Index: trunk/ippTools/share/disttool_pending_raw.sql
===================================================================
--- trunk/ippTools/share/disttool_pending_raw.sql	(revision 25838)
+++ trunk/ippTools/share/disttool_pending_raw.sql	(revision 27455)
@@ -3,11 +3,13 @@
     distRun.label,
     distTarget.dist_group,
-    stage,
-    stage_id,
+    'raw' AS stage,
+    rawExp.exp_id AS stage_id,
     rawImfile.class_id AS component,
     clean,
     rawExp.camera,
-    CONCAT_WS('.', outroot, CONVERT(distRun.dist_id, CHAR)) as outdir,
-    rawImfile.uri as path_base,         -- change this once rawImfile has path_base
+    CONCAT_WS('.', distRun.outroot, CONVERT(distRun.dist_id, CHAR)) as outdir,
+    -- XXX: replace this with rawImfile.path_base once it exists
+    TRIM(TRAILING '.fits' FROM rawImfile.uri) AS path_base,
+    CAST(NULL AS CHAR(255)) AS alt_path_base,
     chipProcessedImfile.path_base as chip_path_base,
     CAST(NULL AS CHAR(255)) AS state,
@@ -15,10 +17,11 @@
     0 as quality,
     distRun.no_magic,
+    distRun.alternate,
     rawImfile.magicked
 FROM distRun
 JOIN distTarget USING(target_id, stage, clean)
-JOIN rawExp ON rawExp.exp_id = stage_id
+JOIN rawExp ON rawExp.exp_id = stage_id AND distTarget.stage = 'raw' AND distRun.alternate = 0
 JOIN rawImfile USING(exp_id)
-JOIN chipRun ON chipRun.exp_id = rawExp.exp_id and chipRun.magicked
+JOIN chipRun ON chipRun.exp_id = rawExp.exp_id AND chipRun.magicked
 JOIN chipProcessedImfile
     USING(chip_id, class_id)
@@ -33,4 +36,45 @@
     AND (rawExp.magicked OR distRun.no_magic)
 UNION
+    -- raw stage alternate inputs
+SELECT
+    distRun.dist_id,
+    distRun.label,
+    distTarget.dist_group,
+    'raw' AS stage,
+    rawExp.exp_id AS stage_id,
+    rawImfile.class_id AS component,
+    clean,
+    rawExp.camera,
+    CONCAT_WS('.', distRun.outroot, CONVERT(distRun.dist_id, CHAR)) as outdir,
+    -- XXX: replace this with rawImfile.path_base once it exists
+    TRIM(TRAILING '.fits' FROM rawImfile.uri) AS path_base,
+    magicDSFile.backup_path_base AS alt_path_base,
+    chipProcessedImfile.path_base AS chip_path_base,
+    CAST('full' AS CHAR(255)) AS state,
+    CAST('full' AS CHAR(255)) AS data_state,
+    0 as quality,
+    distRun.no_magic,
+    distRun.alternate,
+    rawImfile.magicked
+FROM distRun
+JOIN distTarget USING(target_id, stage, clean)
+JOIN rawExp ON rawExp.exp_id = stage_id AND distTarget.stage = 'raw' AND distRun.alternate = 1
+JOIN rawImfile USING(exp_id)
+JOIN magicDSRun ON magicDSRun.stage = 'raw' AND magicDSRun.stage_id = rawExp.exp_id
+JOIN magicDSFile ON magicDSRun.magic_ds_id = magicDSFile.magic_ds_id 
+                AND rawImfile.class_id = magicDSFile.component
+JOIN camRun USING(cam_id)
+JOIN camProcessedExp USING(cam_id)
+JOIN chipProcessedImfile USING(chip_id, class_id)
+LEFT JOIN distComponent 
+    ON distRun.dist_id = distComponent.dist_id 
+    AND rawImfile.class_id = distComponent.component
+WHERE
+    distRun.state = 'new'
+    AND distRun.clean = 0
+    AND distComponent.dist_id IS NULL
+    AND chipProcessedImfile.data_state = 'full'
+    AND chipProcessedImfile.magicked > 0
+UNION
     -- raw stage clean (dbinfo only)
 SELECT
@@ -38,11 +82,12 @@
     distRun.label,
     distTarget.dist_group,
-    stage,
-    stage_id,
+    'raw' AS stage,
+    rawExp.exp_id AS stage_id,
     'exposure' AS component,
     clean,
     rawExp.camera,
-    CONCAT_WS('.', outroot, CONVERT(distRun.dist_id, CHAR)) as outdir,
+    CONCAT_WS('.', distRun.outroot, CONVERT(distRun.dist_id, CHAR)) as outdir,
     CAST(NULL AS CHAR(255)) AS path_base,
+    CAST(NULL AS CHAR(255)) AS alt_path_base,
     CAST(NULL AS CHAR(255)) AS chip_path_base,
     CAST(NULL AS CHAR(255)) AS state,
@@ -50,8 +95,9 @@
     0 as quality,
     distRun.no_magic,
+    distRun.alternate,
     rawExp.magicked
 FROM distRun
 JOIN distTarget USING(target_id, stage, clean)
-JOIN rawExp ON exp_id = stage_id
+JOIN rawExp ON rawExp.exp_id = stage_id
 LEFT JOIN distComponent 
     ON distRun.dist_id = distComponent.dist_id