Access-heme Support

cvr/src/main/java/org/cbioportal/cmo/pipelines/CVRPipeline.java

@@ -67,7 +67,7 @@ private static Options getOptions(String[] args) {
             .addOption("j", "json", false, "To read or not to read. This can be used alone or in combination with --gml")
             .addOption("g", "gml", false, "Run germline job")
             .addOption("s", "skipSeg", false, "Flag to skip fetching seg data")
-            .addOption("i", "study_id", true, "Study identifier (i.e., mskimpact, mskraindance, mskarcher, mskimpact_heme)")
+            .addOption("i", "study_id", true, "Study identifier (i.e., mskimpact, mskraindance, mskarcher, mskimpact_heme, mskaccess, mskaccess_heme)")
             .addOption("t", "test", false, "Flag for running pipeline in testing mode so that samples are not requeued or consumed")
             .addOption("c", "consume_samples", true, "Path to CVR json filename")
             .addOption("r", "max_samples_to_remove", true, "The max number of samples that can be removed from data")

cvr/src/main/java/org/cbioportal/cmo/pipelines/cvr/SessionConfiguration.java

@@ -87,6 +87,12 @@ public class SessionConfiguration {
     @Value("${dmp.tokens.retrieve_master_list.access}")
     private String dmpMasterListAccess;
 
+    @Value("${dmp.tokens.retrieve_variants.accessheme")
+    private String retrieveVariantsAccessHeme;
+
+    @Value("${dmp.tokens.retrieve_master_list.accessheme}")
+    private String dmpMasterListAccessHeme;
+
     private Logger log = Logger.getLogger(SessionConfiguration.class);
 
     @Bean
@@ -106,7 +112,7 @@ public Map<String, String> retrieveVariantTokensMap() {
         map.put("mskimpact_heme", retrieveVariantsHeme);
         map.put("mskarcher", retrieveVariantsArcher);
         map.put("mskaccess", retrieveVariantsAccess);
-
+        map.put("mskaccess_heme", retrieveVariantsAccessHeme);
         return map;
     }
 
@@ -118,7 +124,7 @@ public Map<String, String> masterListTokensMap() {
         map.put("mskimpact_heme", dmpMasterListHeme);
         map.put("mskarcher", dmpMasterListArcher);
         map.put("mskaccess", dmpMasterListAccess);
-
+        map.put("mskaccess_heme", retrieveVariantsAccessHeme);
         return map;
     }
 

import-scripts/backup-redcap-data.sh

@@ -10,11 +10,13 @@ MSKIMPACT_REDCAP_EXPORT_FAIL=0
 HEMEPACT_REDCAP_EXPORT_FAIL=0
 ARCHER_REDCAP_EXPORT_FAIL=0
 ACCESS_REDCAP_EXPORT_FAIL=0
+ACCESSHEME_REDCAP_EXPORT_FAIL=0
 
 MSKIMPACT_VALIDATION_FAIL=0
 HEMEPACT_VALIDATION_FAIL=0
 ARCHER_VALIDATION_FAIL=0
 ACCESS_VALIDATION_FAIL=0
+ACCESSHEME_VALIDATION_FAIL=0
 
 # -----------------------------------------------------------------------------------------------------------
 # FUNCTIONS
@@ -146,6 +148,28 @@ else
     fi
 fi
 
+
+# export and commit ACCESS REDCap data
+$JAVA_BINARY $JAVA_REDCAP_PIPELINE_ARGS -e -r -s mskaccess_heme -d $ACCESSHEME_REDCAP_BACKUP
+if [ $? -gt 0 ]; then
+    echo "Failed to export REDCap data snapshot for ACCESSHEME! Aborting any changes made during export..."
+    cd $ACCESSHEME_REDCAP_BACKUP; $GIT_BINARY checkout -- .
+    ACCESSHEME_REDCAP_EXPORT_FAIL=1
+    sendFailureMessageMskPipelineLogsSlack "ACCESSHEME export"
+else
+    validateRedcapExportForStudy $ACCESSHEME_REDCAP_BACKUP
+    if [ $? -gt 0 ]; then
+        echo "Validation of ACCESS REDCap snapshot failed! Aborting any changes made during export..."
+        ACCESSHEME_VALIDATION_FAIL=1
+        cd $ACCESSHEME_REDCAP_BACKUP; $GIT_BINARY checkout -- .
+        ACCESSHEME_REDCAP_EXPORT_FAIL=1
+        sendFailureMessageMskPipelineLogsSlack "ACCESSHEME validation"
+    else
+        echo "Committing ACCESSHEME REDCap data snapshot"
+        cd $ACCESSHEME_REDCAP_BACKUP; $GIT_BINARY add -A . ; $GIT_BINARY commit -m "ACCESSHEME REDCap Snapshot"
+    fi
+fi
+
 # push outgoing changesets to snapshot repo
 echo "Pushing REDCap snapshot back to git repository..."
 echo $(date)

