From deda89fab404e784b61f8d1cac0a370a3ccc2111 Mon Sep 17 00:00:00 2001
From: James McLaughlin <james@mclgh.net>
Date: Sun, 22 Dec 2024 12:05:06 +0000
Subject: [PATCH] move materialised queries to top of repo

---
 dataload/08_run_queries/run_queries.slurm.py                  | 4 ++--
 dataload/materialised_queries/ebi_monarch_xspecies/.gitkeep   | 0
 dataload/scripts/dataload_codon.sh                            | 1 +
 dataload/scripts/dataload_local.sh                            | 1 +
 dataload/scripts/dataload_saturos.sh                          | 1 +
 .../impc_x_gwas => materialised_queries}/impc_x_gwas.yaml     | 3 +++
 6 files changed, 8 insertions(+), 2 deletions(-)
 delete mode 100644 dataload/materialised_queries/ebi_monarch_xspecies/.gitkeep
 rename {dataload/materialised_queries/impc_x_gwas => materialised_queries}/impc_x_gwas.yaml (96%)

diff --git a/dataload/08_run_queries/run_queries.slurm.py b/dataload/08_run_queries/run_queries.slurm.py
index 0cc7e4e..758f66a 100644
--- a/dataload/08_run_queries/run_queries.slurm.py
+++ b/dataload/08_run_queries/run_queries.slurm.py
@@ -35,7 +35,7 @@ def main():
             '--bind ' + shlex.quote(neo_data_path) + ':/data',
             '--bind ' + shlex.quote(neo_logs_path) + ':/logs',
             '--bind ' + os.path.abspath(os.path.join(os.environ['GREBI_DATALOAD_HOME'], '08_run_queries/run_queries.dockerpy')) + ':/run_queries.py',
-            '--bind ' + os.path.abspath(os.path.join(os.environ['GREBI_DATALOAD_HOME'], 'materialised_queries', os.environ['GREBI_SUBGRAPH'] )) + ':/materialised_queries',
+            '--bind ' + os.path.abspath(os.environ['QUERY_YAMLS_PATH']) + ':/materialised_queries',
             '--bind ' + os.path.abspath(args.out_sqlites_path) + ':/out',
             '--writable-tmpfs',
             '--network=none',
@@ -50,7 +50,7 @@ def main():
             '-v ' + shlex.quote(neo_data_path) + ':/data',
             '-v ' + shlex.quote(neo_logs_path) + ':/logs',
             '-v ' + os.path.abspath(os.path.join(os.environ['GREBI_DATALOAD_HOME'], '08_run_queries/run_queries.dockerpy')) + ':/run_queries.py',
-            '-v ' + os.path.abspath(os.path.join(os.environ['GREBI_DATALOAD_HOME'], 'materialised_queries', os.environ['GREBI_SUBGRAPH'] )) + ':/materialised_queries',
+            '-v ' + os.path.abspath(os.environ['QUERY_YAMLS_PATH']) + ':/materialised_queries',
             '-v ' + os.path.abspath(args.out_sqlites_path) + ':/out',
             '-e NEO4J_AUTH=none',
             'ghcr.io/ebispot/grebi_neo4j_with_extras:5.18.0',
diff --git a/dataload/materialised_queries/ebi_monarch_xspecies/.gitkeep b/dataload/materialised_queries/ebi_monarch_xspecies/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/dataload/scripts/dataload_codon.sh b/dataload/scripts/dataload_codon.sh
index 65a0dc6..ac2426f 100755
--- a/dataload/scripts/dataload_codon.sh
+++ b/dataload/scripts/dataload_codon.sh
@@ -1,5 +1,6 @@
 #!/bin/bash
 export GREBI_DATALOAD_HOME=/nfs/production/parkinso/spot/grebi/dataload
+export GREBI_QUERY_YAMLS_PATH=/nfs/production/parkinso/spot/grebi/materialised_queries
 export GREBI_TMP=/hps/nobackup/parkinso/spot/grebi/tmp
 export GREBI_CONFIG=ebi
 export GREBI_IS_EBI=true
diff --git a/dataload/scripts/dataload_local.sh b/dataload/scripts/dataload_local.sh
index 4a3b52a..faf9943 100755
--- a/dataload/scripts/dataload_local.sh
+++ b/dataload/scripts/dataload_local.sh
@@ -1,5 +1,6 @@
 #!/bin/bash
 export GREBI_DATALOAD_HOME=~/grebi/dataload
+export GREBI_QUERY_YAMLS_PATH=~/grebi/materialised_queries
 export GREBI_TMP=$(pwd)
 export GREBI_CONFIG=ebi
 export GREBI_IS_EBI=false
diff --git a/dataload/scripts/dataload_saturos.sh b/dataload/scripts/dataload_saturos.sh
index 34654aa..3f2f966 100755
--- a/dataload/scripts/dataload_saturos.sh
+++ b/dataload/scripts/dataload_saturos.sh
@@ -1,5 +1,6 @@
 #!/bin/bash
 export GREBI_DATALOAD_HOME=/home/james/grebi/dataload
+export GREBI_QUERY_YAMLS_PATH=/home/james/grebi/materialised_queries
 export GREBI_TMP=/data/grebi_tmp
 export GREBI_CONFIG=ebi
 export GREBI_IS_EBI=false
diff --git a/dataload/materialised_queries/impc_x_gwas/impc_x_gwas.yaml b/materialised_queries/impc_x_gwas.yaml
similarity index 96%
rename from dataload/materialised_queries/impc_x_gwas/impc_x_gwas.yaml
rename to materialised_queries/impc_x_gwas.yaml
index afc2151..409dd75 100644
--- a/dataload/materialised_queries/impc_x_gwas/impc_x_gwas.yaml
+++ b/materialised_queries/impc_x_gwas.yaml
@@ -1,5 +1,8 @@
 title: Human GWAS variants to mouse models in IMPC
 description: Connects human GWAS variants to mouse models in IMPC using multiple different graph paths through phenotype and disease ontologies
+subgraphs:
+  - ebi_monarch_xspecies
+  - impc_x_gwas
 uses_datasources:
   - IMPC
   - GWAS