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FIJI
hpc-workflow-manager
Merge requests
!25
fix: iss1137
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Closed
fix: iss1137
iss1137
into
snakemakeProcessor
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2
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0
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1
Closed
Jan Kožusznik
requested to merge
iss1137
into
snakemakeProcessor
6 years ago
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2
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1
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search also last "Nothing to be done."
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version 1
version 1
d851f758
6 years ago
snakemakeProcessor (base)
and
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ae2baa31
2 commits,
6 years ago
version 1
d851f758
1 commit,
6 years ago
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haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SnakemakeOutputHelper.java
+
8
−
10
Options
@@ -8,6 +8,8 @@ import java.util.Collections;
import
java.util.Comparator
;
import
java.util.List
;
import
java.util.Scanner
;
import
java.util.regex.Matcher
;
import
java.util.regex.Pattern
;
import
java.util.stream.Collectors
;
import
java.util.stream.Stream
;
@@ -55,27 +57,23 @@ class SnakemakeOutputHelper {
private
void
resolveTasksAndNonTaskSpecificErrors
()
{
final
String
OUTPUT_PARSING_JOB_COUNTS
=
"Job counts:"
;
final
String
NOTHING_TO_BE_DONE
=
"Nothing to be done."
;
final
String
OUTPUT_PARSING_TAB_DELIMITER
=
"\\t"
;
final
int
OUTPUT_PARSING_EXPECTED_NUMBER_OF_WORDS_PER_LINE
=
2
;
final
String
OUTPUT_PARSING_WORKFLOW_ERROR
=
"WorkflowError"
;
final
String
OUTPUT_PARSING_VALUE_ERROR
=
"ValueError"
;
processedOutputLength
=
-
1
;
int
readJobCountIndex
=
-
1
;
boolean
found
=
false
;
final
String
output
=
getSnakemakeOutput
();
// Found last job count definition
while
(
true
)
{
readJobCountIndex
=
output
.
indexOf
(
OUTPUT_PARSING_JOB_COUNTS
,
processedOutputLength
+
1
);
if
(
readJobCountIndex
<
0
)
{
break
;
}
final
Pattern
p
=
Pattern
.
compile
(
OUTPUT_PARSING_JOB_COUNTS
+
"|"
+
NOTHING_TO_BE_DONE
);
final
Matcher
m
=
p
.
matcher
(
output
);
while
(
m
.
find
())
{
processedOutputLength
=
m
.
start
();
found
=
true
;
processedOutputLength
=
readJobCountIndex
;
}
// If no job count definition has been found, search through the output and
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