Index: trunk/ippTools/src/flatcorr.c
===================================================================
--- trunk/ippTools/src/flatcorr.c	(revision 19324)
+++ trunk/ippTools/src/flatcorr.c	(revision 19325)
@@ -3,4 +3,5 @@
  *
  * Copyright (C) 2006-2007  Joshua Hoblitt
+ * Copyright (C) 2008  Eugene Magnier
  *
  * This program is free software; you can redistribute it and/or modify it
@@ -31,12 +32,16 @@
 
 #include "pxtools.h"
+#include "pxchip.h"
 #include "flatcorr.h"
 
-static bool newrunMode(pxConfig *config);
-static bool addexpMode(pxConfig *config);
-static bool pendingMode(pxConfig *config);
-static bool flatcorrimfileMode(pxConfig *config);
-static bool doneMode(pxConfig *config);
+static bool definebyqueryMode(pxConfig *config);
+static bool definerunMode(pxConfig *config);
+static bool addchipMode(pxConfig *config);
+static bool addcameraMode(pxConfig *config);
+static bool pendingprocessMode(pxConfig *config);
+static bool addprocessMode(pxConfig *config);
 static bool updaterunMode(pxConfig *config);
+static bool inputexpMode(pxConfig *config);
+static bool inputimfileMode(pxConfig *config);
 
 static bool setflatcorrRunState(pxConfig *config, psS64 corr_id, const char *state);
@@ -60,10 +65,13 @@
 
     switch (config->mode) {
-        MODECASE(FLATCORR_MODE_NEWRUN,      newrunMode);
-        MODECASE(FLATCORR_MODE_ADDEXP,      addexpMode);
-        MODECASE(FLATCORR_MODE_PENDING,     pendingMode);
-        MODECASE(FLATCORR_MODE_FLATCORRIMFILE, flatcorrimfileMode);
-        MODECASE(FLATCORR_MODE_DONE,        doneMode);
-        MODECASE(FLATCORR_MODE_UPDATERUN,   updaterunMode);
+        MODECASE(FLATCORR_MODE_DEFINEBYQUERY,  definebyqueryMode);
+        MODECASE(FLATCORR_MODE_DEFINERUN,      definerunMode);
+        MODECASE(FLATCORR_MODE_ADDCHIP,        addchipMode);
+        MODECASE(FLATCORR_MODE_ADDCAMERA,      addcameraMode);
+        MODECASE(FLATCORR_MODE_PENDINGPROCESS, pendingprocessMode);
+        MODECASE(FLATCORR_MODE_ADDPROCESS,     addprocessMode);
+        MODECASE(FLATCORR_MODE_UPDATERUN,      updaterunMode);
+        MODECASE(FLATCORR_MODE_INPUTEXP,       inputexpMode);
+        MODECASE(FLATCORR_MODE_INPUTIMFILE,    inputimfileMode);
         default:
             psAbort("invalid option (this should not happen)");
@@ -88,50 +96,12 @@
 
 
-static bool newrunMode(pxConfig *config)
+static bool definebyqueryMode(pxConfig *config)
 {
     PS_ASSERT_PTR_NON_NULL(config, false);
 
     psMetadata *where = psMetadataAlloc();
-
-    PXOPT_COPY_S64(config->args, where, "-exp_id", "exp_id", "==");
-    PXOPT_COPY_STR(config->args, where, "-exp_name", "exp_name", "==");
-    PXOPT_COPY_STR(config->args, where, "-inst", "camera", "==");
-    PXOPT_COPY_STR(config->args, where, "-telescope", "telescope", "==");
-    PXOPT_COPY_TIME(config->args, where, "-dateobs_begin", "dateobs", ">=");
-    PXOPT_COPY_TIME(config->args, where, "-dateobs_end", "dateobs", "<=");
-    PXOPT_COPY_STR(config->args, where, "-exp_tag", "exp_tag", "==");
-    PXOPT_COPY_STR(config->args, where, "-exp_type", "exp_type", "==");
-    PXOPT_COPY_STR(config->args, where, "-filelevel", "filelvel", "==");
-    PXOPT_COPY_STR(config->args, where, "-reduction", "reduction", "==");
-    PXOPT_COPY_STR(config->args, where, "-filter", "filter", "==");
-    PXOPT_COPY_F32(config->args, where, "-airmass_min", "airmass", ">=");
-    PXOPT_COPY_F32(config->args, where, "-airmass_max", "airmass", "<");
-    PXOPT_COPY_F64(config->args, where, "-ra_min", "ra", ">=");
-    PXOPT_COPY_F64(config->args, where, "-ra_max", "ra", "<");
-    PXOPT_COPY_F64(config->args, where, "-decl_min", "decl", ">=");
-    PXOPT_COPY_F64(config->args, where, "-decl_max", "decl", "<");
-    PXOPT_COPY_F32(config->args, where, "-exp_time_min", "exp_time", ">=");
-    PXOPT_COPY_F32(config->args, where, "-exp_time_max", "exp_time", "<");
-    PXOPT_COPY_F32(config->args, where, "-sat_pixel_frac_min", "sat_pixel_frac", ">=");
-    PXOPT_COPY_F32(config->args, where, "-sat_pixel_frac_max", "sat_pixel_frac", "<");
-    PXOPT_COPY_F64(config->args, where, "-bg_min", "bt", ">=");
-    PXOPT_COPY_F64(config->args, where, "-bg_max", "bt", "<");
-    PXOPT_COPY_F64(config->args, where, "-bg_stdev_min", "bg_stdev", ">=");
-    PXOPT_COPY_F64(config->args, where, "-bg_stdev_max", "bg_stdev", "<");
-    PXOPT_COPY_F64(config->args, where, "-bg_mean_stdev_min", "bg_mean_stdev", ">=");
-    PXOPT_COPY_F64(config->args, where, "-bg_mean_stdev_max", "bg_mean_stdev", "<");
-    PXOPT_COPY_F64(config->args, where, "-alt_min", "alt", ">=");
-    PXOPT_COPY_F64(config->args, where, "-alt_max", "alt", "<");
-    PXOPT_COPY_F64(config->args, where, "-az_min", "az", ">=");
-    PXOPT_COPY_F64(config->args, where, "-az_max", "az", "<");
-    PXOPT_COPY_F32(config->args, where, "-ccd_temp_min", "ccd_temp", ">=");
-    PXOPT_COPY_F32(config->args, where, "-ccd_temp_max", "ccd_temp", "<");
-    PXOPT_COPY_F64(config->args, where, "-posang_min", "posang", ">=");
-    PXOPT_COPY_F64(config->args, where, "-posang_max", "posang", "<");
-    PXOPT_COPY_STR(config->args, where, "-object", "object", "==");
-    PXOPT_COPY_F32(config->args, where, "-solang_min", "solang", ">=");
-    PXOPT_COPY_F32(config->args, where, "-solang_max", "solang", "<");
-
-    if (where->list->n < 1) {
+    pxchipGetSearchArgs (config, where);
+
+    if (!psListLength(where->list)) {
         psFree(where);
         psError(PXTOOLS_ERR_DATA, false, "search parameters are required");
@@ -146,6 +116,6 @@
     PXOPT_LOOKUP_STR(filter, config->args, "-set_filter", false, false);
     PXOPT_LOOKUP_STR(tess_id, config->args, "-set_tess_id", false, false);
-    PXOPT_LOOKUP_STR(end_stage, config->args, "-set_end_stage", false, false);
     PXOPT_LOOKUP_STR(region, config->args, "-set_region", false, false);
+    // XXX probably should make the region in -set_region match ra_min, ra_max, etc
 