import-scripts/cvr_dmp_endpoint_utility.py

@@ -33,11 +33,13 @@
 MASTERLIST_ARCHER = 'dmp.tokens.retrieve_master_list.archer'
 MASTERLIST_ACCESS = 'dmp.tokens.retrieve_master_list.access'
 MASTERLIST_RAINDANCE = 'dmp.tokens.retrieve_master_list.rdts'
+MASTERLIST_ACCESS_HEME = 'dmp.tokens.retrieve_master_list.accessheme'
 
 RETRIEVE_VARIANTS_MSKIMPMACT = 'dmp.tokens.retrieve_variants.impact'
 RETRIEVE_VARIANTS_HEMEPACT = 'dmp.tokens.retrieve_variants.heme'
 RETRIEVE_VARIANTS_ARCHER = 'dmp.tokens.retrieve_variants.archer'
 RETRIEVE_VARIANTS_ACCESS = 'dmp.tokens.retrieve_variants.access'
+RETRIEVE_VARIANTS_ACCESS_HEME = 'dmp.tokens.retrieve_variants.accessheme'
 RETRIEVE_VARIANTS_RAINDANCE = 'dmp.tokens.retrieve_variants.rdts'
 RETIREVE_GML_VARIANTS = 'dmp.tokens.retrieve_gml_variants'
 
@@ -57,11 +59,13 @@
     MASTERLIST_HEMEPACT,
     MASTERLIST_ARCHER,
     MASTERLIST_ACCESS,
+    MASTERLIST_ACCESS_HEME,
     MASTERLIST_RAINDANCE,
     RETRIEVE_VARIANTS_MSKIMPMACT,
     RETRIEVE_VARIANTS_HEMEPACT,
     RETRIEVE_VARIANTS_ARCHER,
     RETRIEVE_VARIANTS_ACCESS,
+    RETRIEVE_VARIANTS_ACCESS_HEME,
     RETRIEVE_VARIANTS_RAINDANCE,
     RETIREVE_GML_VARIANTS
 ]
@@ -87,7 +91,7 @@
 
 CONSUME_AFFECTED_ROWS = 'affectedRows'
 
-DMP_STUDY_IDS = ['mskimpact', 'mskimpact_heme', 'mskraindance', 'mskarcher', 'mskaccess']
+DMP_STUDY_IDS = ['mskimpact', 'mskimpact_heme', 'mskraindance', 'mskarcher', 'mskaccess', 'mskaccess_heme']
 DMP_SAMPLE_ID_PATTERN = re.compile('P-\d+-(T|N)\d+-(IH|TB|TS|AH|AS|IM|XS)\d+')
 
 MASTERLIST_CHECK_ARG_DESCRIPTION = '[optional] Fetches masterlist for study and reports samples from samples file that are missing from masterlist.'

import-scripts/dmp-import-vars-functions.sh

@@ -270,6 +270,20 @@ function import_access_ddp_to_redcap {
     return $return_value
 }
 
