Preconsume archer-solid-cv4 and add fetch loop (#1129)

* Handle archer-solid-cv4 samples
* Add loop
* move each cohort to its own dir and fix filename

Author: callachennault

import-scripts/detect_samples_with_problematic_metadata.py

@@ -39,7 +39,7 @@ def sample_missing_required_metadata(metadata, problematic_metadata):
         if metadata[required_field] is None:
             problematic_metadata["gene-panel"] = None
             return True
-        if required_field == "gene-panel" and metadata[required_field].casefold() == "unknown":
+        if required_field == "gene-panel" and metadata[required_field].casefold() in {"unknown", "archer-solid-cv4"}:
             problematic_metadata["gene-panel"] = metadata[required_field]
             return True
     return False

import-scripts/preconsume_problematic_samples.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 
 COHORT=$1
-TMP_DIR="/data/portal-cron/tmp/preconsume_problematic_samples"
+FETCH_NUM=1
+TMP_DIR="/data/portal-cron/tmp/preconsume_problematic_samples/${COHORT}"
 CVR_FETCH_PROPERTIES_FILEPATH="/data/portal-cron/git-repos/pipelines-configuration/properties/fetch-cvr/application.properties"
 CVR_USERNAME=$(grep 'dmp.user_name' ${CVR_FETCH_PROPERTIES_FILEPATH} | head -n 1 | sed -E s/[^=][^=]*=//)
 CVR_PASSWORD=$(grep 'dmp.password' ${CVR_FETCH_PROPERTIES_FILEPATH} | head -n 1 | sed -E s/[^=][^=]*=//)
@@ -13,11 +14,11 @@ CVR_HEME_FETCH_URL_PREFIX="${CVR_TUMOR_SERVER}cbio_retrieve_heme_variants"
 CVR_ARCHER_FETCH_URL_PREFIX="${CVR_TUMOR_SERVER}cbio_archer_retrieve_variants"
 CVR_ACCESS_FETCH_URL_PREFIX="${CVR_TUMOR_SERVER}cbio_retrieve_access_variants"
 CVR_CONSUME_SAMPLE_URL_PREFIX="${CVR_TUMOR_SERVER}cbio_consume_sample"
-FETCH_OUTPUT_FILEPATH="$TMP_DIR/cvr_data_${COHORT}.json"
-CONSUME_IDS_FILEPATH="$TMP_DIR/${COHORT}_consume.ids"
-PROBLEMATIC_EVENT_CONSUME_IDS_FILEPATH="$TMP_DIR/problematic_event_consume_${COHORT}.ids"
-PROBLEMATIC_METADATA_CONSUME_IDS_FILEPATH="$TMP_DIR/problematic_metadata_consume_${COHORT}.ids"
-CONSUME_ATTEMPT_OUTPUT_FILEPATH="$TMP_DIR/consume_attempt_output_${COHORT}.json"
+FETCH_OUTPUT_FILEPATH=""
+CONSUME_IDS_FILEPATH="$TMP_DIR/consume.ids"
+PROBLEMATIC_EVENT_CONSUME_IDS_FILEPATH="$TMP_DIR/problematic_event_consume.ids"
+PROBLEMATIC_METADATA_CONSUME_IDS_FILEPATH="$TMP_DIR/problematic_metadata_consume.ids"
+CONSUME_ATTEMPT_OUTPUT_FILEPATH="$TMP_DIR/consume_attempt_output.json"
 DETECT_SAMPLES_WITH_NULL_DP_AD_FIELDS_SCRIPT_FILEPATH=/data/portal-cron/scripts/detect_samples_with_null_dp_ad_fields.py
 DETECT_SAMPLES_WITH_PROBLEMATIC_METADATA_SCRIPT_FILEPATH=/data/portal-cron/scripts/detect_samples_with_problematic_metadata.py
 CVR_MONITOR_SLACK_URI_FILE="/data/portal-cron/pipelines-credentials/cvr-monitor-webhook-uri"
@@ -29,6 +30,9 @@ function make_tmp_dir_if_necessary() {
             echo "Error : could not create tmp directory '$TMP_DIR'" >&2
             exit 1
         fi
+    else
+        # Remove files from last fetch
+        rm $TMP_DIR/*
     fi
 }
 
