:340c73f57fcca6f503403e2e13a0a4ad44bec218feee2e0896be612324394afd",
-                "sha256:cd30261a782824ce543a628ae524480abb4ca6ab4e4a2631477e48baed43b5f2"
+                "sha256:530a4cea3d40a6bd2f15a368ea395beef1ea6dff4491823bc48bd20c7d4da655",
+                "sha256:8c598382e8fb61cfa8f75056197e9b509eb52039ebc291af3b1096241ba2542c"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
-            "version": "==1.34.53"
+            "version": "==1.34.76"
         },
         "botocore": {
             "hashes": [
@@ -3786,19 +3762,18 @@
         },
         "django": {
             "hashes": [
-                "sha256:5dd5b787c3ba39637610fe700f54bf158e33560ea0dba600c19921e7ff926ec5",
-                "sha256:aaee9fb0fb4ebd4311520887ad2e33313d368846607f82a9a0ed461cd4c35b18"
+                "sha256:7ca38a78654aee72378594d63e51636c04b8e28574f5505dff630895b5472777",
+                "sha256:a52ea7fcf280b16f7b739cec38fa6d3f8953a5456986944c3ca97e79882b4e38"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.6'",
-            "version": "==3.2.24"
+            "version": "==3.2.25"
         },
         "django-redis": {
             "hashes": [
                 "sha256:6a02abaa34b0fea8bf9b707d2c363ab6adc7409950b2db93602e6cb292818c42",
                 "sha256:ebc88df7da810732e2af9987f7f426c96204bf89319df4c6da6ca9a2942edd5b"
             ],
-            "markers": "python_version >= '3.6'",
+            "index": "pypi",
             "version": "==5.4.0"
         },
         "django-storages": {
@@ -3807,7 +3782,6 @@
                 "sha256:51b36af28cc5813b98d5f3dfe7459af638d84428c8df4a03990c7d74d1bea4e5"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.7'",
             "version": "==1.14.2"
         },
         "gevent": {
@@ -3855,7 +3829,6 @@
                 "sha256:fbfdce91239fe306772faab57597186710d5699213f4df099d1612da7320d682"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
             "version": "==24.2.1"
         },
         "greenlet": {
@@ -3928,7 +3901,6 @@
                 "sha256:88ec8bff1d634f98e61b9f65bc4bf3cd918a90806c6f5c48bc5603849ec81033"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.5'",
             "version": "==21.2.0"
         },
         "jmespath": {
@@ -3949,29 +3921,34 @@
         },
         "python-dateutil": {
             "hashes": [
-                "sha256:78e73e19c63f5b20ffa567001531680d939dc042bf7850431877645523c66709",
-                "sha256:cbf2f1da5e6083ac2fbfd4da39a25f34312230110440f424a14c7558bb85d82e"
+                "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3",
+                "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"
             ],
             "index": "pypi",
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==2.9.0"
+            "version": "==2.9.0.post0"
+        },
+        "pytz": {
+            "hashes": [
+                "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812",
+                "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"
+            ],
+            "version": "==2024.1"
         },
         "redis": {
             "hashes": [
-                "sha256:3f82cc80d350e93042c8e6e7a5d0596e4dd68715babffba79492733e1f367037",
-                "sha256:4caa8e1fcb6f3c0ef28dba99535101d80934b7d4cd541bbb47f4a3826ee472d1"
+                "sha256:4973bae7444c0fbed64a06b87446f79361cb7e4ec1538c022d696ed7a5015580",
+                "sha256:5da9b8fe9e1254293756c16c008e8620b3d15fcc6dde6babde9541850e72a32d"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.7'",
-            "version": "==5.0.2"
+            "version": "==5.0.3"
         },
         "s3transfer": {
             "hashes": [
-                "sha256:3cdb40f5cfa6966e812209d0994f2a4709b561c88e90cf00c2696d2df4e56b2e",
-                "sha256:d0c8bbf672d5eebbe4e57945e23b972d963f07d82f661cabf678a5c88831595b"
+                "sha256:5683916b4c724f799e600f41dd9e10a9ff19871bf87623cc8f491cb4f5fa0a19",
+                "sha256:ceb252b11bcf87080fb7850a224fb6e05c8a776bab8f2b64b7f25b969464839d"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==0.10.0"
+            "version": "==0.10.1"
         },
         "setuptools": {
             "hashes": [
@@ -3995,7 +3972,6 @@