     PXOPT_LOOKUP_BOOL(pretend, config->args, "-pretend", false);
@@ -156,13 +126,14 @@
     if (!query) {
         psError(PXTOOLS_ERR_DATA, false, "failed to retreive SQL statement");
-        return false;
-    }
-
-    if (where) {
+        psFree(where);
+        return false;
+    }
+
+    if (where && psListLength(where->list)) {
         psString whereClause = psDBGenerateWhereConditionSQL(where, "rawExp");
-        psFree(where);
         psStringAppend(&query, " AND %s", whereClause);
         psFree(whereClause);
     }
+    psFree(where);
 
     if (!p_psDBRunQuery(config->dbh, query)) {
@@ -179,5 +150,5 @@
     }
     if (!psArrayLength(output)) {
-        psTrace("chiptool", PS_LOG_INFO, "no rows found");
+        psTrace("flatcorr", PS_LOG_INFO, "no rows found");
         psFree(output);
         return true;
@@ -185,14 +156,12 @@
 
     if (pretend) {
-        // negative simple so the default is true
-    for (int i = 0; i < output->n; i++) {
-        psMetadata *md = output->data[i];
-        psMetadataConfigPrint (stdout, md);
-    }
-//        if (!rawExpPrintObjects(stdout, output, !simple)) {
-//            psError(PS_ERR_UNKNOWN, false, "failed to print array");
-//            psFree(output);
-//            return false;
-//        }
+	for (long i = 0; i < psArrayLength(output); i++) {
+	    // negative simple so the default is true
+	    if (!ippdbPrintMetadataRaw(stdout, output->data[i], !simple)) {
+		psError(PS_ERR_UNKNOWN, false, "failed to print array");
+		psFree(output);
+		return false;
+	    }
+	}
         psFree(output);
         return true;
@@ -216,4 +185,5 @@
             label,
             NULL,   // stats
+            reduction,
             region
         )) {
@@ -243,6 +213,6 @@
         }
 
-        // queue the exp
-        psS64 chip_id = pxchipQueueByExpTag(config, exp_id, workdir, label, reduction, expgroup, dvodb, tess_id, end_stage);
+        // queue the exp : force this to stop at the chip stage
+        psS64 chip_id = pxchipQueueByExpTag(config, exp_id, workdir, label, reduction, expgroup, dvodb, tess_id, "chip");
         if (!chip_id) {
             if (!psDBRollback(config->dbh)) {
@@ -255,9 +225,6 @@
         }
 
-        // add a flatcorrExp to the flatcorr Run we just created
-        if (!flatcorrExpInsert(config->dbh,
-                corr_id,
-                chip_id
-            )) {
+        // add a flatcorrChipLink to the flatcorr Run we just created
+        if (!flatcorrChipLinkInsert(config->dbh, corr_id, chip_id)) {
             if (!psDBRollback(config->dbh)) {
                 psError(PS_ERR_UNKNOWN, false, "database error");
@@ -270,6 +237,6 @@
     psFree(output);
 
-    // set the flatcorrRun to a state of 'run'
-    if (!setflatcorrRunState(config, corr_id, "run")) {
+    // set the flatcorrRun to a state of 'new'
+    if (!setflatcorrRunState(config, corr_id, "new")) {
         if (!psDBRollback(config->dbh)) {
             psError(PS_ERR_UNKNOWN, false, "database error");
@@ -287,72 +254,87 @@
 }
 
