From 2b775ed96f56ac4d23ab3efd8f2c05fe74488a55 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Sun, 14 Jul 2024 17:09:51 +0000 Subject: [PATCH 01/12] Update README with XMI structure and query breakdowns --- model/queries_execution_notebook.ipynb | 226 ++++++++++++------------- 1 file changed, 113 insertions(+), 113 deletions(-) diff --git a/model/queries_execution_notebook.ipynb b/model/queries_execution_notebook.ipynb index 8ba8078f2..03e26f540 100644 --- a/model/queries_execution_notebook.ipynb +++ b/model/queries_execution_notebook.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "be35de5a", + "id": "779e5ef4", "metadata": {}, "source": [ "# Query Execution Notebook" @@ -11,7 +11,7 @@ { "cell_type": "code", "execution_count": null, - "id": "0bc0eec1", + "id": "eb0b307f", "metadata": {}, "outputs": [], "source": [ @@ -20,7 +20,7 @@ }, { "cell_type": "markdown", - "id": "b9e63956", + "id": "033c7ed8", "metadata": {}, "source": [ "## anatomy_query\n", @@ -30,7 +30,7 @@ { "cell_type": "code", "execution_count": null, - "id": "62ef69fc", + "id": "969267c7", "metadata": {}, "outputs": [], "source": [ @@ -57,7 +57,7 @@ }, { "cell_type": "markdown", - "id": "e84756cd", + "id": "5a4cf7ae", "metadata": {}, "source": [ "## anat_image_query\n", @@ -67,7 +67,7 @@ { "cell_type": "code", "execution_count": null, - "id": "9b07502b", + "id": "5c26fb13", "metadata": {}, "outputs": [], "source": [ @@ -94,7 +94,7 @@ }, { "cell_type": "markdown", - "id": "32c752e2", + "id": "d0ec2506", "metadata": {}, "source": [ "## Get other cluster members\n", @@ -104,7 +104,7 @@ { "cell_type": "code", "execution_count": null, - "id": "cfd2bf55", + "id": "3b0b33d3", "metadata": {}, "outputs": [], "source": [ @@ -131,7 +131,7 @@ }, { "cell_type": "markdown", - "id": "f9995af0", + "id": "0b9f6159", "metadata": {}, "source": [ "## Fetch all example individuals for Class\n", @@ -141,7 +141,7 @@ { "cell_type": "code", "execution_count": null, - "id": "8ecb3bcb", + "id": "decc9fdf", "metadata": {}, "outputs": [], "source": [ @@ -168,7 +168,7 @@ }, { "cell_type": "markdown", - "id": "a9b1e773", + "id": "79dd953e", "metadata": {}, "source": [ "## Find domain individuals for template id\n", @@ -178,7 +178,7 @@ { "cell_type": "code", "execution_count": null, - "id": "766e5e60", + "id": "ff15b560", "metadata": {}, "outputs": [], "source": [ @@ -205,7 +205,7 @@ }, { "cell_type": "markdown", - "id": "6402e2a2", + "id": "cec3c038", "metadata": {}, "source": [ "## Get cluster members\n", @@ -215,7 +215,7 @@ { "cell_type": "code", "execution_count": null, - "id": "bc2556f8", + "id": "8fde8694", "metadata": {}, "outputs": [], "source": [ @@ -242,7 +242,7 @@ }, { "cell_type": "markdown", - "id": "5d2282a2", + "id": "d5b1d23e", "metadata": {}, "source": [ "## Find images for dataset\n", @@ -252,7 +252,7 @@ { "cell_type": "code", "execution_count": null, - "id": "29e38eff", + "id": "c46973a6", "metadata": {}, "outputs": [], "source": [ @@ -279,7 +279,7 @@ }, { "cell_type": "markdown", - "id": "a420db86", + "id": "2c03f5c2", "metadata": {}, "source": [ "## Find images aligned to template id\n", @@ -289,7 +289,7 @@ { "cell_type": "code", "execution_count": null, - "id": "ae7d0d48", + "id": "757950ec", "metadata": {}, "outputs": [], "source": [ @@ -316,7 +316,7 @@ }, { "cell_type": "markdown", - "id": "c3ed67a5", + "id": "aeb8f17c", "metadata": {}, "source": [ "## Test Query for Exp from Anatomy\n", @@ -326,7 +326,7 @@ { "cell_type": "code", "execution_count": null, - "id": "7cda1c51", + "id": "035b9bf7", "metadata": {}, "outputs": [], "source": [ @@ -353,7 +353,7 @@ }, { "cell_type": "markdown", - "id": "9b7aeb1d", + "id": "c3f92a80", "metadata": {}, "source": [ "## Query for Anatomy from Exp\n", @@ -363,7 +363,7 @@ { "cell_type": "code", "execution_count": null, - "id": "8fa0c3ee", + "id": "bf3934cb", "metadata": {}, "outputs": [], "source": [ @@ -390,7 +390,7 @@ }, { "cell_type": "markdown", - "id": "4e435325", + "id": "6c67342a", "metadata": {}, "source": [ "## Test Query for Anatomy from Exp\n", @@ -400,7 +400,7 @@ { "cell_type": "code", "execution_count": null, - "id": "28054007", + "id": "e51119d4", "metadata": {}, "outputs": [], "source": [ @@ -427,7 +427,7 @@ }, { "cell_type": "markdown", - "id": "d7213764", + "id": "f04cb867", "metadata": {}, "source": [ "## Query for Exp from Anatomy\n", @@ -437,7 +437,7 @@ { "cell_type": "code", "execution_count": null, - "id": "4cc5ed44", + "id": "8737a357", "metadata": {}, "outputs": [], "source": [ @@ -464,7 +464,7 @@ }, { "cell_type": "markdown", - "id": "806160f1", + "id": "0b732d01", "metadata": {}, "source": [ "## template_2_datasets_query\n", @@ -474,7 +474,7 @@ { "cell_type": "code", "execution_count": null, - "id": "61a552e0", + "id": "fa9a43d2", "metadata": {}, "outputs": [], "source": [ @@ -501,7 +501,7 @@ }, { "cell_type": "markdown", - "id": "29b030ef", + "id": "a3e56e8a", "metadata": {}, "source": [ "## test_all_datasets_query\n", @@ -511,7 +511,7 @@ { "cell_type": "code", "execution_count": null, - "id": "c6163015", + "id": "dbdcead9", "metadata": {}, "outputs": [], "source": [ @@ -538,7 +538,7 @@ }, { "cell_type": "markdown", - "id": "71d6bec0", + "id": "4b480901", "metadata": {}, "source": [ "## Query for Exp from Anatomy\n", @@ -548,7 +548,7 @@ { "cell_type": "code", "execution_count": null, - "id": "8cfb20cc", + "id": "45c5d97c", "metadata": {}, "outputs": [], "source": [ @@ -575,7 +575,7 @@ }, { "cell_type": "markdown", - "id": "c7fb4e07", + "id": "a6880d79", "metadata": {}, "source": [ "## neuron_region_connectivity_query\n", @@ -585,7 +585,7 @@ { "cell_type": "code", "execution_count": null, - "id": "20aefe4a", + "id": "72a50409", "metadata": {}, "outputs": [], "source": [ @@ -612,7 +612,7 @@ }, { "cell_type": "markdown", - "id": "9238d2c4", + "id": "32f79461", "metadata": {}, "source": [ "## neuron_neuron_connectivity_query\n", @@ -622,7 +622,7 @@ { "cell_type": "code", "execution_count": null, - "id": "775943cd", + "id": "01898cd1", "metadata": {}, "outputs": [], "source": [ @@ -649,7 +649,7 @@ }, { "cell_type": "markdown", - "id": "64ff9c19", + "id": "4d1b5f91", "metadata": {}, "source": [ "## NBLAST_anat_image_query\n", @@ -659,7 +659,7 @@ { "cell_type": "code", "execution_count": null, - "id": "9d22395c", + "id": "5277e4d7", "metadata": {}, "outputs": [], "source": [ @@ -686,7 +686,7 @@ }, { "cell_type": "markdown", - "id": "5cbed346", + "id": "2d93d24a", "metadata": {}, "source": [ "## Fetch all entities for pub\n", @@ -696,7 +696,7 @@ { "cell_type": "code", "execution_count": null, - "id": "64550344", + "id": "daade1a9", "metadata": {}, "outputs": [], "source": [ @@ -723,7 +723,7 @@ }, { "cell_type": "markdown", - "id": "baab6bba", + "id": "922cb139", "metadata": {}, "source": [ "## NBLAST_anat_image_query_exp\n", @@ -733,7 +733,7 @@ { "cell_type": "code", "execution_count": null, - "id": "bd56edd2", + "id": "b42b9095", "metadata": {}, "outputs": [], "source": [ @@ -760,7 +760,7 @@ }, { "cell_type": "markdown", - "id": "683a77d4", + "id": "02d21feb", "metadata": {}, "source": [ "## NB_anat_image_query\n", @@ -770,7 +770,7 @@ { "cell_type": "code", "execution_count": null, - "id": "9e7053f5", + "id": "40b2c749", "metadata": {}, "outputs": [], "source": [ @@ -797,7 +797,7 @@ }, { "cell_type": "markdown", - "id": "389ac5b8", + "id": "02a42acf", "metadata": {}, "source": [ "## Get JSON for cluster expression query\n", @@ -807,7 +807,7 @@ { "cell_type": "code", "execution_count": null, - "id": "2e9a5800", + "id": "733e2ff3", "metadata": {}, "outputs": [], "source": [ @@ -834,7 +834,7 @@ }, { "cell_type": "markdown", - "id": "b63d6af9", + "id": "202c4cd1", "metadata": {}, "source": [ "## Get JSON for anat scRNAseq query\n", @@ -844,7 +844,7 @@ { "cell_type": "code", "execution_count": null, - "id": "b5548d99", + "id": "ca92b11b", "metadata": {}, "outputs": [], "source": [ @@ -871,7 +871,7 @@ }, { "cell_type": "markdown", - "id": "7a1eaed3", + "id": "e12bdc38", "metadata": {}, "source": [ "## Get JSON for dataset scRNAseq query\n", @@ -881,7 +881,7 @@ { "cell_type": "code", "execution_count": null, - "id": "4d694ee2", + "id": "5122b0bf", "metadata": {}, "outputs": [], "source": [ @@ -908,7 +908,7 @@ }, { "cell_type": "markdown", - "id": "f332cb4a", + "id": "27e54839", "metadata": {}, "source": [ "## Get JSON for cluster expression query\n", @@ -918,7 +918,7 @@ { "cell_type": "code", "execution_count": null, - "id": "9e9b2fad", + "id": "728e578b", "metadata": {}, "outputs": [], "source": [ @@ -945,7 +945,7 @@ }, { "cell_type": "markdown", - "id": "53c4d882", + "id": "cd3809c1", "metadata": {}, "source": [ "## Get term core info\n", @@ -955,7 +955,7 @@ { "cell_type": "code", "execution_count": null, - "id": "fb5081fa", + "id": "08aedb25", "metadata": {}, "outputs": [], "source": [ @@ -982,7 +982,7 @@ }, { "cell_type": "markdown", - "id": "619e3081", + "id": "bb51fe22", "metadata": {}, "source": [ "## Get baseline term info\n", @@ -992,7 +992,7 @@ { "cell_type": "code", "execution_count": null, - "id": "fa98e90b", + "id": "25b0a81f", "metadata": {}, "outputs": [], "source": [ @@ -1019,7 +1019,7 @@ }, { "cell_type": "markdown", - "id": "a01cd6ed", + "id": "ecfbb2e6", "metadata": {}, "source": [ "## Get JSON for Class\n", @@ -1029,7 +1029,7 @@ { "cell_type": "code", "execution_count": null, - "id": "271de81b", + "id": "b58180fe", "metadata": {}, "outputs": [], "source": [ @@ -1056,7 +1056,7 @@ }, { "cell_type": "markdown", - "id": "fd1d836a", + "id": "8607bad5", "metadata": {}, "source": [ "## Get JSON for Neuron Class\n", @@ -1066,7 +1066,7 @@ { "cell_type": "code", "execution_count": null, - "id": "66bcc1ca", + "id": "b7a7ced1", "metadata": {}, "outputs": [], "source": [ @@ -1093,7 +1093,7 @@ }, { "cell_type": "markdown", - "id": "feccb163", + "id": "f7d2a878", "metadata": {}, "source": [ "## Get JSON for Split Class\n", @@ -1103,7 +1103,7 @@ { "cell_type": "code", "execution_count": null, - "id": "41e595bf", + "id": "fcd6b85f", "metadata": {}, "outputs": [], "source": [ @@ -1130,7 +1130,7 @@ }, { "cell_type": "markdown", - "id": "26d4c046", + "id": "4a4f032a", "metadata": {}, "source": [ "## Get JSON for Individual\n", @@ -1140,7 +1140,7 @@ { "cell_type": "code", "execution_count": null, - "id": "5135666a", + "id": "22465198", "metadata": {}, "outputs": [], "source": [ @@ -1167,7 +1167,7 @@ }, { "cell_type": "markdown", - "id": "d786128e", + "id": "20eed0d3", "metadata": {}, "source": [ "## Get JSON for Cluster\n", @@ -1177,7 +1177,7 @@ { "cell_type": "code", "execution_count": null, - "id": "8001bf6f", + "id": "ee0ad66d", "metadata": {}, "outputs": [], "source": [ @@ -1204,7 +1204,7 @@ }, { "cell_type": "markdown", - "id": "ed51a87e", + "id": "8b381712", "metadata": {}, "source": [ "## Get JSON for Template\n", @@ -1214,7 +1214,7 @@ { "cell_type": "code", "execution_count": null, - "id": "299b54d9", + "id": "75847e22", "metadata": {}, "outputs": [], "source": [ @@ -1241,7 +1241,7 @@ }, { "cell_type": "markdown", - "id": "792603cf", + "id": "66160240", "metadata": {}, "source": [ "## Get JSON for pub\n", @@ -1251,7 +1251,7 @@ { "cell_type": "code", "execution_count": null, - "id": "96e1cd55", + "id": "5a6372e1", "metadata": {}, "outputs": [], "source": [ @@ -1278,7 +1278,7 @@ }, { "cell_type": "markdown", - "id": "a8170f2a", + "id": "55e73620", "metadata": {}, "source": [ "## Get JSON for DataSet\n", @@ -1288,7 +1288,7 @@ { "cell_type": "code", "execution_count": null, - "id": "7bc0690d", + "id": "7e4965c1", "metadata": {}, "outputs": [], "source": [ @@ -1315,7 +1315,7 @@ }, { "cell_type": "markdown", - "id": "2b81ab03", + "id": "498eb0e1", "metadata": {}, "source": [ "## Get JSON for License\n", @@ -1325,7 +1325,7 @@ { "cell_type": "code", "execution_count": null, - "id": "3e6e1ec7", + "id": "ed30c9ca", "metadata": {}, "outputs": [], "source": [ @@ -1352,7 +1352,7 @@ }, { "cell_type": "markdown", - "id": "932d6bf2", + "id": "be0337cf", "metadata": {}, "source": [ "## Owlery Part of\n", @@ -1362,7 +1362,7 @@ { "cell_type": "code", "execution_count": null, - "id": "c72aa25c", + "id": "9902d832", "metadata": {}, "outputs": [], "source": [ @@ -1385,7 +1385,7 @@ }, { "cell_type": "markdown", - "id": "ea2c5a95", + "id": "6e3d4646", "metadata": {}, "source": [ "## Owlery Neuron class with part here\n", @@ -1395,7 +1395,7 @@ { "cell_type": "code", "execution_count": null, - "id": "a2ad71da", + "id": "ebc3cf38", "metadata": {}, "outputs": [], "source": [ @@ -1418,7 +1418,7 @@ }, { "cell_type": "markdown", - "id": "2028a2da", + "id": "f6b3d04a", "metadata": {}, "source": [ "## Owlery Neurons Synaptic\n", @@ -1428,7 +1428,7 @@ { "cell_type": "code", "execution_count": null, - "id": "8f56a78d", + "id": "93d9e23d", "metadata": {}, "outputs": [], "source": [ @@ -1451,7 +1451,7 @@ }, { "cell_type": "markdown", - "id": "6036dad0", + "id": "947b80a8", "metadata": {}, "source": [ "## Owlery Neurons Presynaptic\n", @@ -1461,7 +1461,7 @@ { "cell_type": "code", "execution_count": null, - "id": "0a84b7e9", + "id": "7491157f", "metadata": {}, "outputs": [], "source": [ @@ -1484,7 +1484,7 @@ }, { "cell_type": "markdown", - "id": "b810269f", + "id": "fd0ffc9e", "metadata": {}, "source": [ "## Owlery Neurons Postsynaptic\n", @@ -1494,7 +1494,7 @@ { "cell_type": "code", "execution_count": null, - "id": "74123342", + "id": "e4c1015f", "metadata": {}, "outputs": [], "source": [ @@ -1517,7 +1517,7 @@ }, { "cell_type": "markdown", - "id": "def179c4", + "id": "40fc97c2", "metadata": {}, "source": [ "## Owlery Neuron classes fasciculating here\n", @@ -1527,7 +1527,7 @@ { "cell_type": "code", "execution_count": null, - "id": "90fe4d98", + "id": "52f0a138", "metadata": {}, "outputs": [], "source": [ @@ -1550,7 +1550,7 @@ }, { "cell_type": "markdown", - "id": "2a9f3a1c", + "id": "6399d00c", "metadata": {}, "source": [ "## Owlery tracts in\n", @@ -1560,7 +1560,7 @@ { "cell_type": "code", "execution_count": null, - "id": "c2a9cc04", + "id": "cdbb1d99", "metadata": {}, "outputs": [], "source": [ @@ -1583,7 +1583,7 @@ }, { "cell_type": "markdown", - "id": "ba2fda89", + "id": "2bbeb6a9", "metadata": {}, "source": [ "## Owlery Subclasses of\n", @@ -1593,7 +1593,7 @@ { "cell_type": "code", "execution_count": null, - "id": "b254cc81", + "id": "a99fd033", "metadata": {}, "outputs": [], "source": [ @@ -1616,7 +1616,7 @@ }, { "cell_type": "markdown", - "id": "2aabb413", + "id": "2365e502", "metadata": {}, "source": [ "## Owlery Lineage Clones\n", @@ -1626,7 +1626,7 @@ { "cell_type": "code", "execution_count": null, - "id": "26a3d94f", + "id": "5d412f8c", "metadata": {}, "outputs": [], "source": [ @@ -1649,7 +1649,7 @@ }, { "cell_type": "markdown", - "id": "c477f572", + "id": "c522f36f", "metadata": {}, "source": [ "## subClassOf cell that overlaps some X\n", @@ -1659,7 +1659,7 @@ { "cell_type": "code", "execution_count": null, - "id": "58302ecb", + "id": "f92e0fb3", "metadata": {}, "outputs": [], "source": [ @@ -1682,7 +1682,7 @@ }, { "cell_type": "markdown", - "id": "d5b30ba0", + "id": "931af77f", "metadata": {}, "source": [ "## subClassOf overlaps some X\n", @@ -1692,7 +1692,7 @@ { "cell_type": "code", "execution_count": null, - "id": "c14dc922", + "id": "7206f21d", "metadata": {}, "outputs": [], "source": [ @@ -1715,7 +1715,7 @@ }, { "cell_type": "markdown", - "id": "6f41e045", + "id": "76ab7392", "metadata": {}, "source": [ "## subClassOf cell overlaps some X\n", @@ -1725,7 +1725,7 @@ { "cell_type": "code", "execution_count": null, - "id": "c22d62f8", + "id": "cf1a9392", "metadata": {}, "outputs": [], "source": [ @@ -1748,7 +1748,7 @@ }, { "cell_type": "markdown", - "id": "6bb80f8a", + "id": "9d20ea06", "metadata": {}, "source": [ "## Owlery Images of neurons with some part here (clustered)\n", @@ -1758,7 +1758,7 @@ { "cell_type": "code", "execution_count": null, - "id": "a3abe9ed", + "id": "4bad2bba", "metadata": {}, "outputs": [], "source": [ @@ -1781,7 +1781,7 @@ }, { "cell_type": "markdown", - "id": "2a616a5a", + "id": "1ba60c6e", "metadata": {}, "source": [ "## Owlery Images of neurons with some part here\n", @@ -1791,7 +1791,7 @@ { "cell_type": "code", "execution_count": null, - "id": "8c62b1cd", + "id": "34c94ea6", "metadata": {}, "outputs": [], "source": [ @@ -1814,7 +1814,7 @@ }, { "cell_type": "markdown", - "id": "52b540c2", + "id": "5dc017fb", "metadata": {}, "source": [ "## Owlery individual parts\n", @@ -1824,7 +1824,7 @@ { "cell_type": "code", "execution_count": null, - "id": "7be68e40", + "id": "0d12511e", "metadata": {}, "outputs": [], "source": [ @@ -1847,7 +1847,7 @@ }, { "cell_type": "markdown", - "id": "26b3a5d7", + "id": "80a09ab3", "metadata": {}, "source": [ "## Get anat_query\n", @@ -1857,7 +1857,7 @@ { "cell_type": "code", "execution_count": null, - "id": "1fbe1c79", + "id": "6caba432", "metadata": {}, "outputs": [], "source": [ @@ -1880,7 +1880,7 @@ }, { "cell_type": "markdown", - "id": "9987f181", + "id": "69e047b7", "metadata": {}, "source": [ "## Get user NBLAST results\n", @@ -1890,7 +1890,7 @@ { "cell_type": "code", "execution_count": null, - "id": "5a8cb7cb", + "id": "7a0aa7af", "metadata": {}, "outputs": [], "source": [ @@ -1913,7 +1913,7 @@ }, { "cell_type": "markdown", - "id": "d36f86f8", + "id": "7fe08352", "metadata": {}, "source": [ "## Get term info\n", @@ -1923,7 +1923,7 @@ { "cell_type": "code", "execution_count": null, - "id": "39431399", + "id": "7446f028", "metadata": {}, "outputs": [], "source": [ @@ -1946,7 +1946,7 @@ }, { "cell_type": "markdown", - "id": "2983c1f5", + "id": "6d8da019", "metadata": {}, "source": [ "## Get cached VFB_JSON for Term\n", @@ -1956,7 +1956,7 @@ { "cell_type": "code", "execution_count": null, - "id": "522b2b9a", + "id": "ec0af57f", "metadata": {}, "outputs": [], "source": [ @@ -1981,4 +1981,4 @@ "metadata": {}, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} From ec373ca4c6715b48b1faf1fd99d664d6054dadd5 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Tue, 15 Oct 2024 21:57:49 +0100 Subject: [PATCH 02/12] using latest query processor --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 9f620a166..5e9c13c3b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,7 +17,7 @@ ARG geppettoDatasourceRelease=passingSOLR ARG geppettoModelSwcRelease=v1.0.1 ARG geppettoFrontendRelease=VFBv2.1.0.3 ARG geppettoClientRelease=VFBv2.2.5 -ARG ukAcVfbGeppettoRelease=v2.2.4.3 +ARG ukAcVfbGeppettoRelease=v2.2.4.4 ARG mvnOpt="-Dhttps.protocols=TLSv1.2 -DskipTests --quiet -Pmaster" From 549bcbcf35fdbf29e4a9f3b82e40a6d26a2d4776 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Tue, 15 Oct 2024 22:00:47 +0100 Subject: [PATCH 03/12] v4 --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 3178fe649..c78230fd6 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -27,7 +27,7 @@ jobs: steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 # Decide based on branch which servers to use - name: Pass branch From 52ed7edb5809b41a3e049b5bc297f3f768261182 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Tue, 15 Oct 2024 22:01:42 +0100 Subject: [PATCH 04/12] v4 --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c78230fd6..cf033766a 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -198,7 +198,7 @@ jobs: fi - name: Stop VFB server run: docker stop testServer - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 if: ${{ failure() }} with: name: test_fails From f1cad61c7f194a5151741d46d77a634ded4934fe Mon Sep 17 00:00:00 2001 From: Rob Court Date: Tue, 19 Nov 2024 20:17:47 +0000 Subject: [PATCH 05/12] swapping to VFBv2.2.6 client with fixed OBJloader --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 5e9c13c3b..c7a14de22 100644 --- a/Dockerfile +++ b/Dockerfile @@ -16,7 +16,7 @@ ARG geppettoSimulationRelease=VFBv2.1.0.2 ARG geppettoDatasourceRelease=passingSOLR ARG geppettoModelSwcRelease=v1.0.1 ARG geppettoFrontendRelease=VFBv2.1.0.3 -ARG geppettoClientRelease=VFBv2.2.5 +ARG geppettoClientRelease=VFBv2.2.6 ARG ukAcVfbGeppettoRelease=v2.2.4.4 ARG mvnOpt="-Dhttps.protocols=TLSv1.2 -DskipTests --quiet -Pmaster" From b6cf22a07ed75e64fcff91929e405a5760baa9c5 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Mon, 2 Dec 2024 15:06:23 +0000 Subject: [PATCH 06/12] fixing three to 0.153.0 --- package-lock.json | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/package-lock.json b/package-lock.json index 