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.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
artemis-18.1.0+dfsg/etc/options-1180- SGN_gene \
artemis-18.1.0+dfsg/etc/options:1181: SGN_germplasm \
artemis-18.1.0+dfsg/etc/options-1182- SGN_ref \
##############################################
artemis-18.1.0+dfsg/etc/results_to_netscape-48-# sanger hack:
artemis-18.1.0+dfsg/etc/results_to_netscape:49:file_arg=`echo $file_arg | sed 's@^/tmp_mnt/nfs/@/nfs/@' | sed 's@^/tmp_mnt/tmp_nfs/@/nfs/@'`
artemis-18.1.0+dfsg/etc/results_to_netscape-50-# fix for pcs3:
artemis-18.1.0+dfsg/etc/results_to_netscape:51:file_arg=`echo $file_arg | sed 's@^/yeastpub4/@/nfs/disk222/yeastpub4/@'`
artemis-18.1.0+dfsg/etc/results_to_netscape-52-# fix for pcs4:
artemis-18.1.0+dfsg/etc/results_to_netscape:53:file_arg=`echo $file_arg | sed 's@^/.automount/pcs3/root/nfs/@/nfs/@'`
artemis-18.1.0+dfsg/etc/results_to_netscape:54:file_arg=`echo $file_arg | sed 's@^/.automount/evs-users2/root/@/nfs/@'`
artemis-18.1.0+dfsg/etc/results_to_netscape-55-
##############################################
artemis-18.1.0+dfsg/etc/results_to_netscape-66-# sanger fix for /nfs/repository which isn't mounted on workstations:
artemis-18.1.0+dfsg/etc/results_to_netscape:67:REPOSITORY=`echo $new_file | sed -n -e 's|^\/nfs\/repository\/\(.*\)\(\/\)\(.*\)$|\3|p'`
artemis-18.1.0+dfsg/etc/results_to_netscape-68-
##############################################
artemis-18.1.0+dfsg/etc/run_blastn-28-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_blastn:29:#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_blastn-30-eval EXPANDED_DATABASE="$DATABASE"
##############################################
artemis-18.1.0+dfsg/etc/run_blastn-49-
artemis-18.1.0+dfsg/etc/run_blastn:50: EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_blastn-51-
##############################################
artemis-18.1.0+dfsg/etc/run_blastn-67-
artemis-18.1.0+dfsg/etc/run_blastn:68: DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`
artemis-18.1.0+dfsg/etc/run_blastn-69-
##############################################
artemis-18.1.0+dfsg/etc/run_blastn-121-then
artemis-18.1.0+dfsg/etc/run_blastn:122: for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_blastn-123- do
##############################################
artemis-18.1.0+dfsg/etc/run_blastp-28-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_blastp:29:#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_blastp-30-eval EXPANDED_DATABASE="$DATABASE"
##############################################
artemis-18.1.0+dfsg/etc/run_blastp-49-
artemis-18.1.0+dfsg/etc/run_blastp:50: EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_blastp-51-
##############################################
artemis-18.1.0+dfsg/etc/run_blastp-67-
artemis-18.1.0+dfsg/etc/run_blastp:68: DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`
artemis-18.1.0+dfsg/etc/run_blastp-69-
##############################################
artemis-18.1.0+dfsg/etc/run_blastp-120-then
artemis-18.1.0+dfsg/etc/run_blastp:121: for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_blastp-122- do
##############################################
artemis-18.1.0+dfsg/etc/run_blastx-29-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_blastx:30:#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_blastx-31-eval EXPANDED_DATABASE="$DATABASE"
##############################################
artemis-18.1.0+dfsg/etc/run_blastx-50-
artemis-18.1.0+dfsg/etc/run_blastx:51: EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_blastx-52-
##############################################
artemis-18.1.0+dfsg/etc/run_blastx-68-
artemis-18.1.0+dfsg/etc/run_blastx:69: DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`
artemis-18.1.0+dfsg/etc/run_blastx-70-
##############################################
artemis-18.1.0+dfsg/etc/run_blastx-121-then
artemis-18.1.0+dfsg/etc/run_blastx:122: for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_blastx-123- do
##############################################
artemis-18.1.0+dfsg/etc/run_hth-29-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_hth:30:EXPANDED_PARAMETERS=`echo "echo $PARAMETERS" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_hth-31-
##############################################
artemis-18.1.0+dfsg/etc/run_hth-71-then
artemis-18.1.0+dfsg/etc/run_hth:72: for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_hth-73- do
##############################################
artemis-18.1.0+dfsg/etc/run_hth-82-then
artemis-18.1.0+dfsg/etc/run_hth:83: PEPFILES=`cat $1`
artemis-18.1.0+dfsg/etc/run_hth-84-else
##############################################
artemis-18.1.0+dfsg/etc/run_netblastp-10-
artemis-18.1.0+dfsg/etc/run_netblastp:11:PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
artemis-18.1.0+dfsg/etc/run_netblastp-12-
##############################################
artemis-18.1.0+dfsg/etc/run_netblastp-31-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_netblastp:32:EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_netblastp-33-
##############################################
artemis-18.1.0+dfsg/etc/run_netblastp-44-