+# Function for importing access cvr files to redcap
+function import_accessheme_cvr_to_redcap {
+    return_value=0
+    if ! import_project_to_redcap $MSK_ACCESS_DATA_HOME/data_clinical_mskaccess_heme_data_clinical.txt mskaccess_heme_data_clinical ; then return_value=1 ; fi
+    return $return_value
+}
+
+# Function for importing access supp date files to redcap
+function import_accessheme_supp_date_to_redcap {
+    return_value=0
+    if ! import_project_to_redcap $MSK_ACCESS_DATA_HOME/data_clinical_mskaccess_heme_data_clinical_supp_date.txt mskaccess_heme_data_clinical_supp_date ; then return_value=1 ; fi
+    return $return_value
+}
+
 # Function for removing raw clinical and timeline files from study directory
 function remove_raw_clinical_timeline_data_files {
     STUDY_DIRECTORY=$1
@@ -340,6 +354,11 @@ function consumeSamplesAfterSolidHemeImport {
         $JAVA_BINARY $JAVA_CVR_FETCHER_ARGS -c $MSK_ACCESS_PRIVATE_DATA_HOME/cvr_data.json -z $drop_dead_instant_string
         rm -f $MSK_ACCESS_CONSUME_TRIGGER
     fi
+    if [ -f $MSK_ACCESSHEME_CONSUME_TRIGGER ] ; then
+        echo "Consuming mskaccessheme samples from cvr"
+        $JAVA_BINARY $JAVA_CVR_FETCHER_ARGS -c $MSK_ACCESSHEME_PRIVATE_DATA_HOME/cvr_data.json -z $drop_dead_instant_string
+        rm -f $MSK_ACCESSHEME_CONSUME_TRIGGER
+    fi
 }
 
 # Function for consuming fetched samples after successful archer import

import-scripts/fetch-dmp-data-for-import.sh

@@ -20,6 +20,7 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/fetch-dmp-data-for-import.lock"
     IMPORT_STATUS_HEME=0
     IMPORT_STATUS_ARCHER=0
     IMPORT_STATUS_ACCESS=0
+    IMPORT_STATUS_ACCESSHEME=0
 
     # Flags for ARCHER structural variants merge failure
     ARCHER_MERGE_IMPACT_FAIL=0
@@ -30,12 +31,14 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/fetch-dmp-data-for-import.lock"
     EXPORT_SUPP_DATE_HEME_FAIL=0
     EXPORT_SUPP_DATE_ARCHER_FAIL=0
     EXPORT_SUPP_DATE_ACCESS_FAIL=0
+    EXPORT_SUPP_DATE_ACCESSHEME_FAIL=0
 
     # Assume fetchers have failed until they complete successfully
     FETCH_CVR_IMPACT_FAIL=1
     FETCH_CVR_HEME_FAIL=1
     FETCH_CVR_ARCHER_FAIL=1
     FETCH_CVR_ACCESS_FAIL=1
+    FETCH_CVR_ACCESSHEME_FAIL=1
 
     UNLINKED_ARCHER_SUBSET_FAIL=0
     MIXEDPACT_MERGE_FAIL=0
@@ -146,6 +149,13 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/fetch-dmp-data-for-import.lock"
         sendPreImportFailureMessageMskPipelineLogsSlack "ACCESS Redcap export of mskaccess_data_clinical_supp_date"
     fi
 
+    echo "exporting accessheme data_clinical_supp_date.txt from redcap"
+    export_project_from_redcap $MSK_ACCESSHEME_DATA_HOME mskaccess_heme_data_clinical_supp_date
+    if [ $? -gt 0 ] ; then
+        EXPORT_SUPP_DATE_ACCESSHEME_FAIL=1
+        sendPreImportFailureMessageMskPipelineLogsSlack "ACCESS Redcap export of mskaccess_heme_data_clinical_supp_date"
+    fi
+
     # IF WE CANCEL ANY IMPORT, LET REDCAP GET AHEAD OF CURRENCY, BUT DON'T LET THE REPOSITORY HEAD ADVANCE [REVERT]
     printTimeStampedDataProcessingStepMessage "export of cvr clinical files from redcap"
     echo "exporting impact data_clinical.txt from redcap"
@@ -176,6 +186,12 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/fetch-dmp-data-for-import.lock"
         sendPreImportFailureMessageMskPipelineLogsSlack "ACCESS Redcap export of mskaccess_data_clinical_cvr"
     fi
 
+    echo "exporting accessheme data_clinical.txt from redcap"
+    export_project_from_redcap $MSK_ACCESSHEME_DATA_HOME mskaccess_heme_data_clinical
+    if [ $? -gt 0 ] ; then
+        IMPORT_STATUS_ACCESSHEME=1
+        sendPreImportFailureMessageMskPipelineLogsSlack "ACCESS Redcap export of mskaccess_heme_data_clinical_cvr"
+    fi
     # -----------------------------------------------------------------------------------------------------------
     # MSKIMPACT DATA FETCHES
     # TODO: move other pre-import/data-fetch steps here (i.e exporting raw files from redcap)
@@ -396,6 +412,40 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/fetch-dmp-data-for-import.lock"
         fi
     fi
 
