renamed env vars

JaneliaSciComp · Dec 18, 2023 · 2945025 · 2945025
1 parent 00ae971
commit 2945025
Show file tree

Hide file tree

Showing 4 changed files with 32 additions and 9 deletions.
diff --git a/precompute-scripts/step0-import-cdm/import-params.sh b/precompute-scripts/step0-import-cdm/import-params.sh
@@ -8,12 +8,20 @@ export JACS_URL=${JACS_URL:="http://<host>/api/rest-v2"}
 export JACS_AUTH_TYPE=${JACS_AUTH_TYPE:="APIKEY"}
 export JACS_AUTH_TOKEN=${JACS_AUTH_TOKEN:="tokenvalue"}
 
-export IMPORT_TAG=${IMPORT_TAG:=}
+if [[ -z ${IMPORT_TAG} ]] ; then
+    echo "IMPORT_TAG must be set in your .env file"
+    exit 1
+fi
+
+export IMPORT_TAG=${IMPORT_TAG}
 
 export SEARCHABLE_SUBFOLDER=${SEARCHABLE_SUBFOLDER:=segmentation}
+export GRAD_SUBFOLDER=${GRAD_SUBFOLDER:=grad}
+export ZGAP_SUBFOLDER=${ZGAP_SUBFOLDER:=zgap}
+
 export SEARCHABLE_MIPS=${SEARCHABLE_MIPS:=${LIBNAME}:searchable_neurons:${LIBDIR}/${SEARCHABLE_SUBFOLDER}}
-export GRAD_MIPS=${GRAD_MIPS:=${LIBNAME}:gradient:${LIBDIR}/grad}
-export ZGAP_MIPS=${ZGAP_MIPS:=${LIBNAME}:zgap:${LIBDIR}/zgap}
+export GRAD_MIPS=${GRAD_MIPS:=${LIBNAME}:gradient:${LIBDIR}/${GRAD_SUBFOLDER}}
+export ZGAP_MIPS=${ZGAP_MIPS:=${LIBNAME}:zgap:${LIBDIR}/${ZGAP_SUBFOLDER}}
 
 export EXCLUDED_LIBS=${EXCLUDED_LIBS:=flylight_splitgal4_drivers}
 export PUBLISHED_NAMES_FILTER=${PUBLISHED_NAMES_FILTER:=}

diff --git a/precompute-scripts/step1-run-cds/cds-params.sh b/precompute-scripts/step1-run-cds/cds-params.sh
@@ -19,7 +19,12 @@ export TARGETS_TAGS=${TARGETS_TAGS:=""}
 export UPDATE_RESULTS=${UPDATE_RESULTS:="false"}
 
 # Color depth search params
-export CDS_TAG=${CDS_TAG:="3.1.0"}
+if [[ -z ${CDS_TAG} ]] ; then
+    echo "CDS_TAG must be set in your .env file"
+    exit 1
+fi
+
+export CDS_TAG=${CDS_TAG}
 export PROCESSING_PARTITION_SIZE=${PROCESSING_PARTITION_SIZE:=1000}
 export MASK_THRESHOLD=${MASK_THRESHOLD:=20}
 export DATA_THRESHOLD=${MASK_THRESHOLD:=20}

diff --git a/precompute-scripts/step2-run-gradscore/ga-params.sh b/precompute-scripts/step2-run-gradscore/ga-params.sh
@@ -10,7 +10,9 @@ export NEURONS_PER_JOB=$((${NEURONS_PER_JOB:=${MASKS_PER_JOB}}))
 export TOTAL_JOBS=$(((TOTAL_MASK_NEURONS - START_MASK_NEURON_INDEX) / NEURONS_PER_JOB + 1))
 
 export MASK_NEURONS_FILTER=${MASK_NEURONS_FILTER:=""}
-export MASK_TAGS=${MASK_TAGS:=""}
+export MASKS_TAGS=${MASKS_TAGS:=""}
+export TARGETS_TAGS=${TARGETS_TAGS:=""}
+export CDS_TAG=${CDS_TAG:=""}
 export TARGET_NEURONS_FILTER=${TARGET_NEURONS_FILTER:=""}
 export MATCHES_TAGS=${MATCHES_TAGS:=""}
 

diff --git a/precompute-scripts/step2-run-gradscore/run-ga-job.sh b/precompute-scripts/step2-run-gradscore/run-ga-job.sh
@@ -22,18 +22,25 @@ function run_ga_job {
     else
         MASK_NEURONS_FILTER_ARG=""
     fi
-    if [[ -n ${MASK_TAGS} ]]; then
-        MASK_TAGS_ARG="--mask-tags ${MASK_TAGS}"
+    if [[ -n ${MASKS_TAGS} ]]; then
+        MASKS_TAGS_ARG="--mask-tags ${MASKS_TAGS}"
     else
-        MASK_TAGS_ARG=""
+        MASKS_TAGS_ARG=""
     fi
     if [[ -n ${TARGET_NEURONS_FILTER} ]]; then
         TARGET_NEURONS_FILTER_ARG="--targets-published-names ${TARGET_NEURONS_FILTER}"
     else
         TARGET_NEURONS_FILTER_ARG=""
     fi
+    if [[ -n ${TARGETS_TAGS} ]]; then
+        TARGETS_TAGS_ARG="--target-tags ${TARGETS_TAGS}"
+    else
+        TARGETS_TAGS_ARG=""
+    fi
     if [[ -n ${MATCHES_TAGS} ]]; then
         MATCHES_TAGS_ARG="--match-tags ${MATCHES_TAGS}"
+    elif [[ -n ${CDS_TAG} ]]; then
+        MATCHES_TAGS_ARG="--match-tags ${CDS_TAG}"
     else
         MATCHES_TAGS_ARG=""
     fi
@@ -79,9 +86,10 @@ function run_ga_job {
         ${AS_ARG} \
         ${MASKS_ARG} \
         ${MASK_NEURONS_FILTER_ARG} \
-        ${MASK_TAGS_ARG} \
+        ${MASKS_TAGS_ARG} \
         ${TARGETS_ARG} \
         ${TARGET_NEURONS_FILTER_ARG} \
+        ${TARGETS_TAGS_ARG} \
         ${MATCHES_TAGS_ARG} \
         --nBestLines ${TOP_RESULTS} \
         --nBestSamplesPerLine ${SAMPLES_PER_LINE} \