From 63265008b106fe3309595fdf85e2b75898919387 Mon Sep 17 00:00:00 2001
From: Pedro Madrigal <8195212+pmb59@users.noreply.github.com>
Date: Tue, 10 Oct 2023 12:02:53 +0100
Subject: [PATCH] dirname: missing operand error in SCXA loading due to
 undefined $BASH_SOURCE (#68)

* Update load_db_scxa_dimred.sh

* using ${BASH_SOURCE:-$0}  to avoid cases where BASH_SOURCE is not defined

* edit SCRATCH_DIR in bin/load_db_scxa_dimred.sh

* Related to PR #66
---
 bin/add_exps_to_collection.sh     | 2 +-
 bin/create_collection.sh          | 2 +-
 bin/delete_collection.sh          | 2 +-
 bin/delete_exp_from_collection.sh | 2 +-
 bin/get_experiment_info.sh        | 2 +-
 bin/load_db_scxa_analytics.sh     | 2 +-
 bin/load_db_scxa_analytics_pg9.sh | 2 +-
 bin/load_db_scxa_cell_clusters.sh | 2 +-
 bin/load_db_scxa_dimred.sh        | 5 +++--
 bin/load_db_scxa_marker_genes.sh  | 2 +-
 bin/load_exp_design.sh            | 2 +-
 bin/load_experiment_web_cli.sh    | 2 +-
 bin/modify_collection.sh          | 2 +-
 bin/update_experiment_web_cli.sh  | 2 +-
 fixtures/generate-fixtures.sh     | 2 +-
 fixtures/generate-tsv-fixture.sh  | 2 +-
 tests/run_tests.sh                | 4 ++--
 tests/test_dimred_load.sh         | 4 ++--
 18 files changed, 22 insertions(+), 21 deletions(-)

diff --git a/bin/add_exps_to_collection.sh b/bin/add_exps_to_collection.sh
index 3a7bd0e..e2c7429 100755
--- a/bin/add_exps_to_collection.sh
+++ b/bin/add_exps_to_collection.sh
@@ -2,7 +2,7 @@
 
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 dbConnection=${dbConnection:-$1}
diff --git a/bin/create_collection.sh b/bin/create_collection.sh
index bc88cf1..db11521 100755
--- a/bin/create_collection.sh
+++ b/bin/create_collection.sh
@@ -2,7 +2,7 @@
 
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 dbConnection=${dbConnection:-$1}
diff --git a/bin/delete_collection.sh b/bin/delete_collection.sh
index 546b927..2a8fab2 100755
--- a/bin/delete_collection.sh
+++ b/bin/delete_collection.sh
@@ -2,7 +2,7 @@
 
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 dbConnection=${dbConnection:-$1}
diff --git a/bin/delete_exp_from_collection.sh b/bin/delete_exp_from_collection.sh
index c6d43a8..dcf0624 100755
--- a/bin/delete_exp_from_collection.sh
+++ b/bin/delete_exp_from_collection.sh
@@ -2,7 +2,7 @@
 
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 dbConnection=${dbConnection:-$1}
diff --git a/bin/get_experiment_info.sh b/bin/get_experiment_info.sh
index 4096cf1..d2bb3a1 100755
--- a/bin/get_experiment_info.sh
+++ b/bin/get_experiment_info.sh
@@ -2,7 +2,7 @@
 