artemis-18.1.0+dfsg/etc/run_netblastp:45: EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_netblastp-46-
##############################################
artemis-18.1.0+dfsg/etc/run_netblastp-94-then
artemis-18.1.0+dfsg/etc/run_netblastp:95: for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_netblastp-96- do
##############################################
artemis-18.1.0+dfsg/etc/run_pepstats-66-then
artemis-18.1.0+dfsg/etc/run_pepstats:67: for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_pepstats-68- do
##############################################
artemis-18.1.0+dfsg/etc/run_sigcleave-67-then
artemis-18.1.0+dfsg/etc/run_sigcleave:68: for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_sigcleave-69- do
##############################################
artemis-18.1.0+dfsg/etc/run_tblastn-29-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_tblastn:30:#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_tblastn-31-eval EXPANDED_DATABASE="$DATABASE"
##############################################
artemis-18.1.0+dfsg/etc/run_tblastn-50-
artemis-18.1.0+dfsg/etc/run_tblastn:51: EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_tblastn-52-
##############################################
artemis-18.1.0+dfsg/etc/run_tblastn-68-
artemis-18.1.0+dfsg/etc/run_tblastn:69: DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`
artemis-18.1.0+dfsg/etc/run_tblastn-70-
##############################################
artemis-18.1.0+dfsg/etc/run_tblastn-121-then
artemis-18.1.0+dfsg/etc/run_tblastn:122: for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_tblastn-123- do
##############################################
artemis-18.1.0+dfsg/etc/run_tblastx-29-# expand any ~ or environment variables
artemis-18.1.0+dfsg/etc/run_tblastx:30:#EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
artemis-18.1.0+dfsg/etc/run_tblastx-31-eval EXPANDED_DATABASE="$DATABASE"
##############################################
artemis-18.1.0+dfsg/etc/run_tblastx-50-
artemis-18.1.0+dfsg/etc/run_tblastx:51: EXEC=${EXEC-`which $PROG 2>/dev/null`}
artemis-18.1.0+dfsg/etc/run_tblastx-52-
##############################################
artemis-18.1.0+dfsg/etc/run_tblastx-68-
artemis-18.1.0+dfsg/etc/run_tblastx:69: DATABASE=`echo $DATABASE_ARG | sed 's|\%||'`
artemis-18.1.0+dfsg/etc/run_tblastx-70-
##############################################
artemis-18.1.0+dfsg/etc/run_tblastx-120-then
artemis-18.1.0+dfsg/etc/run_tblastx:121: for i in `cat $1`
artemis-18.1.0+dfsg/etc/run_tblastx-122- do
##############################################
artemis-18.1.0+dfsg/etc/writedb_entry-30- then
artemis-18.1.0+dfsg/etc/writedb_entry:31: PROXY_SETTINGS="${PROXY_SETTINGS} -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/etc/writedb_entry-32- fi
##############################################
artemis-18.1.0+dfsg/etc/writedb_entry-70-
artemis-18.1.0+dfsg/etc/writedb_entry:71:JAVA_VERSION=`${JAVA} -version 2>&1`
artemis-18.1.0+dfsg/etc/writedb_entry-72-echo ${JAVA_VERSION}
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Cv.xml-20- <select id="selectCv" resultMap="select-cv">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Cv.xml:21: SELECT * FROM cv WHERE cv_id=$cvId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Cv.xml-22- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Db.xml-32- <select id="getDbByDbId" resultClass="Db">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Db.xml:33: SELECT * FROM db WHERE db_id=$db_id$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Db.xml-34- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml-37- <select id="getDbXRefByDbXRefIdLazy" resultMap="select-dbxref-lazy">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml:38: SELECT * FROM dbxref WHERE dbxref_id=$dbXRefId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml-39- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml-41- <select id="getDbXRefByDbXRefId" resultMap="select-dbxref">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml:42: SELECT * FROM dbxref LEFT JOIN db ON dbxref.db_id=db.db_id WHERE dbxref_id=$dbXRefId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/DbXRef.xml-43- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-360- FROM feature f
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:361: WHERE f.feature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-362- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-380- LEFT JOIN db ON dbxref.db_id=db.db_id
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:381: WHERE f.feature_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-382- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-407- ( SELECT feature_id FROM featureloc WHERE srcfeature_id IN
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:408: ( SELECT feature_id FROM featureloc WHERE srcfeature_id=$value$) )
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-409- ORDER BY f.feature_id
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-469- LEFT JOIN feature ON cvterm.cvterm_id=feature.type_id
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:470: WHERE <isNotNull> feature.organism_id=$value$ AND </isNotNull>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-471- residues notnull AND residues != '' AND