-
-static bool addexpMode(pxConfig *config)
+static bool definerunMode(pxConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(config, false);
+
+    PXOPT_LOOKUP_STR(workdir, config->args, "-set_workdir", false, false);
+    PXOPT_LOOKUP_STR(label, config->args, "-set_label", false, false);
+    PXOPT_LOOKUP_STR(reduction, config->args, "-set_reduction", false, false);
+    PXOPT_LOOKUP_STR(expgroup, config->args, "-set_expgroup", false, false);
+    PXOPT_LOOKUP_STR(dvodb, config->args, "-set_dvodb", false, false);
+    PXOPT_LOOKUP_STR(filter, config->args, "-set_filter", false, false);
+    PXOPT_LOOKUP_STR(tess_id, config->args, "-set_tess_id", false, false);
+    PXOPT_LOOKUP_STR(region, config->args, "-set_region", false, false);
+    // XXX probably should make the region in -set_region match ra_min, ra_max, etc
+
+    PXOPT_LOOKUP_BOOL(simple, config->args, "-simple", false);
+
+    // start a transaction so we don't end up with an exp without any associted
+    // imfiles
+    if (!psDBTransaction(config->dbh)) {
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        return false;
+    }
+
+    // create a new flatcorrRun
+    flatcorrRunRow *row = flatcorrRunRowAlloc(
+	0,      // corr_id
+	dvodb,
+	filter,
+	"reg",  // state
+	workdir,
+	label,
+	NULL,   // stats
+	reduction,
+	region
+        );
+
+    // create a new flatcorrRun
+    if (!flatcorrRunInsertObject(config->dbh,row)) {
+        if (!psDBRollback(config->dbh)) {
+            psError(PS_ERR_UNKNOWN, false, "database error");
+        }
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        return false;
+    }
+    
+    // figure out the ID of the flatcorrRun we just created
+    psS64 corr_id = psDBLastInsertID(config->dbh);
+    row->corr_id = corr_id;
+
+    flatcorrRunPrintObject (stdout, row, !simple);
+    return true;
+}
+
+static bool addchipMode(pxConfig *config)
 {
     PS_ASSERT_PTR_NON_NULL(config, false);
 
     // required
-    PXOPT_LOOKUP_STR(corr_id, config->args, "-corr_id", true, false);
-    PXOPT_LOOKUP_STR(chip_id, config->args, "-chip_id", true, false);
-
-    if (!flatcorrExpInsert(config->dbh,
-            (psS64)atoll(corr_id),
-            (psS64)atoll(chip_id)
-        )) {
-        psError(PS_ERR_UNKNOWN, false, "database error");
-        return false;
-    }
-
-    return true;
-}
-
-
-static bool pendingMode(pxConfig *config)
-{
-    PS_ASSERT_PTR_NON_NULL(config, false);
-
-    PXOPT_LOOKUP_BOOL(simple, config->args, "-simple", false);
-    PXOPT_LOOKUP_BOOL(limit, config->args, "-limit", false);
-
-    // create a temp table to hold completely processed chipRuns
-    {
-	psString query = pxDataGet("flatcorr_create_tmp_chiprundone.sql");
-	if (!query) {
-	    psError(PXTOOLS_ERR_DATA, false, "failed to retreive SQL statement");
-	    return false;
-	}
-
-	if (!p_psDBRunQuery(config->dbh, query)) {
-	    psError(PS_ERR_UNKNOWN, false, "database error");
-	    psFree(query);
-	    return false;
-	}
-
-	psFree(query);
-    }
-   
-    // find all completed chipRuns
-    {
-	psString query = pxDataGet("flatcorr_completely_processed_chiprun.sql");
-	if (!query) {
-	    psError(PXTOOLS_ERR_DATA, false, "failed to retreive SQL statement");
-	    return false;
-	}
-
-	if (!p_psDBRunQuery(config->dbh, query)) {
-	    psError(PS_ERR_UNKNOWN, false, "database error");
-	    psFree(query);
-	    return false;
-	}
-
-	psFree(query);
-    }
-
-    // find flatcorrRun's that have had all of their chipRun's completed by
-    // comparing against the temp table
-    psString query = pxDataGet("flatcorr_find_completed_floatcorruns.sql");
+    PXOPT_LOOKUP_S64(corr_id, config->args, "-corr_id", true, false);
+    PXOPT_LOOKUP_S64(chip_id, config->args, "-chip_id", true, false);
+
+    if (!flatcorrChipLinkInsert(config->dbh, corr_id, chip_id)) {
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        return false;
+    }
+
+    return true;
+}
+
+// select the flatcorr chip runs that have completed and for which there is no camera entry
+// queue a new camera run for them
+static bool addcameraMode(pxConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(config, false);
+
+    PXOPT_LOOKUP_BOOL(simple,  config->args, "-simple",  false);
+    PXOPT_LOOKUP_BOOL(limit,   config->args, "-limit",   false);
+    PXOPT_LOOKUP_BOOL(pretend, config->args, "-pretend", false);
+
+    psString query = pxDataGet("flatcorr_chiprundone.sql");
     if (!query) {
-        psError(PXTOOLS_ERR_DATA, false, "failed to retreive SQL statement");
-        return false;
+	psError(PXTOOLS_ERR_DATA, false, "failed to retreive SQL statement");
+	return false;
     }
 
@@ -372,25 +354,16 @@
     psArray *output = p_psDBFetchResult(config->dbh);
     if (!output) {
-        psErrorCode err = psErrorCodeLast();
-        switch (err) {
-	  case PS_ERR_DB_CLIENT:
-	    psError(PXTOOLS_ERR_SYS, false, "database error");
-	  case PS_ERR_DB_SERVER:
-	    psError(PXTOOLS_ERR_PROG, false, "database error");
-	  default:
-	    psError(PXTOOLS_ERR_PROG, false, "unknown error");
-        }
-
+        psError(PS_ERR_UNKNOWN, false, "database error");
         return false;
     }
     if (!psArrayLength(output)) {
-        psTrace("regtool", PS_LOG_INFO, "no rows found");
+        psTrace("flatcorr", PS_LOG_INFO, "no rows found");
         psFree(output);
         return true;
     }
 