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 postgres_scripts_dir=$scriptDir/../postgres_routines
diff --git a/bin/load_db_scxa_analytics.sh b/bin/load_db_scxa_analytics.sh
index 05779a7..18c6348 100755
--- a/bin/load_db_scxa_analytics.sh
+++ b/bin/load_db_scxa_analytics.sh
@@ -12,7 +12,7 @@
 # - Postprocess table and attach it to the main scxa-analytics table.
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 postgres_scripts_dir=$scriptDir/../postgres_routines
diff --git a/bin/load_db_scxa_analytics_pg9.sh b/bin/load_db_scxa_analytics_pg9.sh
index ca89825..95ec151 100755
--- a/bin/load_db_scxa_analytics_pg9.sh
+++ b/bin/load_db_scxa_analytics_pg9.sh
@@ -10,7 +10,7 @@
 #   PG10, which loads each experiment into a different partition.
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 dbConnection=${dbConnection:-$1}
diff --git a/bin/load_db_scxa_cell_clusters.sh b/bin/load_db_scxa_cell_clusters.sh
index 7c1c4d7..dff3bf2 100755
--- a/bin/load_db_scxa_cell_clusters.sh
+++ b/bin/load_db_scxa_cell_clusters.sh
@@ -5,7 +5,7 @@
 # scxa_cell_group_membership table of AtlasProd.
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 dbConnection=${dbConnection:-$1}
diff --git a/bin/load_db_scxa_dimred.sh b/bin/load_db_scxa_dimred.sh
index 31f17b6..e0ed5ba 100755
--- a/bin/load_db_scxa_dimred.sh
+++ b/bin/load_db_scxa_dimred.sh
@@ -5,7 +5,7 @@
 # parameterisations, and loads it into the scxa_coords table of AtlasProd.
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 dbConnection=${dbConnection:-$1}
@@ -13,7 +13,8 @@ EXP_ID=${EXP_ID:-$2}
 DIMRED_TYPE=${DIMRED_TYPE:-$3}
 DIMRED_FILE_PATH=${DIMRED_FILE_PATH:-$4}
 DIMRED_PARAM_JSON=${DIMRED_PARAM_JSON:-$5}
-SCRATCH_DIR=${SCRATCH_DIR:-"$(dirname ${DIMRED_FILE_PATH})"}
+#SCRATCH_DIR=${SCRATCH_DIR:-"$(dirname ${DIMRED_FILE_PATH})"}
+SCRATCH_DIR=${SCRATCH_DIR:-"$DIMRED_FILE_PATH"}
 
 # Check that necessary environment variables are defined.
 [ -n ${dbConnection+x} ] || (echo "Env var dbConnection for the database connection needs to be defined. This includes the database name." && exit 1)
diff --git a/bin/load_db_scxa_marker_genes.sh b/bin/load_db_scxa_marker_genes.sh
index 89067fb..dc70d05 100755
--- a/bin/load_db_scxa_marker_genes.sh
+++ b/bin/load_db_scxa_marker_genes.sh
@@ -6,7 +6,7 @@
 # scxa_cell_groups_marker_genes table of AtlasProd.
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 dbConnection=${dbConnection:-$1}
diff --git a/bin/load_exp_design.sh b/bin/load_exp_design.sh
index 6ed6458..bd86df3 100755
--- a/bin/load_exp_design.sh
+++ b/bin/load_exp_design.sh
@@ -2,7 +2,7 @@
 
 set -e
 
-scriptDir=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+scriptDir=$(cd "$( dirname "${BASH_SOURCE[0]:-$0}" )" && pwd )
 source $scriptDir/db_scxa_common.sh
 
 dbConnection=${dbConnection:-$1}
diff --git a/bin/load_experiment_web_cli.sh b/bin/load_experiment_web_cli.sh
index d0cebc6..f550dbb 100755
--- a/bin/load_experiment_web_cli.sh
+++ b/bin/load_experiment_web_cli.sh
@@ -11,7 +11,7 @@
 
 jar_dir=$CONDA_PREFIX/share/atlas-cli
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/common_routines.sh
 
 echo "CONDA_PREFIX: $CONDA_PREFIX"
diff --git a/bin/modify_collection.sh b/bin/modify_collection.sh
index e7f08e4..2ca68be 100755
--- a/bin/modify_collection.sh
+++ b/bin/modify_collection.sh
@@ -2,7 +2,7 @@
 