@@ -57,6 +61,7 @@ function set_cvr_fetch_url_prefix() {
 }
 
 function fetch_currently_queued_samples() {
+    FETCH_OUTPUT_FILEPATH="$TMP_DIR/cvr_data_${FETCH_NUM}.json"
     dmp_token=$(curl $CVR_CREATE_SESSION_URL | grep session_id | sed -E 's/",[[:space:]]*$//' | sed -E 's/.*"//')
     curl "${CVR_FETCH_URL_PREFIX}/${dmp_token}/0" > ${FETCH_OUTPUT_FILEPATH}
 }
@@ -69,10 +74,13 @@ function detect_samples_with_problematic_metadata() {
     $DETECT_SAMPLES_WITH_PROBLEMATIC_METADATA_SCRIPT_FILEPATH ${FETCH_OUTPUT_FILEPATH} ${PROBLEMATIC_METADATA_CONSUME_IDS_FILEPATH}
 }
 
-function exit_if_no_problems_detected() {
+function problems_were_detected() {
     if [ ! -s ${PROBLEMATIC_EVENT_CONSUME_IDS_FILEPATH} ] && [ ! -s ${PROBLEMATIC_METADATA_CONSUME_IDS_FILEPATH} ] ; then
-        echo "no problematic samples detected .. exiting"
-        exit 0
+        echo "no problematic samples detected"
+        return 1
+    else
+        echo "problematic samples were detected"
+        return 0
     fi
 }
 
@@ -108,41 +116,57 @@ function attempt_to_consume_problematic_sample() {
     dmp_token="$1"
     sample_id="$2"
     type_of_problem="$3" # pass 'e' for event problems and 'm' for metadata problems
+    register_attempt="$4"
     HTTP_STATUS=$(curl -sSL -w '%{http_code}' -o "$CONSUME_ATTEMPT_OUTPUT_FILEPATH" "${CVR_CONSUME_SAMPLE_URL_PREFIX}/${dmp_token}/${sample_id}")
     if [[ $HTTP_STATUS =~ ^2 ]] ; then
         if ! grep '"error": "' "$CONSUME_ATTEMPT_OUTPUT_FILEPATH" ; then
             if grep --silent 'affectedRows": 1' "$CONSUME_ATTEMPT_OUTPUT_FILEPATH" ; then
-                register_successful_consumption "${sample_id}" "$type_of_problem"
-                continue
+                if [ "$register_attempt" == true ] ; then
+                    register_successful_consumption "${sample_id}" "$type_of_problem"
+                    continue
+                fi
             fi
         fi
     fi
-    register_failed_consumption "${sample_id}" "$type_of_problem"
+    if [ "$register_attempt" == true ] ; then
+        register_failed_consumption "${sample_id}" "$type_of_problem"
+    fi
 }
 
 function attempt_to_consume_problematic_samples() {
+    register_attempt=${1:-true}
     dmp_token=$(curl $CVR_CREATE_SESSION_URL | grep session_id | sed -E 's/",[[:space:]]*$//' | sed -E 's/.*"//')
     while read sample_id ; do
-        attempt_to_consume_problematic_sample "$dmp_token" "$sample_id" "e"
+        attempt_to_consume_problematic_sample "$dmp_token" "$sample_id" "e" "$register_attempt"
     done < ${PROBLEMATIC_EVENT_CONSUME_IDS_FILEPATH}
     while read sample_id ; do
-        attempt_to_consume_problematic_sample "$dmp_token" "$sample_id" "m"
+        attempt_to_consume_problematic_sample "$dmp_token" "$sample_id" "m" "$register_attempt"
     done < ${PROBLEMATIC_METADATA_CONSUME_IDS_FILEPATH}
 }
 