-    if (psArrayLength(output)) {
+    if (pretend) {
         // negative simple so the default is true
-        if (!ippdbPrintMetadatas(stdout, output, "flatcorrPending", !simple)) {
+        if (!ippdbPrintMetadatas(stdout, output, "flatcorr_addcamera", !simple)) {
             psError(PS_ERR_UNKNOWN, false, "failed to print array");
             psFree(output);
@@ -399,39 +372,99 @@
     }
 
+    // start a transaction so we don't end up with an exp without any associted
+    // imfiles
+    if (!psDBTransaction(config->dbh)) {
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        psFree(output);
+        return false;
+    }
+
+    // loop over our list of chipRun rows
+    for (long i = 0; i < psArrayLength(output); i++) {
+        psMetadata *md = output->data[i];
+
+        bool status;
+        psS64 corr_id = psMetadataLookupS64(&status, md, "corr_id");
+        if (!status) {
+            if (!psDBRollback(config->dbh)) {
+                psError(PS_ERR_UNKNOWN, false, "database error");
+            }
+            psError(PS_ERR_UNKNOWN, false, "failed to lookup value for corr_id");
+            psFree(output);
+            return false;
+        }
+
+        chipRunRow *row = chipRunObjectFromMetadata(md);
+        if (!row) {
+            psError(PS_ERR_UNKNOWN, false, "failed to convert metadata into chipRun");
+            psFree(output);
+            return false;
+        }
+
+        // queue the exp
+        if (!pxcamQueueByChipID(
+		config,
+		row->chip_id,
+		row->workdir,
+		row->label,
+		row->reduction,
+		row->expgroup,
+		row->dvodb,
+		row->tess_id,
+		"camera")) {
+            if (!psDBRollback(config->dbh)) {
+                psError(PS_ERR_UNKNOWN, false, "database error");
+            }
+            psError(PS_ERR_UNKNOWN, false,
+                    "failed to trying to queue chip_id: %" PRId64, row->chip_id);
+            psFree(row);
+            psFree(output);
+            return false;
+        }
+
+	// figure out the ID of the flatcorrRun we just created
+	psS64 cam_id = psDBLastInsertID(config->dbh);
+
+	// add the camRun entry to the flatcorrCamLink table:
+        if (!flatcorrCamLinkInsert(config->dbh, corr_id, row->chip_id, cam_id)) {
+            if (!psDBRollback(config->dbh)) {
+                psError(PS_ERR_UNKNOWN, false, "database error");
+            }
+            psError(PS_ERR_UNKNOWN, false, "database error");
+            return false;
+        }
+	
+        psFree(row);
+    }
     psFree(output);
 
+    if (!psDBCommit(config->dbh)) {
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        return false;
+    }
+
     return false;
 }
 
-
-static bool flatcorrimfileMode(pxConfig *config)
-{
-    PS_ASSERT_PTR_NON_NULL(config, false);
-
-    psMetadata *where = psMetadataAlloc();
-    PXOPT_COPY_S64(config->args, where, "-corr_id", "corr_id", "==");
-
-    PXOPT_LOOKUP_U64(limit, config->args, "-limit", false, false);
-    PXOPT_LOOKUP_BOOL(simple, config->args, "-simple", false);
-
-    // find all rawImfiles matching the default query
-    psString query = pxDataGet("flatcorr_find_processedimfiles.sql");
+// select the flatcorr chip runs that have completed and for which there is no camera entry
+// queue a new camera run for them
+static bool pendingprocessMode(pxConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(config, false);
+
+    PXOPT_LOOKUP_BOOL(simple,  config->args, "-simple",  false);
+    PXOPT_LOOKUP_BOOL(limit,   config->args, "-limit",   false);
+
+    psString query = pxDataGet("flatcorr_pendingprocess.sql");
     if (!query) {
-        psError(PXTOOLS_ERR_DATA, false, "failed to retreive SQL statement");
-        return false;
-    }
-
-    if (psListLength(where->list)) {
-        psString whereClause = psDBGenerateWhereConditionSQL(where, NULL);
-        psStringAppend(&query, " AND %s", whereClause);
-        psFree(whereClause);
-    }
-    psFree(where);
+	psError(PXTOOLS_ERR_DATA, false, "failed to retreive SQL statement");
+	return false;
+    }
 
     // treat limit == 0 as "no limit"
     if (limit) {
-        psString limitString = psDBGenerateLimitSQL(limit);
-        psStringAppend(&query, " %s", limitString);
-        psFree(limitString);
+	psString limitString = psDBGenerateLimitSQL(limit);
+	psStringAppend(&query, " %s", limitString);
+	psFree(limitString);
     }
 
