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
ebi-gene-expression-group · Oct 10, 2023 · 6326500 · 6326500
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commit 6326500
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -5,15 +5,16 @@
 # 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:-$1}
 EXP_ID=${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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -6,15 +6,15 @@ 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'}]'
   load_db_scxa_dimred.sh
 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'}]'