 set -e
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/db_scxa_common.sh
 
 dbConnection=${dbConnection:-$1}
diff --git a/bin/update_experiment_web_cli.sh b/bin/update_experiment_web_cli.sh
index 2c6d8fa..bd2c7bf 100755
--- a/bin/update_experiment_web_cli.sh
+++ b/bin/update_experiment_web_cli.sh
@@ -11,7 +11,7 @@
 
 jar_dir=$CONDA_PREFIX/share/atlas-cli
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 source $scriptDir/common_routines.sh
 
 echo "CONDA_PREFIX: $CONDA_PREFIX"
diff --git a/fixtures/generate-fixtures.sh b/fixtures/generate-fixtures.sh
index 840a621..dbd91f8 100755
--- a/fixtures/generate-fixtures.sh
+++ b/fixtures/generate-fixtures.sh
@@ -22,7 +22,7 @@
 
 # https://stackoverflow.com/questions/59895/how-can-i-get-the-source-directory-of-a-bash-script-from-within-the-script-itsel
 # https://stackoverflow.com/a/246128
-SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )"
 
 export POSTGRES_HOST=${POSTGRES_HOST:-localhost}
 export POSTGRES_PORT=${POSTGRES_PORT:-5432}
diff --git a/fixtures/generate-tsv-fixture.sh b/fixtures/generate-tsv-fixture.sh
index e55bf4b..8bf89eb 100755
--- a/fixtures/generate-tsv-fixture.sh
+++ b/fixtures/generate-tsv-fixture.sh
@@ -10,7 +10,7 @@
 # We choose 100 genes that are expressed in those cells via analytics table
 
 set -e
-SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )"
 
 source ${SCRIPT_DIR}/utils.sh
 
diff --git a/tests/run_tests.sh b/tests/run_tests.sh
index 02a8f18..9b7dc55 100755
--- a/tests/run_tests.sh
+++ b/tests/run_tests.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+scriptDir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}" )" &> /dev/null && pwd )
 export testsDir=$scriptDir
 export PATH=$scriptDir/../bin:$scriptDir/../tests:$PATH
 
@@ -29,7 +29,7 @@ chmod -R a+w /tmp/fixtures/experiment_files/expdesign
 
 
 if [ "$#" -eq 0 ]; then
-	bats --tap "$(dirname "${BASH_SOURCE[0]}")"
+	bats --tap "$(dirname "${BASH_SOURCE[0]:-$0}")"
 else
 	bats random-data-set.bats
 fi
diff --git a/tests/test_dimred_load.sh b/tests/test_dimred_load.sh
index e9f2c1b..46e1dc3 100755
--- a/tests/test_dimred_load.sh
+++ b/tests/test_dimred_load.sh
@@ -6,7 +6,7 @@ delete_db_scxa_dimred.sh
 # do it just for testing
 
 ls ${EXPERIMENT_DIMRED_PATH}/${EXP_ID}.tsne*.tsv | while read -r l; do
-  export DIMRED_TYPE=tsne
+  export DIMRED_TYPE=t-SNE
   export DIMRED_FILE_PATH=$l
   paramval=$(echo "$l" | sed 's/.*[^0-9]\([0-9]*\).tsv/\1/g')
   export DIMRED_PARAM_JSON='[{"perplexity": '$paramval'}]'
@@ -14,7 +14,7 @@ ls ${EXPERIMENT_DIMRED_PATH}/${EXP_ID}.tsne*.tsv | while read -r l; do
 done
 
 ls ${EXPERIMENT_DIMRED_PATH}/${EXP_ID}.umap*.tsv | while read -r l; do
-  export DIMRED_TYPE=umap
+  export DIMRED_TYPE=UMAP
   export DIMRED_FILE_PATH=$l
   paramval=$(echo "$l" | sed 's/.*[^0-9]\([0-9]*\).tsv/\1/g')
   export DIMRED_PARAM_JSON='[{"n_neighbors": '$paramval'}]'