 function consume_hardcoded_samples() {
     rm -f ${PROBLEMATIC_EVENT_CONSUME_IDS_FILEPATH} ${PROBLEMATIC_METADATA_CONSUME_IDS_FILEPATH}
     touch ${PROBLEMATIC_EVENT_CONSUME_IDS_FILEPATH}
     touch ${PROBLEMATIC_METADATA_CONSUME_IDS_FILEPATH}
-
     if [ "$COHORT" == "mskimpact" ] ; then
         echo "P-0025907-N01-IM6" >> "${PROBLEMATIC_METADATA_CONSUME_IDS_FILEPATH}"
     fi
     if [ -f "${PROBLEMATIC_METADATA_CONSUME_IDS_FILEPATH}" ] ; then
-        attempt_to_consume_problematic_samples
+        # Won't register attempt (so it doesn't show up in logs every night)
+        attempt_to_consume_problematic_samples false
     fi
 }
 
+function need_to_log_actions {
+    if [ ${#succeeded_to_consume_problematic_events_sample_list[@]} -gt 0 ] || \
+       [ ${#failed_to_consume_problematic_events_sample_list[@]} -gt 0 ] || \
+       [ ${#succeeded_to_consume_problematic_metadata_sample_list[@]} -gt 0 ] || \
+       [ ${#failed_to_consume_problematic_metadata_sample_list[@]} -gt 0 ] ; then
+            return 0
+    fi
+    return 1
+}
+
 function log_actions() {
     date
     echo -e "${COHORT^^} Problematic Samples"
@@ -158,7 +182,7 @@ function post_slack_message() {
     if [ ${#failed_to_consume_problematic_events_sample_list[@]} -gt 0 ]; then
         MESSAGE="${MESSAGE} Attempted Unsuccessfully To Consume :\n${failed_to_consume_problematic_events_sample_list[*]}"
     fi
-    MESSAGE="${MESSAGE}Warning : the following samples have been preemptively consumed before fetch because they contained problematic metadata where the gene-panel property was unset or had value UNKNOWN.\nSuccessfully Consumed :\n${succeeded_to_consume_problematic_metadata_sample_list[*]}"
+    MESSAGE="${MESSAGE}Warning : the following samples have been preemptively consumed before fetch because they contained problematic metadata where the gene-panel property was unset, invalid, or had value UNKNOWN.\nSuccessfully Consumed :\n${succeeded_to_consume_problematic_metadata_sample_list[*]}"
     if [ ${#failed_to_consume_problematic_metadata_sample_list[@]} -gt 0 ]; then
         MESSAGE="${MESSAGE} Attempted Unsuccessfully To Consume :\n${failed_to_consume_problematic_metadata_sample_list[*]}"
     fi
@@ -168,20 +192,24 @@ function post_slack_message() {
 date
 check_args
 make_tmp_dir_if_necessary
-failed_to_consume_problematic_events_sample_list=() # temporary code
-succeeded_to_consume_problematic_events_sample_list=() # temporary code
-failed_to_consume_problematic_metadata_sample_list=() # temporary code
-succeeded_to_consume_problematic_metadata_sample_list=() # temporary code
 set_cvr_fetch_url_prefix
-consume_hardcoded_samples # temporary code
-fetch_currently_queued_samples
-detect_samples_with_problematic_events
-detect_samples_with_problematic_metadata
-exit_if_no_problems_detected
 failed_to_consume_problematic_events_sample_list=()
 succeeded_to_consume_problematic_events_sample_list=()
 failed_to_consume_problematic_metadata_sample_list=()
 succeeded_to_consume_problematic_metadata_sample_list=()
-attempt_to_consume_problematic_samples
-log_actions
-post_slack_message
+while :
+do
+    consume_hardcoded_samples # temporary code
+    fetch_currently_queued_samples
+    detect_samples_with_problematic_events
+    detect_samples_with_problematic_metadata
+    if ! problems_were_detected ; then
+        break
+    fi
+    attempt_to_consume_problematic_samples
+    ((FETCH_NUM++))
+done
+if need_to_log_actions ; then
+    log_actions
+    post_slack_message
+fi