                 "sha256:d446183e84b8349fa3061f0fe7f06ca94ba65b426946ffebe6e3e8295332420c"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.5'",
             "version": "==0.4.4"
         },
         "typing-extensions": {
@@ -4020,7 +3996,6 @@
                 "sha256:b1f9db9bf67dc183484d760b99f4080185633136a273a03f6436034a41064146"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.8'",
             "version": "==6.6.0"
         },
         "zope.event": {
diff --git a/utils/kickoff_orphaned_annotation_query.py b/utils/kickoff_orphaned_annotation_query.py
index 453a84af0..cb3655ab2 100644
--- a/utils/kickoff_orphaned_annotation_query.py
+++ b/utils/kickoff_orphaned_annotation_query.py
@@ -16,7 +16,7 @@
 #: Endpoint to smallvariant list-create query
 ENDPOINT_SM_LISTCREATE_QUERY = "/variants/api/query/list-create/{case_uuid}"
 #: Endpoint to smallvariant retrieve query
-ENDPOINT_SM_RETRIEVE_QUERY = "/svs/api/query/retrieve-update-destroy/{query_uuid}/"
+ENDPOINT_SM_RETRIEVE_QUERY = "/variants/api/query/retrieve-update-destroy/{query_uuid}/"
 #: Endpoint to structuralvariant query settings
 ENDPOINT_SV_SETTINGS = "/svs/ajax/query-case/query-settings-shortcut/{case_uuid}/?quick_preset=whole_genome&genotype_criteria=default&inheritance=any&frequency=any&impact=any&sv_type=any"
 #: Endpoint to structuralvariant list-create query
diff --git a/utils/projectwide_query.py b/utils/projectwide_query.py
new file mode 100644
index 000000000..890f2f63d
--- /dev/null
+++ b/utils/projectwide_query.py
@@ -0,0 +1,294 @@
+import json
+import os
+import sys
+import time
+
+import click
+import requests
+from rich.console import Console
+import toml
+
+#: Paths to search the global configuration in.
+GLOBAL_CONFIG_PATHS = ("~/.varfishrc.toml",)
+
+#: Endpoint to generate export tsv file
+ENDPOINT_DOWNLOAD_GENERATE_TSV = "/variants/api/query-case/download/generate/tsv/{query_uuid}"
+#: Endpoint to generate export vcf file
+ENDPOINT_DOWNLOAD_GENERATE_VCF = "/variants/api/query-case/download/generate/vcf/{query_uuid}"
+#: Endpoint to generate export xlsx file
+ENDPOINT_DOWNLOAD_GENERATE_XLSX = "/variants/api/query-case/download/generate/xlsx/{query_uuid}"
+#: Endpoint to download file
+ENDPOINT_DOWNLOAD_SERVE = "/variants/api/query-case/download/serve/{sodar_uuid}"
+#: Endpoint to check download status
+ENDPOINT_DOWNLOAD_STATUS = "/variants/api/query-case/download/status/{sodar_uuid}"
+#: Endpoint to case list
+ENDPOINT_CASE_LIST = "/cases/api/case/list/{project_uuid}"
+#: Endpoint to smallvariant query settings
+ENDPOINT_SM_SETTINGS = "/variants/api/query-case/query-settings-shortcut/{case_uuid}"
+#: Endpoint to smallvariant list-create query
+ENDPOINT_SM_LISTCREATE_QUERY = "/variants/api/query/list-create/{case_uuid}"
+#: Endpoint to smallvariant retrieve query
+ENDPOINT_SM_RETRIEVE_QUERY = "/variants/api/query/retrieve-update-destroy/{query_uuid}/"
+#: Endpoint to structuralvariant query settings
+ENDPOINT_SV_SETTINGS = "/svs/ajax/query-case/query-settings-shortcut/{case_uuid}/?quick_preset=whole_genome&genotype_criteria=default&inheritance=any&frequency=any&impact=any&sv_type=any"
+#: Endpoint to structuralvariant list-create query
+ENDPOINT_SV_LISTCREATE_QUERY = "/svs/ajax/sv-query/list-create/{case_uuid}/"
+#: Endpoint to structuralvariant retrieve query
+ENDPOINT_SV_RETRIEVE_QUERY = "/svs/ajax/sv-query/retrieve-update-destroy/{query_uuid}/"
+
+#: Sleep time between starting queries
+SLEEP_RUN = 2
+#: Sleep time between polling queries
+SLEEP_POLL = 5
+
+#: SQL database name for structural variants
+SQL_SV_DB = "svs_structuralvariant"
+#: SQL database name for small variants
+SQL_SM_DB = "variants_smallvariant"
+#: SQL query template to retrieve variants
+SQL_QUERY_TEMPLATE = "select * from {db} left outer join variants_case on variants_case.id={db}.case_id where variants_case.sodar_uuid='{case_uuid}' and {db}.release='GRCh37' and chromosome='{chromosome}' and start={start};\n"
+
+
+console = Console()
+
+
+def connect_endpoint(config, endpoint, data=None):
+    token = config.get("global", {}).get("varfish_api_token")
+    base = config.get("global", {}).get("varfish_server_url").rstrip("/")
+    url = f"{base}{endpoint}"
+    headers = {"Authorization": f"Token {token}"}
+    if data:
+        response = requests.post(url, headers=headers, json=data)
+    else:
+        response = requests.get(url, headers=headers)
+    if response.status_code not in (
+        200,
+        201,
+    ):
+        sys.stderr.write(f"Error: {url} responded with {response.status_code}\n")
+        return {}
+    return response
+
+
+def read_toml():
+    for config_path in GLOBAL_CONFIG_PATHS:
+        config_path = os.path.expanduser(os.path.expandvars(config_path))
+        if os.path.exists(config_path):
+            with open(config_path, "rt") as tomlf:
+                return toml.load(tomlf)
+    else:
+        sys.stderr.write(
+            f"Could not find any of the global configuration files {GLOBAL_CONFIG_PATHS}"
+        )
+        sys.exit()
+
+
+def run_query(
+    config,
+    settings_endpoint,
+    query_endpoint,
+    case_uuid,
+    gene,
+    region,
+    quick_preset,
+    inheritance,
+    frequency,
+    impact,
+    verbose,
+):
+    url = settings_endpoint.format(case_uuid=case_uuid)
+    url += f"?quick_preset={quick_preset}"
+    if inheritance:
+        url += f"&inheritance={inheritance}"
+    if frequency:
+        url += f"&frequency={frequency}"
+    if impact:
+        url += f"&impact={impact}"
+    if verbose:
+        console.log(url)
+    response = connect_endpoint(config, url)
+    if not response:
+        return ""
+    response_json = response.json()
+    if gene:
+        response_json["query_settings"]["gene_allowlist"] = [gene]
+    elif region:
+        response_json["query_settings"]["genomic_region"] = region
+    url = query_endpoint.format(case_uuid=case_uuid)
+    response = connect_endpoint(config, url, data=response_json)
+    if not response:
+        return ""
+    response_json = response.json()
+    if not response_json.get("sodar_uuid"):
+        console.log(f"[bold red]Error: got no query uuid for case {case_uuid}[/bold red]")
+        return ""
+    time.sleep(SLEEP_RUN)
+    return response_json["sodar_uuid"]
+
+
+def poll_query(config, query_endpoint, query_uuid):
+    url = query_endpoint.format(query_uuid=query_uuid)
+    response = connect_endpoint(config, url)
+    if not response:
+        return {"query_state": "fetching_failed"}
+    return response.json()
+
+
+def poll_queries(config, query_endpoint, query_uuids):
+    poll_running = []
+    for query_uuid, data in query_uuids.items():
+        if not data["running"]:
+            continue
+        query_data = poll_query(config, query_endpoint, query_uuid)
+        data["state"] = query_data["query_state"]
+        data["logs"] = query_data["logs"]
+        data["running"] = query_data["query_state"] == "running"
+        poll_running.append(data["running"])
+    return any(poll_running)
+
+
+def get_case_list(config, project_uuid):
+    url = ENDPOINT_CASE_LIST.format(project_uuid=project_uuid)
+    url_appendix = ""
+    case_query = {}
+    while True:
+        response = connect_endpoint(config, url + ("?" + (url_appendix if url_appendix else "")))
+        response_json = response.json()
+        for case in response_json["results"]:
+            case_query[case["sodar_uuid"]] = {"name": case["name"], "query": None}
+        if not response_json["next"]:
+            break
+        url_appendix = response_json["next"].split("?")[1]
+    return case_query
+
+
+def download_generate(config, query_uuid, export_format):
+    if export_format == "tsv":
+        url = ENDPOINT_DOWNLOAD_GENERATE_TSV.format(query_uuid=query_uuid)
+    elif export_format == "vcf":
+        url = ENDPOINT_DOWNLOAD_GENERATE_VCF.format(query_uuid=query_uuid)
+    elif export_format == "xlsx":
+        url = ENDPOINT_DOWNLOAD_GENERATE_XLSX.format(query_uuid=query_uuid)
+    response = connect_endpoint(config, url)
+    if not response:
+        return
+    return response.json()["export_job__sodar_uuid"]
+
+
+def download_status(config, sodar_uuid):
+    url = ENDPOINT_DOWNLOAD_STATUS.format(sodar_uuid=sodar_uuid)
+    response = connect_endpoint(config, url)
+    if not response:
+        return {}
+    return response.json()["status"]
+
+
+def download_serve(config, sodar_uuid, name):
+    url = ENDPOINT_DOWNLOAD_SERVE.format(sodar_uuid=sodar_uuid)