@@ -441,54 +474,123 @@
         return false;
     }
-    psFree(query);
-    
+
     psArray *output = p_psDBFetchResult(config->dbh);
     if (!output) {
-        psErrorCode err = psErrorCodeLast();
-        switch (err) {
-            case PS_ERR_DB_CLIENT:
-                psError(PXTOOLS_ERR_SYS, false, "database error");
-            case PS_ERR_DB_SERVER:
-                psError(PXTOOLS_ERR_PROG, false, "database error");
-            default:
-                psError(PXTOOLS_ERR_PROG, false, "unknown error");
-        } 
-    
+        psError(PS_ERR_UNKNOWN, false, "database error");
         return false;
     }
     if (!psArrayLength(output)) {
-        psTrace("warptool", PS_LOG_INFO, "no rows found");
-        psFree(output);
-        return true; 
-    }
-
-    if (psArrayLength(output)) {
-        // negative simple so the default is true
-        if (!ippdbPrintMetadatas(stdout, output, "chipProcessedImfile", !simple)) {
-            psError(PS_ERR_UNKNOWN, false, "failed to print array");
-            psFree(output);
-            return false;
-        }
-    }
-
-    psFree(output);
-
-    return true;
-}
-
-
-static bool doneMode(pxConfig *config)
-{
-    PS_ASSERT_PTR_NON_NULL(config, false);
-
-    PXOPT_LOOKUP_STR(corr_id, config->args, "-corr_id", true, false);
-    PXOPT_LOOKUP_STR(stats, config->args, "-stats", true, false);
-
-    if (!psDBTransaction(config->dbh)) {
-        psError(PS_ERR_UNKNOWN, false, "database error");
-        return false;
-    }
-
-    if (!setflatcorrRunState(config, (psS64)atoll(corr_id), "stop")) {
+        psTrace("flatcorr", PS_LOG_INFO, "no rows found");
+        psFree(output);
+        return true;
+    }
+
+    if (!ippdbPrintMetadatas(stdout, output, "flatcorrPending", !simple)) {
+	psError(PS_ERR_UNKNOWN, false, "failed to print array");
+	psFree(output);
+	return false;
+    }
+
+    return true;
+}
+
+// select the flatcorr chip runs that have completed and for which there is no camera entry
+// queue a new camera run for them
+static bool inputexpMode(pxConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(config, false);
+
+    PXOPT_LOOKUP_S64(corr_id, config->args, "-corr_id", true, false);
+    PXOPT_LOOKUP_BOOL(simple,  config->args, "-simple",  false);
+    PXOPT_LOOKUP_BOOL(limit,   config->args, "-limit",   false);
+
+    char *query = psStringCopy ("SELECT * FROM flatcorrChipLink WHERE corr_id = %" PRId64);
+
+    // treat limit == 0 as "no limit"
+    if (limit) {
+	psString limitString = psDBGenerateLimitSQL(limit);
+	psStringAppend(&query, " %s", limitString);
+	psFree(limitString);
+    }
+
+    if (!p_psDBRunQuery(config->dbh, query, corr_id)) {
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        psFree(query);
+        return false;
+    }
+
+    psArray *output = p_psDBFetchResult(config->dbh);
+    if (!output) {
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        return false;
+    }
+    if (!psArrayLength(output)) {
+        psTrace("flatcorr", PS_LOG_INFO, "no rows found");
+        psFree(output);
+        return true;
+    }
+
+    if (!ippdbPrintMetadatas(stdout, output, "flatcorrPending", !simple)) {
+	psError(PS_ERR_UNKNOWN, false, "failed to print array");
+	psFree(output);
+	return false;
+    }
+
+    return true;
+}
+
+// select the flatcorr chip runs that have completed and for which there is no camera entry
+// queue a new camera run for them
+static bool inputimfileMode(pxConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(config, false);
+
+    PXOPT_LOOKUP_S64(chip_id, config->args, "-chip_id", true, false);
+    PXOPT_LOOKUP_BOOL(simple,  config->args, "-simple",  false);
+    PXOPT_LOOKUP_BOOL(limit,   config->args, "-limit",   false);
+
+    char *query = psStringCopy ("SELECT * FROM chipProcessedImfile WHERE chip_id = %" PRId64);
+
+    // treat limit == 0 as "no limit"
+    if (limit) {
+	psString limitString = psDBGenerateLimitSQL(limit);
+	psStringAppend(&query, " %s", limitString);
+	psFree(limitString);
+    }
+
+    if (!p_psDBRunQuery(config->dbh, query, chip_id)) {
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        psFree(query);
+        return false;
+    }
+
+    psArray *output = p_psDBFetchResult(config->dbh);
+    if (!output) {
+        psError(PS_ERR_UNKNOWN, false, "database error");
+        return false;
+    }
+    if (!psArrayLength(output)) {
+        psTrace("flatcorr", PS_LOG_INFO, "no rows found");
+        psFree(output);
+        return true;
+    }
+
+    if (!ippdbPrintMetadatas(stdout, output, "flatcorrPending", !simple)) {
+	psError(PS_ERR_UNKNOWN, false, "failed to print array");
+	psFree(output);
+	return false;
+    }
+
+    return true;
+}
+
+// XXX need a fault state
+static bool addprocessMode(pxConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(config, false);
+
+    PXOPT_LOOKUP_S64(corr_id, config->args, "-corr_id", true, false);
+
+    if (!setflatcorrRunState(config, corr_id, "full")) {
         if (!psDBRollback(config->dbh)) {
             psError(PS_ERR_UNKNOWN, false, "database error");
@@ -498,19 +600,24 @@
     }
 
-    char *query = "UPDATE flatcorrRun SET stats = '%s' WHERE corr_id = %" PRId64;
-    if (!p_psDBRunQuery(config->dbh, query, stats, (psS64)atoll(corr_id))) {
-        psError(PS_ERR_UNKNOWN, false,
-                "failed to change state for corr_id %" PRId64, (psS64)atoll(corr_id));
-        return false;
-    }
-
-    if (!psDBCommit(config->dbh)) {
-        psError(PS_ERR_UNKNOWN, false, "database error");
-        return false;
-    }
-
-    return false;
-}
-
+    return true;
+}
+
+static bool updaterunMode(pxConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(config, false);
+
+    PXOPT_LOOKUP_S64(corr_id, config->args, "-corr_id", true, false);
+    PXOPT_LOOKUP_STR(state, config->args, "-state", true, false);
+
+    if (!setflatcorrRunState(config, corr_id, state)) {
+        if (!psDBRollback(config->dbh)) {
+            psError(PS_ERR_UNKNOWN, false, "database error");
+        }
+        psError(PS_ERR_UNKNOWN, false, "failed to set run state");
+        return false;
+    }
+
+    return true;
+}
 
 static bool setflatcorrRunState(pxConfig *config, psS64 corr_id, const char *state)
@@ -520,10 +627,8 @@
 