+    # -----------------------------------------------------------------------------------------------------------
+    # ACCESSHEME DATA FETCHES
+    printTimeStampedDataProcessingStepMessage "ACCESSHEME data processing"
+
+    if [ $IMPORT_STATUS_ACCESSHEME -eq 0 ] ; then
+        # fetch new/updated access samples using CVR Web service (must come after git fetching).
+        drop_dead_instant_step=$(date --date="+3hours" -Iseconds) # nearly 3 hours from now
+        drop_dead_instant_string=$(find_earlier_instant "$drop_dead_instant_step" "$DROP_DEAD_INSTANT_END_TO_END")
+        printTimeStampedDataProcessingStepMessage "CVR fetch for accessheme"
+        # access has -b option to block warnings for samples with zero variants (all samples will have zero variants)
+        $JAVA_BINARY $JAVA_CVR_FETCHER_ARGS -d $MSK_ACCESSHEME_DATA_HOME -p $MSK_ACCESSHEME_PRIVATE_DATA_HOME -n data_clinical_mskaccessheme_data_clinical.txt -i mskaccess_heme -s -b -r 50 $CVR_TEST_MODE_ARGS -z $drop_dead_instant_string
+        if [ $? -gt 0 ] ; then
+            echo "CVR ACCESSHEME fetch failed!"
+            echo "This will not affect importing of mskimpact"
+            cd $DMP_DATA_HOME ; $GIT_BINARY reset HEAD --hard
+            cd $DMP_PRIVATE_DATA_HOME ; $GIT_BINARY reset HEAD --hard
+            sendPreImportFailureMessageMskPipelineLogsSlack "ACCESSHEME CVR Fetch"
+            IMPORT_STATUS_ACCESSHEME=1
+        else
+            # check for PHI
+            $PYTHON_BINARY $PORTAL_HOME/scripts/phi-scanner.py -a $PIPELINES_CONFIG_HOME/properties/fetch-cvr/phi-scanner-attributes.txt -j $MSK_ACCESSHEME_PRIVATE_DATA_HOME/cvr_data.json
+            if [ $? -gt 0 ] ; then
+                echo "PHI attributes found in $MSK_ACCESS_PRIVATE_DATA_HOME/cvr_data.json! ACCESSHEME will not be imported!"
+                cd $DMP_DATA_HOME ; $GIT_BINARY reset HEAD --hard
+                cd $DMP_PRIVATE_DATA_HOME ; $GIT_BINARY reset HEAD --hard
+                sendPreImportFailureMessageMskPipelineLogsSlack "ACCESSHEME PHI attributes scan failed on $MSK_ACCESSHEME_PRIVATE_DATA_HOME/cvr_data.json"
+                IMPORT_STATUS_ACCESSHEME=1
+            else
+                FETCH_CVR_ACCESSHEME_FAIL=0
+                cd $MSK_ACCESSHEME_DATA_HOME ; $GIT_BINARY add ./* ; $GIT_BINARY commit -m "Latest ACCESSHEME dataset"
+                cd $MSK_ACCESSHEME_PRIVATE_DATA_HOME ; $GIT_BINARY add ./* ; $GIT_BINARY commit -m "Latest ACCESSHEME dataset"
+            fi
+        fi
+    fi
     # -----------------------------------------------------------------------------------------------------------
     # GENERATE CANCER TYPE CASE LISTS AND SUPP DATE ADDED FILES
     # NOTE: Even though cancer type case lists are not needed for MSKIMPACT, HEMEPACT for the portal
@@ -447,6 +497,18 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/fetch-dmp-data-for-import.lock"
         cd $DMP_DATA_HOME ; $GIT_BINARY reset HEAD --hard
     fi
 