+    response = connect_endpoint(config, url)
+    if not response:
+        return
+    with open(name, "wb") as fh:
+        fh.write(response.content)
+
+
+@click.command()
+@click.argument("project-uuid")
+@click.option(
+    "--export-format",
+    default="xlsx",
+    type=click.Choice(["tsv", "vcf", "xlsx"], case_sensitive=False),
+)
+@click.option("--gene", default=None, help="Gene to filter on")
+@click.option("--region", default=None, help="Region to filter on")
+@click.option("--quick-preset", default="default", help="Quick preset to use")
+@click.option("--inheritance", default=None, help="Inheritance preset to use")
+@click.option("--frequency", default=None, help="Frequency preset to use")
+@click.option("--impact", default=None, help="Impact preset to use")
+@click.option("--verbose", is_flag=False, help="Verbose output")
+def main(
+    project_uuid, export_format, gene, region, quick_preset, inheritance, frequency, impact, verbose
+):
+    config = read_toml()
+    query_results = {}
+    case_query = {}
+
+    with console.status("[bold green]Starting ..."):
+        case_query = get_case_list(config, project_uuid)
+        console.log("Getting cases from project [bold green]done[/bold green]")
+
+    tasks = [
+        f"Starting query for [bold]{case_query[n]['name']}[/bold] ({n})" for n in case_query.keys()
+    ]
+    with console.status("[bold green]Starting queries ..."):
+        for case_uuid in case_query.keys():
+            rich_query_start = tasks.pop(0)
+            query_uuid = run_query(
+                config,
+                ENDPOINT_SM_SETTINGS,
+                ENDPOINT_SM_LISTCREATE_QUERY,
+                case_uuid,
+                gene,
+                region,
+                quick_preset,
+                inheritance,
+                frequency,
+                impact,
+                verbose,
+            )
+            if not query_uuid:
+                console.log(f"{rich_query_start} [bold red]failed[/bold red]")
+                continue
+            query_results[query_uuid] = {
+                "running": True,
+                "state": "initial",
+                "case_uuid": case_uuid,
+                "logs": [],
+            }
+            case_query[case_uuid]["query"] = query_uuid
+            console.log(f"{rich_query_start} [bold green]done[/bold green]")
+
+    with console.status("[bold green]Waiting for queries to finish ..."):
+        while True:
+            polls_running = poll_queries(config, ENDPOINT_SM_RETRIEVE_QUERY, query_results)
+            if not polls_running:
+                break
+            time.sleep(SLEEP_POLL)
+
+        if verbose:
+            with open("query_logs.json", "w") as fh:
+                json.dump(query_results, fh, indent=1)
+
+    download_uuids = {}
+    tasks = [
+        f"Starting generation of export file for [bold]{case_query[query_results[n]['case_uuid']]['name']}[/bold] ({n})"
+        for n in query_results.keys()
+    ]
+    with console.status("[bold green]Starting generation of export files ..."):
+        for query_uuid, data in query_results.items():
+            if data["state"] == "done":
+                download_uuid = download_generate(config, query_uuid, export_format)
+                if not download_uuid:
+                    console.log(f"{tasks.pop(0)} [bold red]failed[/bold red]")
+                    continue
+                download_uuids[download_uuid] = case_query[data["case_uuid"]]["name"]
+                console.log(f"{tasks.pop(0)} [bold green]done[/bold green]")
+            else:
+                console.log(f"{tasks.pop(0)} [bold red]failed[/bold red]")
+
+    downloads_running = [True] * len(download_uuids)
+    tasks = [f"Downloading file for [bold]{n}[/bold]" for n in download_uuids.values()]
+    with console.status("[bold green]Waiting for downloads to finish ..."):
+        while any(downloads_running):
+            for i, download_uuid in enumerate(download_uuids):
+                downloads_running[i] = download_status(config, download_uuid) == "running"
+            time.sleep(SLEEP_POLL)
+
+        for download_uuid, name in download_uuids.items():
+            download_serve(config, download_uuid, f"{name}.{export_format}")