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-483- JOIN featureprop using (feature_id)
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:484: WHERE <isNotNull> feature.organism_id=$value$ AND </isNotNull>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-485- featureprop.type_id in (
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-529- <isNotNull property="timeLastModified"> , timelastmodified=#timeLastModified# </isNotNull>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:530: WHERE feature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-531- </update>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-576- seqlen=(seqLen+$seqLen$)
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:577: WHERE feature_id=$featureLoc.featureBySrcFeatureId.featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-578- </update>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-584- DELETE FROM feature
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:585: WHERE uniquename=#uniqueName# AND type_id=$cvTerm.cvTermId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-586- </delete>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-590- DELETE FROM feature
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml:591: WHERE feature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Feature.xml-592- </delete>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-64- WHERE feature_id IN
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml:65: (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-66- <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND">
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-76- WHERE feature_id IN
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml:77: (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-78- <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND">
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-131- SET rank=$rank$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml:132: WHERE feature_cvterm_id=$featureCvTermId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTerm.xml-133- </update>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml-42- WHERE feature_id IN
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml:43: (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml-44- <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND">
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml-54- LEFT JOIN db ON db.db_id=dbx.db_id
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml:55: WHERE feature_cvterm_id=$feature_cvterm_id$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermDbXRef.xml-56- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermPub.xml-39- WHERE feature_id IN
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermPub.xml:40: (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureCvTermPub.xml-41- <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND">
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-41- <isGreaterThan property="featureId" compareValue="0">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml:42: WHERE dbx_f.feature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-43- </isGreaterThan>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-53- <!-- RIGHT JOIN feature f ON dbx_f.feature_id=f.feature_id -->
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml:54: WHERE dbx_f.feature_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-55- ORDER BY dbx_f.feature_id
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-66- LEFT JOIN db ON db.db_id=dbx.db_id
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml:67: WHERE srcfeature_id = $featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureDbXRef.xml-68- <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND">
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml-46- FROM featureloc
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml:47: WHERE featureloc.feature_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml-48- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml-95- </isNull>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml:96: WHERE fmin >= $startBase$ AND srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureLoc.xml-97- </update>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml-59- LEFT JOIN cvterm ON fp.type_id=cvterm_id
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml:60: WHERE f.feature_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml-61- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml-66- SET value=#value#
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml:67: WHERE rank=$rank$ AND type_id=$cvTerm.cvTermId$ AND
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureProp.xml-68- feature_id=(SELECT feature_id FROM feature WHERE uniquename=#feature.uniqueName#)
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml-40- WHERE f.feature_id IN
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml:41: (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml-42- <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND">