+    # generate case lists by cancer type and add "DATE ADDED" info to clinical data for ACCESSHEME
+    if [ $IMPORT_STATUS_ACCESSHEME -eq 0 ] && [ $FETCH_CVR_ACCESSHEME_FAIL -eq 0 ] ; then
+        # TODO: double check args for this
+        addCancerTypeCaseLists $MSK_ACCESSHEME_DATA_HOME "mskaccess_heme" "data_clinical_mskaccess_heme_data_clinical.txt"
+        cd $MSK_ACCESSHEME_DATA_HOME ; $GIT_BINARY add case_lists ; $GIT_BINARY commit -m "Latest ACCESSHEME Dataset: Case Lists"
+        if [ $EXPORT_SUPP_DATE_ACCESSHEME_FAIL -eq 0 ] ; then
+            addDateAddedData $MSK_ACCESSHEME_DATA_HOME "data_clinical_mskaccess_heme_data_clinical.txt" "data_clinical_mskaccess_heme_data_clinical_supp_date.txt"
+            cd $MSK_ACCESSHEME_DATA_HOME ; $GIT_BINARY add data_clinical_mskaccess_heme_data_clinical_supp_date.txt ; $GIT_BINARY commit -m "Latest ACCESSHEME Dataset: SUPP DATE ADDED"
+        fi
+        cd $DMP_DATA_HOME ; $GIT_BINARY reset HEAD --hard
+    fi
+
     # -----------------------------------------------------------------------------------------------------------
     # ADDITIONAL PROCESSING
 
@@ -563,6 +625,23 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/fetch-dmp-data-for-import.lock"
         fi
     fi
 
+    ## ACCESSHEME imports
+
+    # imports access cvr data into redcap
+    if [ $FETCH_CVR_ACCESSHEME_FAIL -eq 0 ] ; then
+        import_accessheme_cvr_to_redcap
+        if [ $? -gt 0 ] ; then
+            IMPORT_STATUS_ACCESSHEME=1
+            sendPreImportFailureMessageMskPipelineLogsSlack "ACCESSHEME CVR Redcap Import"
+        fi
+        if [ $EXPORT_SUPP_DATE_ACCESSHEME_FAIL -eq 0 ] ; then
+            import_accessheme_supp_date_to_redcap
+            if [ $? -gt 0 ] ; then
+                sendPreImportFailureMessageMskPipelineLogsSlack "ACCESSHEME Supp Date Redcap Import. Project is now empty, data restoration required"
+            fi
+        fi
+    fi
+
     echo "Import into redcap finished"
 
     # -------------------------------------------------------------
@@ -580,8 +659,11 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/fetch-dmp-data-for-import.lock"
     echo "removing raw clinical & timeline files for mskaccess"
     remove_raw_clinical_timeline_data_files $MSK_ACCESS_DATA_HOME
 
+    echo "removing raw clinical & timeline files for mskaccess"
+    remove_raw_clinical_timeline_data_files $MSK_ACCESSHEME_DATA_HOME
+
     # commit raw file cleanup - study staging directories should only contain files for portal import
-    $GIT_BINARY commit -m "Raw clinical and timeline file cleanup: MSKIMPACT, HEMEPACT, ARCHER, ACCESS"
+    $GIT_BINARY commit -m "Raw clinical and timeline file cleanup: MSKIMPACT, HEMEPACT, ARCHER, ACCESS, ACCESSHEME"
 
     # -------------------------------------------------------------
     # REDCAP EXPORTS - CBIO STAGING FORMATS
@@ -661,6 +743,19 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/fetch-dmp-data-for-import.lock"
         fi
     fi
 
+    printTimeStampedDataProcessingStepMessage "export of redcap data for accessheme"
+    if [ $IMPORT_STATUS_ACCESSHEME -eq 0 ] ; then
+        export_stable_id_from_redcap mskaccess_heme $MSK_ACCESSHEME_DATA_HOME
+        if [ $? -gt 0 ] ; then
+            IMPORT_STATUS_ACCESSHEME=1
+            cd $DMP_DATA_HOME ; $GIT_BINARY reset HEAD --hard
+            sendPreImportFailureMessageMskPipelineLogsSlack "ACCESSHEME Redcap Export"
+        else
+            touch $MSK_ACCESSHEME_CONSUME_TRIGGER
+            cd $MSK_ACCESSHEME_DATA_HOME ; $GIT_BINARY add * ; $GIT_BINARY commit -m "Latest ACCESSHEME Dataset: Clinical and Timeline"
+        fi
+    fi
+
     # -------------------------------------------------------------
     # UNLINKED ARCHER DATA PROCESSING
     # NOTE: This processing should only occur if (1) PROCESS_UNLINKED_ARCHER_STUDY=1 and
@@ -734,9 +829,9 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/fetch-dmp-data-for-import.lock"
         echo $(date)
     fi
 