     // check that state is a valid string value
-    if (!(
-            (strncmp(state, "run", 4) == 0)
-            || (strncmp(state, "stop", 5) == 0)
-            || (strncmp(state, "reg", 4) == 0)
-        )
-    ) {
+    if (!strcmp(state, "reg") && 
+	!strcmp(state, "new") && 
+	!strcmp(state, "full"))
+    {
         psError(PS_ERR_UNKNOWN, false, "invalid state: %s", state);
         return false;
@@ -541,16 +646,2 @@
 
 
-static bool updaterunMode(pxConfig *config)
-{
-    PS_ASSERT_PTR_NON_NULL(config, false);
-
-    PXOPT_LOOKUP_STR(corr_id, config->args, "-corr_id", true, false);
-    PXOPT_LOOKUP_STR(state, config->args, "-state", true, false);
-
-    if (state) {
-        // set detRun.state to state
-        return setflatcorrRunState(config, (psS64)atoll(corr_id), state);
-    }
-
-    return true;
-}
Index: trunk/ippTools/src/flatcorr.h
===================================================================
--- trunk/ippTools/src/flatcorr.h	(revision 19324)
+++ trunk/ippTools/src/flatcorr.h	(revision 19325)
@@ -25,10 +25,13 @@
 typedef enum {
     FLATCORR_MODE_NONE           = PXTOOL_MODE_NONE,
-    FLATCORR_MODE_NEWRUN,
-    FLATCORR_MODE_ADDEXP,
-    FLATCORR_MODE_PENDING,
-    FLATCORR_MODE_FLATCORRIMFILE,
-    FLATCORR_MODE_DONE,
-    FLATCORR_MODE_UPDATERUN
+    FLATCORR_MODE_DEFINEBYQUERY,
+    FLATCORR_MODE_DEFINERUN,
+    FLATCORR_MODE_ADDCHIP,
+    FLATCORR_MODE_ADDCAMERA,
+    FLATCORR_MODE_PENDINGPROCESS,
+    FLATCORR_MODE_ADDPROCESS,
+    FLATCORR_MODE_UPDATERUN,
+    FLATCORR_MODE_INPUTEXP,
+    FLATCORR_MODE_INPUTIMFILE
 } flatcorrMode;
 
Index: trunk/ippTools/src/flatcorrConfig.c
===================================================================
--- trunk/ippTools/src/flatcorrConfig.c	(revision 19324)
+++ trunk/ippTools/src/flatcorrConfig.c	(revision 19325)
@@ -45,84 +45,69 @@
     psTime *now = psTimeGetNow(PS_TIME_TAI);
 
-    // -newrun
-    psMetadata *newrunArgs = psMetadataAlloc();
+    // -definebyquery
+    psMetadata *definebyqueryArgs = psMetadataAlloc();
     // XXX need to allow multiple exp_ids
-    psMetadataAddS64(newrunArgs, PS_LIST_TAIL, "-exp_id",  0,            "search by exp_id", 0);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-exp_name",  0,            "search by exp_name", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-inst",  0,            "search for camera", NULL); 
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-telescope",  0,            "search for telescope", NULL);
-    psMetadataAddTime(newrunArgs, PS_LIST_TAIL, "-dateobs_begin", 0,               "search for exposures by time (>=)", NULL);
-    psMetadataAddTime(newrunArgs, PS_LIST_TAIL, "-dateobs_end", 0,            "search for exposures by time (<)", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-exp_tag",  0,            "search by exp_tag", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-exp_type",  0,            "search by exp_type", "object");
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-filelevel",  0,            "search by filelevel", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-reduction",  0,            "search by reduction class", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-filter",  0,            "search for filter", NULL); 
-    psMetadataAddF32(newrunArgs, PS_LIST_TAIL, "-airmass_min",  0,            "define min airmass", NAN);
-    psMetadataAddF32(newrunArgs, PS_LIST_TAIL, "-airmass_max",  0,            "define max airmass", NAN); 
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-ra_min",  0,            "define min", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-ra_max",  0,            "define max", NAN); 
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-decl_min",  0,            "define min", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-decl_max",  0,            "define max", NAN); 
-    psMetadataAddF32(newrunArgs, PS_LIST_TAIL, "-exp_time_min",  0,            "define min", NAN);
-    psMetadataAddF32(newrunArgs, PS_LIST_TAIL, "-exp_time_max",  0,            "define max", NAN); 
-    psMetadataAddF32(newrunArgs, PS_LIST_TAIL, "-sat_pixel_frac_min",  0,            "define max fraction of saturated pixels", NAN);
-    psMetadataAddF32(newrunArgs, PS_LIST_TAIL, "-sat_pixel_frac_max",  0,            "define min fraction of saturated pixels", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-bg_min",  0,            "define max", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-bg_max",  0,            "define max", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-bg_stdev_min",  0,            "define max", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-bg_stdev_max",  0,            "define max", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-bg_mean_stdev_min",  0,            "define max", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-bg_mean_stdev_max",  0,            "define max", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-alt_min",  0,            "define min", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-alt_max",  0,            "define max", NAN); 
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-az_min",  0,            "define min", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-az_max",  0,            "define max", NAN);
-    psMetadataAddF32(newrunArgs, PS_LIST_TAIL, "-ccd_temp_min",  0,               "define min ccd tempature", NAN);
-    psMetadataAddF32(newrunArgs, PS_LIST_TAIL, "-ccd_temp_max",  0,            "define max ccd tempature", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-posang_min",  0,            "define min rotator position angle", NAN);
-    psMetadataAddF64(newrunArgs, PS_LIST_TAIL, "-posang_max",  0,            "define max rotator position angle", NAN);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-object",  0,            "search by exposure object", NULL);
-    psMetadataAddF32(newrunArgs, PS_LIST_TAIL, "-solang_min",  0,            "define min solar angle", NAN);
-    psMetadataAddF32(newrunArgs, PS_LIST_TAIL, "-solang_max",  0,            "define max solar angle", NAN);
+    pxchipSetSearchArgs (definebyqueryArgs);
 
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-set_workdir",  0,            "define workdir", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-set_label",  0,            "define label", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-set_reduction",  0,            "define reduction class", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-set_expgroup",  0,            "define exposure group", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-set_dvodb",  0,            "define DVO db", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-set_filter",  0,            "define filter", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-set_tess_id",  0,            "define tessalation", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-set_end_stage",  0,            "define processing end stage", NULL);
-    psMetadataAddStr(newrunArgs, PS_LIST_TAIL, "-set_region",  0,            "define region", NULL);
+    psMetadataAddStr(definebyqueryArgs, PS_LIST_TAIL, "-set_workdir",  0,            "define workdir", NULL);
+    psMetadataAddStr(definebyqueryArgs, PS_LIST_TAIL, "-set_label",    0,            "define label", NULL);
+    psMetadataAddStr(definebyqueryArgs, PS_LIST_TAIL, "-set_reduction",0,            "define reduction class", NULL);
+    psMetadataAddStr(definebyqueryArgs, PS_LIST_TAIL, "-set_expgroup", 0,            "define exposure group", NULL);
+    psMetadataAddStr(definebyqueryArgs, PS_LIST_TAIL, "-set_dvodb",    0,            "define DVO db", NULL);
+    psMetadataAddStr(definebyqueryArgs, PS_LIST_TAIL, "-set_filter",   0,            "define filter", NULL);
+    psMetadataAddStr(definebyqueryArgs, PS_LIST_TAIL, "-set_tess_id",  0,            "define tessalation", NULL);
+    psMetadataAddStr(definebyqueryArgs, PS_LIST_TAIL, "-set_region",   0,            "define region", NULL);
 
-    psMetadataAddBool(newrunArgs, PS_LIST_TAIL, "-pretend",  0,            "print the exposures that would be included in the detrend run and exit", false);
-    psMetadataAddBool(newrunArgs, PS_LIST_TAIL, "-simple", 0,            "use the simple output format", false);
+    psMetadataAddBool(definebyqueryArgs, PS_LIST_TAIL, "-pretend",  0,            "print the exposures that would be included in the detrend run and exit", false);
+    psMetadataAddBool(definebyqueryArgs, PS_LIST_TAIL, "-simple", 0,            "use the simple output format", false);
 
-    // -addexp
-    psMetadata *addexpArgs = psMetadataAlloc();
-    psMetadataAddStr(addexpArgs, PS_LIST_TAIL, "-corr_id", 0,            "define Flat Correction ID (required)", NULL);
-    psMetadataAddStr(addexpArgs, PS_LIST_TAIL, "-chip_id", 0,            "define Chip ID (required)", NULL);
+    // -definerun
+    psMetadata *definerunArgs = psMetadataAlloc();
+    psMetadataAddStr(definerunArgs, PS_LIST_TAIL, "-set_workdir",  0,            "define workdir", NULL);
+    psMetadataAddStr(definerunArgs, PS_LIST_TAIL, "-set_label",  0,            "define label", NULL);
+    psMetadataAddStr(definerunArgs, PS_LIST_TAIL, "-set_reduction",  0,            "define reduction class", NULL);
+    psMetadataAddStr(definerunArgs, PS_LIST_TAIL, "-set_expgroup",  0,            "define exposure group", NULL);
+    psMetadataAddStr(definerunArgs, PS_LIST_TAIL, "-set_dvodb",  0,            "define DVO db", NULL);
+    psMetadataAddStr(definerunArgs, PS_LIST_TAIL, "-set_filter",  0,            "define filter", NULL);
+    psMetadataAddStr(definerunArgs, PS_LIST_TAIL, "-set_tess_id",  0,            "define tessalation", NULL);
+    psMetadataAddStr(definerunArgs, PS_LIST_TAIL, "-set_region",  0,            "define region", NULL);
+    psMetadataAddBool(definerunArgs, PS_LIST_TAIL, "-simple", 0,            "use the simple output format", false);
 
-    // -pending
-    psMetadata *pendingArgs = psMetadataAlloc();
-    psMetadataAddU64(pendingArgs, PS_LIST_TAIL, "-limit",  0,            "limit result set to N items", 0);
-    psMetadataAddBool(pendingArgs, PS_LIST_TAIL, "-simple", 0,            "use the simple output format", false);
+    // -addchip
+    psMetadata *addchipArgs = psMetadataAlloc();
+    psMetadataAddS64(addchipArgs, PS_LIST_TAIL, "-corr_id", 0,            "define Flat Correction ID (required)", 0);
+    psMetadataAddS64(addchipArgs, PS_LIST_TAIL, "-chip_id", 0,            "define Chip ID (required)", 0);
 
-    // -flatcorrimfile
-    psMetadata *flatcorrimfileArgs = psMetadataAlloc();
-    psMetadataAddStr(flatcorrimfileArgs, PS_LIST_TAIL, "-corr_id",  0,            "search by flat correction ID (required)", NULL);
-    psMetadataAddU64(flatcorrimfileArgs, PS_LIST_TAIL, "-limit",  0,            "limit result set to N items", 0);
-    psMetadataAddBool(flatcorrimfileArgs, PS_LIST_TAIL, "-simple", 0,            "use the simple output format", false);
+    // -addcamera
+    psMetadata *addcameraArgs = psMetadataAlloc();
+    psMetadataAddU64 (addcameraArgs, PS_LIST_TAIL, "-limit",   0, "limit result set to N items", 0);
+    psMetadataAddBool(addcameraArgs, PS_LIST_TAIL, "-simple",  0, "use the simple output format", false);
+    psMetadataAddBool(addcameraArgs, PS_LIST_TAIL, "-pretend", 0, "use the simple output format", false);
 
-    // -done
-    psMetadata *doneArgs = psMetadataAlloc();
-    psMetadataAddStr(doneArgs, PS_LIST_TAIL, "-corr_id",  0,            "define correction id (required)", NULL);
-    psMetadataAddStr(doneArgs, PS_LIST_TAIL, "-stats",  0,            "define stats (required)", NULL);
+    // -pendingprocess
+    psMetadata *pendingprocessArgs = psMetadataAlloc();
+    psMetadataAddU64 (pendingprocessArgs, PS_LIST_TAIL, "-limit",  0, "limit result set to N items", 0);
+    psMetadataAddBool(pendingprocessArgs, PS_LIST_TAIL, "-simple", 0, "use the simple output format", false);
+
+    // -addprocess (XXX need to add fault and stats)
+    psMetadata *addprocessArgs = psMetadataAlloc();
+    psMetadataAddS64 (addprocessArgs, PS_LIST_TAIL, "-corr_id", 0, "add complete run for specified corr_id (required)", 0);
 
     // -updaterun
     psMetadata *updaterunArgs = psMetadataAlloc();
-    psMetadataAddStr(updaterunArgs, PS_LIST_TAIL, "-corr_id",  0,            "define correction id (required)", NULL);
-    psMetadataAddStr(updaterunArgs, PS_LIST_TAIL, "-state", 0,            "set state (required)", NULL);
+    psMetadataAddS64(updaterunArgs, PS_LIST_TAIL, "-corr_id", 0, "define correction id (required)", 0);
+    psMetadataAddStr(updaterunArgs, PS_LIST_TAIL, "-state",   0, "set state (required)", NULL);
+
+    // -inputexp
+    psMetadata *inputexpArgs = psMetadataAlloc();
+    psMetadataAddS64(inputexpArgs, PS_LIST_TAIL, "-corr_id", 0, "define correction id (required)", 0);
+    psMetadataAddBool(inputexpArgs, PS_LIST_TAIL, "-simple", 0, "use the simple output format", false);
+    psMetadataAddU64(inputexpArgs, PS_LIST_TAIL, "-limit",   0, "limit result set to N items", 0);
+
+    // -inputimfile
+    psMetadata *inputimfileArgs = psMetadataAlloc();
+    psMetadataAddS64(inputimfileArgs, PS_LIST_TAIL, "-chip_id", 0, "define chip id (required)", 0);
+    psMetadataAddBool(inputimfileArgs, PS_LIST_TAIL, "-simple", 0, "use the simple output format", false);
+    psMetadataAddU64(inputimfileArgs, PS_LIST_TAIL, "-limit",   0, "limit result set to N items", 0);
 
     psFree(now);
@@ -131,10 +116,13 @@
     psMetadata *modes = psMetadataAlloc();
 
-    PXOPT_ADD_MODE("-newrun",  "start a new flat correction run",        FLATCORR_MODE_NEWRUN,       newrunArgs);
-    PXOPT_ADD_MODE("-addexp",  "add an exp to a flat correction run",        FLATCORR_MODE_ADDEXP,       addexpArgs);
-    PXOPT_ADD_MODE("-pending", "show flat correction runs needing to be processed",        FLATCORR_MODE_PENDING,      pendingArgs);
-    PXOPT_ADD_MODE("-flatcorrimfile", "list all the imfiles in a flat correction run",        FLATCORR_MODE_FLATCORRIMFILE, flatcorrimfileArgs);
-    PXOPT_ADD_MODE("-done",  "change a flat calibration run's state",        FLATCORR_MODE_DONE,         doneArgs);
-    PXOPT_ADD_MODE("-updaterun",  "change a flat calibration run's state",        FLATCORR_MODE_UPDATERUN,   updaterunArgs);
+    PXOPT_ADD_MODE("-definebyquery",  "create a new, populated flat correction run",       FLATCORR_MODE_DEFINEBYQUERY,  definebyqueryArgs);
+    PXOPT_ADD_MODE("-definerun",      "create a new, empty flat correction run",           FLATCORR_MODE_DEFINERUN,      definerunArgs);
+    PXOPT_ADD_MODE("-addchip",        "add a chip to a flat correction run",               FLATCORR_MODE_ADDCHIP,        addchipArgs);
+    PXOPT_ADD_MODE("-addcamera",      "migrate completed chips to camera stage analysis",  FLATCORR_MODE_ADDCAMERA,      addcameraArgs);
+    PXOPT_ADD_MODE("-pendingprocess", "show flat correction runs needing to be processed", FLATCORR_MODE_PENDINGPROCESS, pendingprocessArgs);
+    PXOPT_ADD_MODE("-addprocess",     "report completed flat correction analysis",         FLATCORR_MODE_ADDPROCESS,     addprocessArgs);
+    PXOPT_ADD_MODE("-updaterun",      "change a flat calibration run's state",             FLATCORR_MODE_UPDATERUN,      updaterunArgs);
+    PXOPT_ADD_MODE("-inputexp",       "list exposures for a correction run",               FLATCORR_MODE_INPUTEXP,       inputexpArgs);
+    PXOPT_ADD_MODE("-inputimfile",    "list imfiles for a chip run",                       FLATCORR_MODE_INPUTIMFILE,    inputimfileArgs);
 
     if (!pxGetOptions(stderr, argc, argv, config, modes, argSets)) {