47f28c1c1..448f9048a 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,7 +11,7 @@ "requires": { "accessor-fn": "1", "kapsule": "1", - "three": ">=0.118 <1", + "three": "0.153.0", "three-forcegraph": "1", "three-render-objects": "1" }, @@ -1349,7 +1349,7 @@ "stats.js": "^0.17.0", "styled-components": "^4.3.2", "text": "^0.1.0", - "three": "^0.87.0", + "three": "0.153.0", "three-render-objects": "1.13.3", "typeahead.js": "^0.11.1", "typeface-roboto": "^0.0.54", @@ -2893,7 +2893,7 @@ "nifti-reader-js": "v0.5.3", "nrrd-js": "^0.2.1", "pako": "1.0.1", - "three": "^0.153.0" + "three": "0.153.0" }, "dependencies": { "pako": { @@ -17773,10 +17773,10 @@ "dev": true }, "three": { - "version": "0.87.1", - "resolved": "https://registry.npmjs.org/three/-/three-0.87.1.tgz", - "integrity": "sha512-ZwMODnlSi4CRAa4snN6R4FlxUCxlRHkUmCcAgqf0N2L6OGbnIsXPfqpvDyqWzoyqSCKfhjXWWp6tTSXOKwV+XA==" - }, + "version": "0.153.0", + "resolved": "https://registry.npmjs.org/three/-/three-0.153.0.tgz", + "integrity": "sha512-OCP2/uQR6GcDpSLnJt/3a4mdS0kNWcbfUXIwLoEMgLzEUIVIYsSDwskpmOii/AkDM+BBwrl6+CKgrjX9+E2aWg==" + } "three-fly-controls": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/three-fly-controls/-/three-fly-controls-2.0.0.tgz", From b54f2f0c0db2dab70cc0f3ef1f59d9b10ff25b4a Mon Sep 17 00:00:00 2001 From: Rob Court Date: Mon, 2 Dec 2024 15:38:17 +0000 Subject: [PATCH 07/12] typo fix --- package-lock.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package-lock.json b/package-lock.json index 448f9048a..5e497ea28 100644 --- a/package-lock.json +++ b/package-lock.json @@ -17776,7 +17776,7 @@ "version": "0.153.0", "resolved": "https://registry.npmjs.org/three/-/three-0.153.0.tgz", "integrity": "sha512-OCP2/uQR6GcDpSLnJt/3a4mdS0kNWcbfUXIwLoEMgLzEUIVIYsSDwskpmOii/AkDM+BBwrl6+CKgrjX9+E2aWg==" - } + }, "three-fly-controls": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/three-fly-controls/-/three-fly-controls-2.0.0.tgz", From 27268c7002f5ff84004d7fde186eaae76c2a67ae Mon Sep 17 00:00:00 2001 From: Rob Court Date: Mon, 2 Dec 2024 20:18:51 +0000 Subject: [PATCH 08/12] reverting to three 0.115.0 --- package-lock.json | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/package-lock.json b/package-lock.json index 5e497ea28..716ce6ab3 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,15 +11,15 @@ "requires": { "accessor-fn": "1", "kapsule": "1", - "three": "0.153.0", - "three-forcegraph": "1", - "three-render-objects": "1" + "three": "0.115.0", + "three-forcegraph": "1.23.0", + "three-render-objects": "1.11.0" }, "dependencies": { "three": { - "version": "0.153.0", - "resolved": "https://registry.npmjs.org/three/-/three-0.153.0.tgz", - "integrity": "sha512-OCP2/uQR6GcDpSLnJt/3a4mdS0kNWcbfUXIwLoEMgLzEUIVIYsSDwskpmOii/AkDM+BBwrl6+CKgrjX9+E2aWg==" + "version": "0.115.0", + "resolved": "https://registry.npmjs.org/three/-/three-0.115.0.tgz", + "integrity": "sha512-mAV2Ky3RdcbdSbR9capI+tKLvRldWYxd4151PZTT/o7+U2jh9Is3a4KmnYwzyUAhB2ZA3pXSgCd2DOY4Tj5kow==" } } }, @@ -1330,8 +1330,8 @@ "react-dom-factories": "^1.0.2", "react-dropzone": "^8.0.3", "react-fontawesome": "^1.6.1", - "react-force-graph-2d": "^1.12.1", - "react-force-graph-3d": "^1.12.1", + "react-force-graph-2d": "1.12.1", + "react-force-graph-3d": "1.12.1", "react-jsonschema-form": "^1.0.6", "react-lazy-load": "^3.0.13", "react-modal": "^3.8.1", @@ -1349,7 +1349,7 @@ "stats.js": "^0.17.0", "styled-components": "^4.3.2", "text": "^0.1.0", - "three": "0.153.0", + "three": "0.115.0", "three-render-objects": "1.13.3", "typeahead.js": "^0.11.1", "typeface-roboto": "^0.0.54", @@ -2893,7 +2893,7 @@ "nifti-reader-js": "v0.5.3", "nrrd-js": "^0.2.1", "pako": "1.0.1", - "three": "0.153.0" + "three": "0.115.0" }, "dependencies": { "pako": { @@ -2902,9 +2902,9 @@ "integrity": "sha512-ArD3vwgjBSMGLkDM5ktk1FLC0mOAdAFS/EsRY+YSzJu4goVM4ZfuVJ5yOVd+fXm4oO0wd3GPLCQI/mT9kNuP+Q==" }, "three": { - "version": "0.153.0", - "resolved": "https://registry.npmjs.org/three/-/three-0.153.0.tgz", - "integrity": "sha512-OCP2/uQR6GcDpSLnJt/3a4mdS0kNWcbfUXIwLoEMgLzEUIVIYsSDwskpmOii/AkDM+BBwrl6+CKgrjX9+E2aWg==" + "version": "0.115.0", + "resolved": "https://registry.npmjs.org/three/-/three-0.115.0.tgz", + "integrity": "sha512-mAV2Ky3RdcbdSbR9capI+tKLvRldWYxd4151PZTT/o7+U2jh9Is3a4KmnYwzyUAhB2ZA3pXSgCd2DOY4Tj5kow==" } } }, @@ -17773,9 +17773,9 @@ "dev": true }, "three": { - "version": "0.153.0", - "resolved": "https://registry.npmjs.org/three/-/three-0.153.0.tgz", - "integrity": "sha512-OCP2/uQR6GcDpSLnJt/3a4mdS0kNWcbfUXIwLoEMgLzEUIVIYsSDwskpmOii/AkDM+BBwrl6+CKgrjX9+E2aWg==" + "version": "0.115.0", + "resolved": "https://registry.npmjs.org/three/-/three-0.115.0.tgz", + "integrity": "sha512-mAV2Ky3RdcbdSbR9capI+tKLvRldWYxd4151PZTT/o7+U2jh9Is3a4KmnYwzyUAhB2ZA3pXSgCd2DOY4Tj5kow==" }, "three-fly-controls": { "version": "2.0.0", From ad19fa3b318be3f4cb252c224b14e5840752516f Mon Sep 17 00:00:00 2001 From: Rob Court Date: Tue, 3 Dec 2024 11:40:13 +0000 Subject: [PATCH 09/12] swapping three to 0.87.1 --- package-lock.json | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/package-lock.json b/package-lock.json index 716ce6ab3..12fb82bc8 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,15 +11,15 @@ "requires": { "accessor-fn": "1", "kapsule": "1", - "three": "0.115.0", + "three": "0.87.1", "three-forcegraph": "1.23.0", "three-render-objects": "1.11.0" }, "dependencies": { "three": { - "version": "0.115.0", - "resolved": "https://registry.npmjs.org/three/-/three-0.115.0.tgz", - "integrity": "sha512-mAV2Ky3RdcbdSbR9capI+tKLvRldWYxd4151PZTT/o7+U2jh9Is3a4KmnYwzyUAhB2ZA3pXSgCd2DOY4Tj5kow==" + "version": "0.87.1", + "resolved": "https://registry.npmjs.org/three/-/three-0.87.1.tgz", + "integrity": "sha1-Rmo07cRUNFnO2bnX0na2Uhb+K6g=" } } }, @@ -1349,7 +1349,7 @@ "stats.js": "^0.17.0", "styled-components": "^4.3.2", "text": "^0.1.0", - "three": "0.115.0", + "three": "0.87.1", "three-render-objects": "1.13.3", "typeahead.js": "^0.11.1", "typeface-roboto": "^0.0.54", @@ -2893,7 +2893,7 @@ "nifti-reader-js": "v0.5.3", "nrrd-js": "^0.2.1", "pako": "1.0.1", - "three": "0.115.0" + "three": "0.87.1" }, "dependencies": { "pako": { @@ -2902,9 +2902,9 @@ "integrity": "sha512-ArD3vwgjBSMGLkDM5ktk1FLC0mOAdAFS/EsRY+YSzJu4goVM4ZfuVJ5yOVd+fXm4oO0wd3GPLCQI/mT9kNuP+Q==" }, "three": { - "version": "0.115.0", - "resolved": "https://registry.npmjs.org/three/-/three-0.115.0.tgz", - "integrity": "sha512-mAV2Ky3RdcbdSbR9capI+tKLvRldWYxd4151PZTT/o7+U2jh9Is3a4KmnYwzyUAhB2ZA3pXSgCd2DOY4Tj5kow==" + "version": "0.87.1", + "resolved": "https://registry.npmjs.org/three/-/three-0.87.1.tgz", + "integrity": "sha1-Rmo07cRUNFnO2bnX0na2Uhb+K6g=" } } }, @@ -17773,9 +17773,9 @@ "dev": true }, "three": { - "version": "0.115.0", - "resolved": "https://registry.npmjs.org/three/-/three-0.115.0.tgz", - "integrity": "sha512-mAV2Ky3RdcbdSbR9capI+tKLvRldWYxd4151PZTT/o7+U2jh9Is3a4KmnYwzyUAhB2ZA3pXSgCd2DOY4Tj5kow==" + "version": "0.87.1", + "resolved": "https://registry.npmjs.org/three/-/three-0.87.1.tgz", + "integrity": "sha1-Rmo07cRUNFnO2bnX0na2Uhb+K6g=" }, "three-fly-controls": { "version": "2.0.0", From 5c0561c1b4d45c62e2bc0397e2c81064e8a898b7 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Tue, 3 Dec 2024 11:41:16 +0000 Subject: [PATCH 10/12] three-render-objects to 1.13.3 --- package-lock.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package-lock.json b/package-lock.json index 12fb82bc8..12162ad58 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13,7 +13,7 @@ "kapsule": "1", "three": "0.87.1", "three-forcegraph": "1.23.0", - "three-render-objects": "1.11.0" + "three-render-objects": "1.13.3" }, "dependencies": { "three": { From 7c9af298071c0fb829d0cbd577d86f2183c21e11 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Tue, 3 Dec 2024 14:41:21 +0000 Subject: [PATCH 11/12] upgrading three to 0.167.0 and three-render-objects to 1.29.4 --- package-lock.json | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/package-lock.json b/package-lock.json index 12162ad58..6eb52c49b 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,15 +11,15 @@ "requires": { "accessor-fn": "1", "kapsule": "1", - "three": "0.87.1", + "three": "0.167.0", "three-forcegraph": "1.23.0", - "three-render-objects": "1.13.3" + "three-render-objects": "1.29.4" }, "dependencies": { "three": { - "version": "0.87.1", - "resolved": "https://registry.npmjs.org/three/-/three-0.87.1.tgz", - "integrity": "sha1-Rmo07cRUNFnO2bnX0na2Uhb+K6g=" + "version": "0.167.0", + "resolved": "https://registry.npmjs.org/three/-/three-0.167.0.tgz", + "integrity": "sha512-/Mc6vsQxiKb3Le5oUKjvx+YOqDsmGuHSgvoUxnpHs0mlbB8hcfUn8GFh5uGJ8FXkN5DQqU/EHyHo3ahUto8AZw==" } } }, @@ -1349,8 +1349,8 @@ "stats.js": "^0.17.0", "styled-components": "^4.3.2", "text": "^0.1.0", - "three": "0.87.1", - "three-render-objects": "1.13.3", + "three": "0.167.0", + "three-render-objects": "1.29.4", "typeahead.js": "^0.11.1", "typeface-roboto": "^0.0.54", "underscore": "~1.9.1", @@ -2893,7 +2893,7 @@ "nifti-reader-js": "v0.5.3", "nrrd-js": "^0.2.1", "pako": "1.0.1", - "three": "0.87.1" + "three": "0.167.0" }, "dependencies": { "pako": { @@ -2902,9 +2902,9 @@ "integrity": "sha512-ArD3vwgjBSMGLkDM5ktk1FLC0mOAdAFS/EsRY+YSzJu4goVM4ZfuVJ5yOVd+fXm4oO0wd3GPLCQI/mT9kNuP+Q==" }, "three": { - "version": "0.87.1", - "resolved": "https://registry.npmjs.org/three/-/three-0.87.1.tgz", - "integrity": "sha1-Rmo07cRUNFnO2bnX0na2Uhb+K6g=" + "version": "0.167.0", + "resolved": "https://registry.npmjs.org/three/-/three-0.167.0.tgz", + "integrity": "sha512-/Mc6vsQxiKb3Le5oUKjvx+YOqDsmGuHSgvoUxnpHs0mlbB8hcfUn8GFh5uGJ8FXkN5DQqU/EHyHo3ahUto8AZw==" } } }, @@ -17773,9 +17773,9 @@ "dev": true }, "three": { - "version": "0.87.1", - "resolved": "https://registry.npmjs.org/three/-/three-0.87.1.tgz", - "integrity": "sha1-Rmo07cRUNFnO2bnX0na2Uhb+K6g=" + "version": "0.167.0", + "resolved": "https://registry.npmjs.org/three/-/three-0.167.0.tgz", + "integrity": "sha512-/Mc6vsQxiKb3Le5oUKjvx+YOqDsmGuHSgvoUxnpHs0mlbB8hcfUn8GFh5uGJ8FXkN5DQqU/EHyHo3ahUto8AZw==" }, "three-fly-controls": { "version": "2.0.0", @@ -17805,9 +17805,9 @@ "integrity": "sha512-hIWxGoHqIbeq0S2lA14m9VRzo7SamKKVJ9mKMT/rdh0Qa3nV5Umvhlx4zsHl0Y6jLKVZhjatJfeD/K08Tr/g4A==" }, "three-render-objects": { - "version": "1.13.3", - "resolved": "https://registry.npmjs.org/three-render-objects/-/three-render-objects-1.13.3.tgz", - "integrity": "sha512-fAwJoHuotMiJrgXb/BH+LqW3gsTwG54vjoJJ8NvckSVhHoMYib+rSSlh+zwnzDJpMmsHKqwwLgBebawIo0FfDg==", + "version": "1.29.4", + "resolved": "https://registry.npmjs.org/three-render-objects/-/three-render-objects-1.29.4.tgz", + "integrity": "sha512-uv5yD/854yFAgFyTQqVFi8uC+N3r0yjgYhJYWEQ+R5tEiTgvAPMl7q+SsLuHbfzK7RnhFGgQIVhynlj42jm5g==", "requires": { "@tweenjs/tween.js": "^18.5.0", "accessor-fn": "^1.3.0", From 8af8b64a879a18a7908aa8a7bc4c4d27b588f693 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Wed, 4 Dec 2024 12:52:25 +0000 Subject: [PATCH 12/12] hash fix --- package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 6eb52c49b..2997b36af 100644 --- a/package-lock.json +++ b/package-lock.json @@ -19,7 +19,7 @@ "three": { "version": "0.167.0", "resolved": "https://registry.npmjs.org/three/-/three-0.167.0.tgz", - "integrity": "sha512-/Mc6vsQxiKb3Le5oUKjvx+YOqDsmGuHSgvoUxnpHs0mlbB8hcfUn8GFh5uGJ8FXkN5DQqU/EHyHo3ahUto8AZw==" + "integrity": "sha512-9Y1a66fpjqF3rhq7ivKTaKtjQLZ97Hj/lZ00DmZWaKHaQFH4uzYT1znwRDWQOcgMmCcOloQzo61gDmqO8l9xmA==" } } }, @@ -2904,7 +2904,7 @@ "three": { "version": "0.167.0", "resolved": "https://registry.npmjs.org/three/-/three-0.167.0.tgz", - "integrity": "sha512-/Mc6vsQxiKb3Le5oUKjvx+YOqDsmGuHSgvoUxnpHs0mlbB8hcfUn8GFh5uGJ8FXkN5DQqU/EHyHo3ahUto8AZw==" + "integrity": "sha512-9Y1a66fpjqF3rhq7ivKTaKtjQLZ97Hj/lZ00DmZWaKHaQFH4uzYT1znwRDWQOcgMmCcOloQzo61gDmqO8l9xmA==" } } }, @@ -17775,7 +17775,7 @@ "three": { "version": "0.167.0", "resolved": "https://registry.npmjs.org/three/-/three-0.167.0.tgz", - "integrity": "sha512-/Mc6vsQxiKb3Le5oUKjvx+YOqDsmGuHSgvoUxnpHs0mlbB8hcfUn8GFh5uGJ8FXkN5DQqU/EHyHo3ahUto8AZw==" + "integrity": "sha512-9Y1a66fpjqF3rhq7ivKTaKtjQLZ97Hj/lZ00DmZWaKHaQFH4uzYT1znwRDWQOcgMmCcOloQzo61gDmqO8l9xmA==" }, "three-fly-controls": { "version": "2.0.0",