-    printTimeStampedDataProcessingStepMessage "merge of MSK-IMPACT, HEMEPACT, ACCESS data for MSKSOLIDHEME"
+    printTimeStampedDataProcessingStepMessage "merge of MSK-IMPACT, HEMEPACT, ACCESS, ACCESSHEME data for MSKSOLIDHEME"
     # MSKSOLIDHEME merge and check exit code
-    $PYTHON_BINARY $PORTAL_HOME/scripts/merge.py -d $MSK_SOLID_HEME_DATA_HOME -i mskimpact -m "true" -e $MAPPED_ARCHER_SAMPLES_FILE $MSK_IMPACT_DATA_HOME $MSK_HEMEPACT_DATA_HOME $MSK_ACCESS_DATA_HOME
+    $PYTHON_BINARY $PORTAL_HOME/scripts/merge.py -d $MSK_SOLID_HEME_DATA_HOME -i mskimpact -m "true" -e $MAPPED_ARCHER_SAMPLES_FILE $MSK_IMPACT_DATA_HOME $MSK_HEMEPACT_DATA_HOME $MSK_ACCESS_DATA_HOME $MSK_ACCESSHEME_DATA_HOME
     if [ $? -gt 0 ] ; then
         echo "MSKSOLIDHEME merge failed! Study will not be updated in the portal."
         echo $(date)

import-scripts/pipelines_eks/automation-environment.sh

@@ -169,12 +169,14 @@ export MSK_HEMEPACT_DATA_HOME=$DMP_DATA_HOME/mskimpact_heme
 export MSK_ARCHER_DATA_HOME=$DMP_DATA_HOME/mskarcher
 export MSK_ARCHER_UNFILTERED_DATA_HOME=$DMP_DATA_HOME/mskarcher_unfiltered
 export MSK_ACCESS_DATA_HOME=$DMP_DATA_HOME/mskaccess
+export MSK_ACCESSHEME_DATA_HOME=$DMP_DATA_HOME/mskaccess_heme
 export MSK_IMPACT_PRIVATE_DATA_HOME=$DMP_PRIVATE_DATA_HOME/mskimpact_private
 export MSK_RAINDANCE_PRIVATE_DATA_HOME=$DMP_PRIVATE_DATA_HOME/mskraindance_private
 export MSK_HEMEPACT_PRIVATE_DATA_HOME=$DMP_PRIVATE_DATA_HOME/mskimpact_heme_private
 export MSK_ARCHER_PRIVATE_DATA_HOME=$DMP_PRIVATE_DATA_HOME/mskarcher_private
 export MSK_ARCHER_UNFILTERED_PRIVATE_DATA_HOME=$DMP_PRIVATE_DATA_HOME/mskarcher_unfiltered_private
 export MSK_ACCESS_PRIVATE_DATA_HOME=$DMP_PRIVATE_DATA_HOME/mskaccess_private
+export MSK_ACCESSHEME_PRIVATE_DATA_HOME=$DMP_PRIVATE_DATA_HOME/mskaccess_heme_private
 export MSK_MIXEDPACT_DATA_HOME=$DMP_DATA_HOME/mixedpact
 export MSK_SOLID_HEME_DATA_HOME=$DMP_DATA_HOME/msk_solid_heme
 export MSK_KINGS_DATA_HOME=$DMP_DATA_HOME/msk_kingscounty
@@ -205,6 +207,7 @@ export MSKIMPACT_REDCAP_BACKUP=$REDCAP_BACKUP_DATA_HOME/mskimpact
 export HEMEPACT_REDCAP_BACKUP=$REDCAP_BACKUP_DATA_HOME/mskimpact_heme
 export ARCHER_REDCAP_BACKUP=$REDCAP_BACKUP_DATA_HOME/mskarcher
 export ACCESS_REDCAP_BACKUP=$REDCAP_BACKUP_DATA_HOME/mskaccess
+export ACCESSHEME_REDCAP_BACKUP=$REDCAP_BACKUP_DATA_HOME/mskaccess_heme
 
 #######################
 # environment variables used in the import-pdx-data script

import-scripts/preconsume_problematic_samples.sh

@@ -212,4 +212,4 @@ done
 if need_to_log_actions ; then
     log_actions
     post_slack_message
-fi
+fi