+            console.log(f"{tasks.pop(0)} [bold green]done[/bold green]")
+    console.log(":heavy_check_mark: [bold green]All done[/bold green]")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/variants/file_export.py b/variants/file_export.py
index 8b9d43838..f015d5233 100644
--- a/variants/file_export.py
+++ b/variants/file_export.py
@@ -653,8 +653,6 @@ def _write_comment_sheet(self):
                 row = [
                     comment.chromosome,
                     comment.start,
-                    comment.end,
-                    comment.bin,
                     comment.reference,
                     comment.alternative,
                     comment.date_created,
@@ -663,7 +661,7 @@ def _write_comment_sheet(self):
                 ]
                 if self.project_or_cohort:
                     row.insert(0, case.name)
-                self.variant_sheet.write_row(offset, 0, row)
+                self.comment_sheet.write_row(offset, 0, row)
                 offset += 1
 
     def _write_metadata_sheet(self):
diff --git a/variants/serializers/__init__.py b/variants/serializers/__init__.py
index bdae1c874..aef648d12 100644
--- a/variants/serializers/__init__.py
+++ b/variants/serializers/__init__.py
@@ -81,7 +81,7 @@ def _check_gene_list_found(gene_list, label):
     # Validate HPO term list.
     if "prio_hpo_terms" in query_settings:
         missing = []
-        for term in query_settings["prio_hpo_terms"]:
+        for term in query_settings["prio_hpo_terms"] or []:
             if term.startswith("HP"):
                 if not HpoName.objects.filter(hpo_id=term).exists():
                     missing.append(term)
diff --git a/variants/utils.py b/variants/utils.py
index 0e3a10d72..11b158b18 100644
--- a/variants/utils.py
+++ b/variants/utils.py
@@ -285,17 +285,15 @@ def _perform_create(obj):
                 for result_row in result_rows:
                     duplicates.append(
                         {
-                            {
-                                "case_uuid": str(case.sodar_uuid),
-                                "case_name": case.name,
-                                "project": case.project.full_title,
-                                "chromosome": result_row.chromosome,
-                                "start": result_row.start,
-                                "end": result_row.end,
-                                "json": json.dumps(
-                                    model_to_dict(result_row, exclude=("id",)), cls=UUIDEncoder
-                                ),
-                            }
+                            "case_uuid": str(case.sodar_uuid),
+                            "case_name": case.name,
+                            "project": case.project.full_title,
+                            "chromosome": result_row.chromosome,
+                            "start": result_row.start,
+                            "end": result_row.end,
+                            "json": json.dumps(
+                                model_to_dict(result_row, exclude=("id",)), cls=UUIDEncoder
+                            ),
                         }
                     )
 
diff --git a/variants/views/api/__init__.py b/variants/views/api/__init__.py
index 29681e9a0..52452dbee 100644
--- a/variants/views/api/__init__.py
+++ b/variants/views/api/__init__.py
@@ -845,11 +845,17 @@ def get(self, request, *args, **kwargs):
         if self.request.get_full_path() == reverse(
             "variants:ajax-query-case-download-generate-tsv",
             kwargs={"smallvariantquery": query.sodar_uuid},
+        ) or self.request.get_full_path() == reverse(
+            "variants:api-query-case-download-generate-tsv",
+            kwargs={"smallvariantquery": query.sodar_uuid},
         ):
             file_type = "tsv"
         elif self.request.get_full_path() == reverse(
             "variants:ajax-query-case-download-generate-vcf",
             kwargs={"smallvariantquery": query.sodar_uuid},
+        ) or self.request.get_full_path() == reverse(
+            "variants:api-query-case-download-generate-vcf",
+            kwargs={"smallvariantquery": query.sodar_uuid},
         ):
             file_type = "vcf"
         else: