nmparser: guard against NaN for all incoming floats

NONMEM output may contain NaN values for floats.  Since fc3af5b
(nmparser: map NaN's to DefaultFloat64 too, 2022-06-23), the nmparser
code has guarded against NaNs in spots that use the strToFloat helper.
However, that doesn't cover the places that invoke strconv.ParseFloat
directly.  That's a problem because the summary command will error
when trying to encode an NaN to JSON.

Adjust all the remaining strconv.ParseFloat calls to guard against
NaN.  Simply using strToFloat in all these spots isn't a good option
because that silently replaces errors with DefaultFloat64.  Add a new
helper that maps NaN to DefaultFloat64 but, unlike strToFloat, relays
any errors.

If a spot does something with the error [*], use the new helper. On
the other hand, if a spot ignores the error, use strToFloat.

For testing, piggyback on top of summary's existing acop-nan test case
by setting many values in its ext file to NaN.

Thanks to @callistosp for reporting the original failure case.

[*] Unfortunately the spots that process the error panic, while
    ideally they would bubble up the error as a return value.  Still,
    using strToFloat is a step in the wrong direction.

integration/nmless/bbi_summary_test.go

@@ -44,7 +44,7 @@ func TestSummaryHappyPath(tt *testing.T) {
 		"example2_bayes",   // Bayes (5 est methods, from NONMEM examples)
 		"iovmm",            // Mixture model. Also has parameter_near_boundary and final_zero_gradient heuristics.
 		"acop-iov",         // fake model with 62 OMEGAS (fake iov)
-		"acop-nan",         // NaN values for objective function
+		"acop-nan",         // NaN values in several spots
 		"onlysim",          // $SIM with ONLYSIM.
 		"chain",            // CHAIN method that lacks estimation data.
 		"12-empty-problem", // $PROBLEM is an empty string

integration/nmless/testdata/bbi_summary/aa_golden_files/acop-nan.golden.json

@@ -49,12 +49,12 @@
 				"theta": [
 					2.31034,
 					54.9596,
-					464.659,
+					-999999999,
 					-0.0805722,
 					4.1303
 				],
 				"omega": [
-					0.0964407,
+					-999999999,
 					0,
 					0.153571
 				],
@@ -65,14 +65,14 @@
 			"std_err": {
 				"theta": [
 					0.086147,
-					3.32914,
+					-999999999,
 					29.6177,
 					0.0555149,
 					1.35989
 				],
 				"omega": [
 					0.0200146,
-					10000000000,
+					-999999999,
 					0.026733
 				],
 				"sigma": [
@@ -105,7 +105,7 @@
 					0,
 					0,
 					0,
-					0
+					-999999999
 				],
 				"omega": [
 					0,

integration/nmless/testdata/bbi_summary/aa_golden_files/acop-nan.golden.txt

@@ -8,14 +8,14 @@ No Heuristic Problems Detected
 | THETA |  NAME  |  ESTIMATE  |   STDERR (RSE)    |
 +-------+--------+------------+-------------------+
 | TH 1  | THETA1 | 2.31034    | 0.086147 (3.7%)   |
-| TH 2  | THETA2 | 54.9596    | 3.32914 (6.1%)    |
-| TH 3  | THETA3 | 464.659    | 29.6177 (6.4%)    |
+| TH 2  | THETA2 | 54.9596    | -                 |
+| TH 3  | THETA3 | -999999999 | 29.6177 (0.0%)    |
 | TH 4  | THETA4 | -0.0805722 | 0.0555149 (68.9%) |
 | TH 5  | THETA5 | 4.1303     | 1.35989 (32.9%)   |
 +-------+--------+------------+-------------------+
-+------------+------+----------+---------------+
-|   OMEGA    | ETA  | ESTIMATE | SHRINKAGE (%) |
-+------------+------+----------+---------------+
-| OMEGA(1,1) | ETA1 | 0.096441 | 17.511500     |
-| OMEGA(2,2) | ETA2 | 0.153571 | 2.059620      |
-+------------+------+----------+---------------+
++------------+------+-------------------+---------------+
+|   OMEGA    | ETA  |     ESTIMATE      | SHRINKAGE (%) |
++------------+------+-------------------+---------------+
+| OMEGA(1,1) | ETA1 | -999999999.000000 | 17.511500     |
+| OMEGA(2,2) | ETA2 | 0.153571          | 2.059620      |
++------------+------+-------------------+---------------+

integration/nmless/testdata/bbi_summary/acop-nan/acop-nan.ext

@@ -7,10 +7,10 @@ TABLE NO.     1: First Order Conditional Estimation with Interaction: Goal Funct
            20  2.30528E+00  5.58065E+01  4.72255E+02 -8.05144E-02  4.12591E+00  1.00000E+00  9.09862E-02  0.00000E+00  2.06974E-01    2638.5029836424560
            25  2.31302E+00  5.44961E+01  4.65370E+02 -8.07920E-02  4.13612E+00  1.00000E+00  9.61335E-02  0.00000E+00  1.57375E-01    2636.8778706340345
            28  2.31034E+00  5.49596E+01  4.64659E+02 -8.05722E-02  4.13030E+00  1.00000E+00  9.64407E-02  0.00000E+00  1.53571E-01    2636.8457703290751
-  -1000000000  2.31034E+00  5.49596E+01  4.64659E+02 -8.05722E-02  4.13030E+00  1.00000E+00  9.64407E-02  0.00000E+00  1.53571E-01    2636.8457703290751
-  -1000000001  8.61470E-02  3.32914E+00  2.96177E+01  5.55149E-02  1.35989E+00  1.00000E+10  2.00146E-02  1.00000E+10  2.67330E-02    0.0000000000000000
-  -1000000004  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  1.00000E+00  3.10549E-01  0.00000E+00  3.91882E-01    0.0000000000000000
-  -1000000005  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  1.00000E+10  3.22245E-02  1.00000E+10  3.41085E-02    0.0000000000000000
-  -1000000006  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  1.00000E+00  0.00000E+00  1.00000E+00  0.00000E+00    0.0000000000000000
-  -1000000007  0.00000E+00  3.70000E+01  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00    0.0000000000000000
-  -1000000008 -3.39427E-03  1.00007E-04 -7.27007E-04 -1.46088E-01  2.43350E-03  0.00000E+00  4.84108E-02  0.00000E+00 -5.58021E-03    0.0000000000000000
+  -1000000000  2.31034E+00  5.49596E+01     NaN      -8.05722E-02  4.13030E+00  1.00000E+00     NaN       0.00000E+00  1.53571E-01    2636.8457703290751
+  -1000000001  8.61470E-02      NaN      2.96177E+01  5.55149E-02  1.35989E+00  1.00000E+10  2.00146E-02      NaN      2.67330E-02    0.0000000000000000
+  -1000000004     NaN       0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  1.00000E+00  3.10549E-01  0.00000E+00  3.91882E-01    0.0000000000000000
+  -1000000005  0.00000E+00  0.00000E+00  0.00000E+00     NaN       0.00000E+00  1.00000E+10  3.22245E-02  1.00000E+10  3.41085E-02    0.0000000000000000
+  -1000000006  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00      NaN      1.00000E+00  0.00000E+00  1.00000E+00  0.00000E+00    0.0000000000000000
+  -1000000007  0.00000E+00  3.70000E+01  0.00000E+00  0.00000E+00  0.00000E+00     NaN       0.00000E+00  0.00000E+00  0.00000E+00    0.0000000000000000
+  -1000000008 -3.39427E-03  1.00007E-04 -7.27007E-04 -1.46088E-01  2.43350E-03  0.00000E+00  4.84108E-02  0.00000E+00     NaN         0.0000000000000000

parsers/nmparser/get_model_output.go

@@ -4,7 +4,6 @@ import (
 	"errors"
 	"fmt"
 	"path/filepath"
-	"strconv"
 	"strings"
 
 	"github.com/metrumresearchgroup/bbi/utils"
@@ -90,7 +89,7 @@ func GetModelOutput(lstPath string, ext ModelOutputFile, grd bool, shk bool) (Su
 		log.Trace("error reading cpu file: ", err)
 	} else {
 		results.RunDetails.OutputFilesUsed = append(results.RunDetails.OutputFilesUsed, filepath.Base(cpuFilePath))
-		cpuTime, err := strconv.ParseFloat(strings.TrimSpace(cpuLines[0]), 64)
+		cpuTime, err := parseFloatReplaceNaN(strings.TrimSpace(cpuLines[0]))
 		if err != nil {
 			// this is set to trace as don't want it to log normally as could screw up json output that
 			log.Trace("error parsing cpu time: ", err)

parsers/nmparser/parse_lst_file.go

@@ -105,7 +105,7 @@ func getMatrixData(lines []string, start int) MatrixData {
 		// populate matrix
 		for j, row := range rows {
 			for k, cell := range strings.Fields(row) {
-				value, err := strconv.ParseFloat(cell, 64)
+				value, err := parseFloatReplaceNaN(cell)
 				if err == nil {
 					matrix[j][k] = value
 				} else {
@@ -418,7 +418,7 @@ func mustCalculateConditionNumber(lines []string, start int) float64 {
 
 		eigenstarted = true
 		for _, s := range strings.Fields(line) {
-			eigenvalue, err := strconv.ParseFloat(s, 64)
+			eigenvalue, err := parseFloatReplaceNaN(s)
 			if err != nil {
 				panic(fmt.Sprintf("Attempting to calculate condition number but could not parse eigenvalues -- %v", err))
 			}

parsers/nmparser/parse_run_details.go

@@ -58,7 +58,7 @@ func ParseRunDetails(lines []string) RunDetails {
 		case strings.Contains(line, "NO. OF FUNCTION EVALUATIONS USED"):
 			runDetails.FunctionEvaluations, _ = strconv.ParseInt(replaceTrim(line, "NO. OF FUNCTION EVALUATIONS USED:"), 10, 64)
 		case strings.Contains(line, "NO. OF SIG. DIGITS IN FINAL EST.:"):
-			runDetails.SignificantDigits, _ = strconv.ParseFloat(replaceTrim(line, "NO. OF SIG. DIGITS IN FINAL EST.:"), 64)
+			runDetails.SignificantDigits = strToFloat(replaceTrim(line, "NO. OF SIG. DIGITS IN FINAL EST.:"))
 		case strings.Contains(line, "Elapsed estimation"):
 			runDetails.EstimationTime = append(runDetails.EstimationTime,
 				parseFinalTime(line))
@@ -68,7 +68,7 @@ func ParseRunDetails(lines []string) RunDetails {
 		case strings.Contains(line, "Elapsed postprocess"):
 			runDetails.PostprocessTime = parseFinalTime(line)
 		case strings.Contains(line, " #CPUT: Total CPU Time in Seconds,"):
-			runDetails.CpuTime, _ = strconv.ParseFloat(replaceTrim(line, " #CPUT: Total CPU Time in Seconds,"), 64)
+			runDetails.CpuTime = strToFloat(replaceTrim(line, " #CPUT: Total CPU Time in Seconds,"))
 		case strings.Contains(line, "Started"):
 			runDetails.RunStart = replaceTrim(line, "Started")
 		case strings.HasPrefix(lineTrimmed, "Finished "):

parsers/nmparser/read_cov.go

@@ -1,7 +1,6 @@
 package parser
 
 import (
-	"strconv"
 	"strings"
 )
 
@@ -51,7 +50,7 @@ func getThetaMatrix(lines []string) [][]float64 {
 			thetas := make([]float64, len)
 
 			for n := 1; n <= len; n++ {
-				if f, err := strconv.ParseFloat(fields[n], 64); err == nil {
+				if f, err := parseFloatReplaceNaN(fields[n]); err == nil {
 					thetas[n-1] = f
 				} else {
 					panic("error converting value in cov file to number: " + fields[n])

parsers/nmparser/read_ext.go

@@ -98,7 +98,7 @@ func ParseParamsExt(ed ExtData) ([]ParametersData, ParameterNames) {
 					// this is the OBJ which we've gotten elsewhere
 					continue
 				}
-				if n, err := strconv.ParseFloat(val, 64); err == nil {
+				if n, err := parseFloatReplaceNaN(val); err == nil {
 					result[i-1] = n
 				} else {
 					log.Println("Did you use a non-default format parameter? bbi does not support non-default format parameters.")
@@ -163,7 +163,7 @@ func ParseConditionNumberExt(ed ExtData) []ConditionNumDetails {
 			fields := strings.Fields(line)
 			step, _ := strconv.Atoi(fields[0])
 			if step == -1000000003 {
-				condNum, _ = strconv.ParseFloat(fields[1], 64)
+				condNum = strToFloat(fields[1])
 
 				break
 			} else {

parsers/nmparser/read_grd.go

@@ -1,7 +1,6 @@
 package parser
 
 import (
-	"strconv"
 	"strings"
 )
 
@@ -64,7 +63,7 @@ func ParseGrdData(ed ExtData) ([]ParametersData, ParameterNames) {
 					if i == 0 {
 						continue
 					}
-					if n, err := strconv.ParseFloat(val, 64); err == nil {
+					if n, err := parseFloatReplaceNaN(val); err == nil {
 						result[i-1] = n
 					} else {
 						panic("error converting value in grd file to number: " + val)

parsers/nmparser/utils.go

@@ -73,3 +73,15 @@ func strToFloat(s string) float64 {
 
 	return f
 }
+
+// parseFloatReplaceNaN converts s to a float64.  If the result is NaN,
+// DefaultFloat64 is returned as the value.  Any errors are relayed as is from
+// strconv.ParseFloat.
+func parseFloatReplaceNaN(s string) (float64, error) {
+	f, err := strconv.ParseFloat(s, 64)
+	if math.IsNaN(f) {
+		f = DefaultFloat64
+	}
+
+	return f, err
+}