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml-56- <isGreaterThan property="featureId" compareValue="0">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml:57: WHERE f.feature_id = $featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeaturePub.xml-58- </isGreaterThan>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureRelationship.xml-133- LEFT JOIN cvterm AS fr2_cvterm ON fr2_cvterm.cvterm_id=fr2.type_id
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureRelationship.xml:134: WHERE subject_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureRelationship.xml-135- AND (fr2_cvterm.name='derives_from' OR fr2_cvterm.name='part_of' OR fr2_cvterm.name='proper_part_of'))
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml-87- LEFT JOIN featureloc fl ON fl.feature_id=fs.feature_id AND srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml:88: WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml-89- <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND">
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml-97- WHERE f.feature_id IN
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml:98: (SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/FeatureSynonym.xml-99- <isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND">
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml-30- <select id="getGraphs" resultMap="select-graph">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml:31: SELECT graph_id, feature_id, name, description FROM graph.graph WHERE feature_id=$featureId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml-32- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml-34- <select id="getGraph" resultMap="select-graphdata">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml:35: SELECT * FROM graph.graph WHERE graph_id=$graphId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Graph.xml-36- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Pub.xml-33- <select id="selectPub" resultMap="select-pub">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Pub.xml:34: SELECT * FROM pub WHERE pub_id=$pub_id$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Pub.xml-35- </select>
##############################################
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Synonym.xml-42- <delete id="deleteAlias" parameterClass="FeatureSynonym">
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Synonym.xml:43: DELETE FROM synonym WHERE synonym_id=$synonym.synonymId$
artemis-18.1.0+dfsg/src/main/resources/artemis_sqlmap/Synonym.xml-44- </delete>
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3658- EntryGroup entryGroup0 = mock(EntryGroup.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3659: doReturn("uk.ac.sanger.artemis.FilteredEntryGroup", "1_O!1w+4", "`6uh$GzN\"/V~J:0", "D-fBu$%JA,$", "`6uh$GzN\"/V~J:0").when(entryGroup0).toString();
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3660- doReturn(entryVector0, (EntryVector) null).when(entryGroup0).getActiveEntries();
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3661- FeaturePredicate featurePredicate0 = mock(FeaturePredicate.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3662: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(entryGroup0, featurePredicate0, "<M8`)Xz>~:$>0k`LzI");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3663- assertEquals(0, filteredEntryGroup0.size());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3664: assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup0.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3665- assertEquals(0, filteredEntryGroup0.refCount());
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3668- FeatureVector featureVector0 = mock(FeatureVector.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3669: FilteredEntryGroup filteredEntryGroup1 = new FilteredEntryGroup(filteredEntryGroup0, featureVector0, "<M8`)Xz>~:$>0k`LzI");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3670- assertEquals(0, filteredEntryGroup0.size());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3671: assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup0.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3672- assertEquals(0, filteredEntryGroup0.refCount());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3673: assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup1.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3674- assertEquals(0, filteredEntryGroup1.size());
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3680- assertEquals(0, filteredEntryGroup0.size());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3681: assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup0.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3682- assertEquals(0, filteredEntryGroup0.refCount());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3683: assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup1.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3684- assertEquals(0, filteredEntryGroup1.size());
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3693- assertEquals(0, filteredEntryGroup0.size());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3694: assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup0.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3695- assertEquals(0, filteredEntryGroup0.refCount());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:3696: assertEquals("<M8`)Xz>~:$>0k`LzI", filteredEntryGroup1.getFilterName());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-3697- assertEquals(0, filteredEntryGroup1.size());
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-4107- EntryGroup entryGroup0 = mock(EntryGroup.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:4108: doReturn("mo!$>TPLf}x`ejqHx", "r0.{'#UE(!", "mo!$>TPLf}x`ejqHx", "", "uk.ac.sanger.artemis.FilteredEntryGroup$2").when(entryGroup0).toString();
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-4109- doReturn(entryVector0).when(entryGroup0).getActiveEntries();
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-7349- FeaturePredicate featurePredicate0 = mock(FeaturePredicate.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:7350: FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(entryGroup0, featurePredicate0, "<M8`)Xz>~:$>0k`LzI");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-7351- FeatureVector featureVector0 = mock(FeatureVector.class, new ViolatedAssumptionAnswer());
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java:7352: FilteredEntryGroup filteredEntryGroup1 = new FilteredEntryGroup(filteredEntryGroup0, featureVector0, "<M8`)Xz>~:$>0k`LzI");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/FilteredEntryGroup_ESTest.java-7353- filteredEntryGroup1.features();
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/components/RunBlastAtNCBI_ESTest.java-87- public void test7() throws Throwable {
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/components/RunBlastAtNCBI_ESTest.java:88: String string0 = RunBlastAtNCBI.constructRequest("$q^+H", "11", "n.ae`3jzQU$Qamd:", "11", "$q^+H", "n.ae`3jzQU$Qamd:", "", (String) null, "k*4*");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/components/RunBlastAtNCBI_ESTest.java-89- assertEquals("CMD=Put&QUERY=11&DATABASE=n.ae%603jzQU%24Qamd%3A&HITLIST_SIZE=11&FILTER=%24q%5E%2BH&EXPECT=n.ae%603jzQU%24Qamd%3A&FORMAT_TYPE=HTML&PROGRAM=%24q%5E%2BH&CLIENT=web&SERVICE=&GAPCOSTS=null+k*4*", string0);
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java-293- MockFile mockFile0 = new MockFile("${vqx\"ta`Rd=`Rm1R9@");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java:294: MockFile.createTempFile("${vqx\"ta`Rd=`Rm1R9@", "${vqx\"ta`Rd=`Rm1R9@", (File) mockFile0);
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java-295- ZipFileDocument zipFileDocument0 = new ZipFileDocument(mockFile0, "${vqx\"ta`Rd=`Rm1R9@");
##############################################
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java-314- MockFile mockFile0 = new MockFile("${vqx\"ta`Rd=`Rm1R9@");
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java:315: MockFile.createTempFile("${vqx\"ta`Rd=`Rm1R9@", "${vqx\"ta`Rd=`Rm1R9@", (File) mockFile0);
artemis-18.1.0+dfsg/src/test/evosuite/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java-316- mockFile0.setReadable(false, false);
##############################################
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-27-- then
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch:28:- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-29-- fi
##############################################
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-117-- then
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch:118:- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-119-- fi
##############################################
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-207-- then
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch:208:- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-209-- fi
##############################################
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-289-- then
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch:290:- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/debian/patches/debianize_launcher_scripts.patch-291-- fi
##############################################
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/act-54- then
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/act:55: APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/act-56- fi
##############################################
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/art-60- then
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/art:61: APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/art-62- fi
##############################################
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/bamview-22- then
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/bamview:23: APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/bamview-24- fi
##############################################
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/dnaplotter-41- then
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/dnaplotter:42: APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
artemis-18.1.0+dfsg/.pc/debianize_launcher_scripts.patch/dnaplotter-43- fi