From 98746e431f4cdfad4aa13a10a57cc453e35a9522 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=9Ckpepper=E2=80=9D?= <kp11@sanger.ac.uk>
Date: Mon, 9 Oct 2017 15:14:08 +0100
Subject: [PATCH] Changes to new unit tests
---
.classpath | 5 +-
.gitignore | 5 +
AUTHORS | 1 +
INSTALL | 2 +-
Makefile | 2 +-
test/RunAllUnitTests.sh | 3 +-
test/RunEvoSuiteUnitTests.sh | 3 +-
test/RunManualUnitTestsOnly.sh | 3 +-
test/build-test.xml | 19 +-
test/data/options | 895 ------------------
.../artemis/ExternalProgram_ESTest.java | 4 +-
.../uk/ac/sanger/artemis/Options_ESTest.java | 24 +-
.../circular/EmbossCirdnaReader_ESTest.java | 10 +-
...EmbossCirdnaReader_ESTest_scaffolding.java | 4 +-
.../digest/EmbossDigestParser_ESTest.java | 7 +-
...EmbossDigestParser_ESTest_scaffolding.java | 6 +-
.../components/Splash_ESTest_scaffolding.java | 6 +-
.../components/alignment/BamFrame_ESTest.java | 4 +-
.../alignment/FileSelectionDialog_ESTest.java | 12 +-
...ileSelectionDialog_ESTest_scaffolding.java | 7 +-
.../components/filetree/FileNode_ESTest.java | 5 +-
.../filetree/FileNode_ESTest_scaffolding.java | 7 +-
.../genebuilder/cv/WrapTextArea_ESTest.java | 7 -
.../components/variant/IOUtils_ESTest.java | 4 +-
.../variant/IOUtils_ESTest_scaffolding.java | 5 +-
.../variant/TabixReader_ESTest.java | 10 +-
.../TabixReader_ESTest_scaffolding.java | 7 +-
.../artemis/editor/BrowserControl_ESTest.java | 7 +-
.../ac/sanger/artemis/io/EmblMisc_ESTest.java | 3 +-
.../sanger/artemis/io/GffToEMBL_ESTest.java | 10 +-
.../io/GffToEMBL_ESTest_scaffolding.java | 7 +-
.../artemis/io/IndexFastaStream_ESTest.java | 8 +-
.../IndexFastaStream_ESTest_scaffolding.java | 5 +-
.../util/FTPSeekableStream_ESTest.java | 3 +-
.../FTPSeekableStream_ESTest_scaffolding.java | 1 +
.../artemis/util/ZipFileDocument_ESTest.java | 6 +-
test/uk/ac/sanger/artemis/FeatureTest.java | 1 +
37 files changed, 137 insertions(+), 981 deletions(-)
delete mode 100644 test/data/options
diff --git a/.classpath b/.classpath
index bd97ecc58..309409b65 100644
--- a/.classpath
+++ b/.classpath
@@ -1,11 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
- <classpathentry kind="src" path="corba"/>
<classpathentry including="uk" kind="src" path="test"/>
<classpathentry excluding="main/" kind="src" path="ant-build/src"/>
- <classpathentry kind="src" path="lib"/>
- <classpathentry including="nsdb/|seqdb/|type/" kind="src" path="ant-build/src/main"/>
- <classpathentry excluding="ant-build/src/|ant-build/src/main/|uk/ac/sanger/artemis/ExternalProgramUtils.java|test/" including="nsdb/|org/|seqdb/|type/|uk/" kind="src" path=""/>
+ <classpathentry excluding="ant-build/src/|test/|uk/ac/sanger/artemis/ExternalProgramUtils.java" including="org/|uk/" kind="src" path=""/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="lib" path="lib/jemAlign.jar"/>
<classpathentry kind="lib" path="lib/jakarta-regexp-1.2.jar"/>
diff --git a/.gitignore b/.gitignore
index 7775cc6fd..3cb8ac2d1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,8 @@ ant-build
test/ant-build
**/.DS_Store
**/*.log
+test/coverage-report
+test/coverage-report/**
+jar_build
+tar_build
+artemis_compiled.tar
diff --git a/AUTHORS b/AUTHORS
index f3ff3b36b..141608611 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,3 +1,4 @@
+Kevin Pepper (path-help@sanger.ac.uk)
Tim Carver (path-help@sanger.ac.uk)
Sascha Steinbiss (path-help@sanger.ac.uk)
Kim Rutherford (path-help@sanger.ac.uk)
diff --git a/INSTALL b/INSTALL
index a3e2c3cd3..e227ee58f 100644
--- a/INSTALL
+++ b/INSTALL
@@ -68,4 +68,4 @@ Running the test suite
======================
cd test
-ant -f build-test.xml
+RunAllUnitTests.sh
diff --git a/Makefile b/Makefile
index 437cce599..e52f08473 100644
--- a/Makefile
+++ b/Makefile
@@ -57,7 +57,7 @@ manual :
CLASS_FILES := `find org uk -name '*.class' -print`
-OTHER_FILES := `find images/PSUlogo.gif images/icon.gif COPYING README.md`
+OTHER_FILES := `find images/PSUlogo.gif images/icon.gif README.md`
dist :
rm -rf artemis_compiled.tar.gz tar_build
diff --git a/test/RunAllUnitTests.sh b/test/RunAllUnitTests.sh
index d1ae55cf8..6d7f1f50b 100755
--- a/test/RunAllUnitTests.sh
+++ b/test/RunAllUnitTests.sh
@@ -1,4 +1,5 @@
#! /bin/bash
-ant -Dlib=jacoco-lib -DEMBOSS_ROOT=$EMBOSS_ROOT -buildfile build-test.xml test
+SCRIPT_DIR=$(dirname $0)
+ant -Dlib=${SCRIPT_DIR}/jacoco-lib -DEMBOSS_ROOT=$EMBOSS_ROOT -buildfile build-test.xml test
diff --git a/test/RunEvoSuiteUnitTests.sh b/test/RunEvoSuiteUnitTests.sh
index 8d15afb87..c5cfd550e 100755
--- a/test/RunEvoSuiteUnitTests.sh
+++ b/test/RunEvoSuiteUnitTests.sh
@@ -1,4 +1,5 @@
#! /bin/bash
-ant -Dlib=jacoco-lib -DEMBOSS_ROOT=$EMBOSS_ROOT -buildfile build-test.xml run-evosuite-tests
+SCRIPT_DIR=$(dirname $0)
+ant -Dlib=${SCRIPT_DIR}/jacoco-lib -DEMBOSS_ROOT=$EMBOSS_ROOT -buildfile build-test.xml run-evosuite-tests
diff --git a/test/RunManualUnitTestsOnly.sh b/test/RunManualUnitTestsOnly.sh
index 8db7637d1..daebbe4d2 100755
--- a/test/RunManualUnitTestsOnly.sh
+++ b/test/RunManualUnitTestsOnly.sh
@@ -1,4 +1,5 @@
#! /bin/bash
-ant -Dlib=jacoco-lib -DEMBOSS_ROOT=$EMBOSS_ROOT -buildfile build-test.xml jacoco-coverage-report
+SCRIPT_DIR=$(dirname $0)
+ant -Dlib=${SCRIPT_DIR}/jacoco-lib -DEMBOSS_ROOT=$EMBOSS_ROOT -buildfile build-test.xml jacoco-coverage-report
diff --git a/test/build-test.xml b/test/build-test.xml
index ef9bb6f60..b22c9233c 100644
--- a/test/build-test.xml
+++ b/test/build-test.xml
@@ -11,14 +11,19 @@
-Drun.blast.test.flag=true
This ant script can be used to create Evosuite tests
- using the "create-evotests" target, and
+ from scratch using the "create-evotests" target, and
to run them along with the current set of manually
constructed tests, producing coverage reports at the end.
These coverage reports are stored in the :
ant-build/coverage-report
- folder. Jacoco is used for the manual unit tests and Evosuite
+ folder. Note, however, that the EvoSuite tests may need some degree
+ of manual modification after creation as a small number
+ may not be cross-platform compatible and I noticed one instance
+ of heap exhaustion caused by incorrect object sizing.
+
+ Jacoco is used for the manual unit tests and Evosuite
creates its own reports at the unit test creation stage.
Unfortunately, neither Jacoco nor Cobertura work properly with
EvoSuite due to interactions at the bytecode instrumentation
@@ -152,7 +157,7 @@
</path>
<taskdef uri="antlib:org.jacoco.ant" resource="org/jacoco/ant/antlib.xml">
- <classpath path="${src.lib.dir}/jacocoant.jar"/>
+ <classpath path="${jacoco.dir}/jacocoant.jar"/>
</taskdef>
<target name="get-java-version">
@@ -291,10 +296,12 @@
<junit description="Artemis JUnit Manual Tests" fork="yes" showoutput="yes" printsummary="yes" haltonerror="${halt.tests.on.error}">
<jvmarg value="-DEMBOSS_ROOT=${EMBOSS_ROOT}" />
<jvmarg value="-noverify" />
+ <jvmarg value="-Xmx4g" />
<batchtest fork="yes" todir="${junit.reports.dir}">
<fileset dir="${build.src.tests}">
<include name="${artemis.base.package.path}/**/**Test.java" />
<exclude name="${artemis.base.package.path}/**/RunBlastAtNCBITest.java" unless="${run.blast.test.flag}" />
+ <exclude name="**/*_ESTest*" />
</fileset>
</batchtest>
<formatter type="plain" usefile="false" />
@@ -316,11 +323,13 @@
<junit description="Artemis JUnit Headless Manual Tests" fork="yes" showoutput="yes" printsummary="yes" haltonerror="${halt.tests.on.error}">
<jvmarg value="-DEMBOSS_ROOT=${EMBOSS_ROOT}" />
<jvmarg value="-noverify" />
+ <jvmarg value="-Xmx4g" />
<jvmarg value="-Djava.awt.headless=true" />
<batchtest fork="yes" todir="${junit.reports.dir}">
<fileset dir="${build.src.tests}">
<include name="${artemis.base.package.path}/**/**Test.java" />
<exclude name="${artemis.base.package.path}/**/RunBlastAtNCBITest.java" unless="${run.blast.test.flag}" />
+ <exclude name="**/*_ESTest*" />
</fileset>
</batchtest>
<formatter type="plain" usefile="false" />
@@ -373,7 +382,7 @@
</target>
<!-- Create Jacoco reports -->
- <target name="jacoco-coverage-report" depends="run-manual-tests">
+ <target name="jacoco-coverage-report">
<delete dir="${coverage.report.jacoco.dir}" />
<mkdir dir="${coverage.report.jacoco.dir}" />
@@ -407,7 +416,7 @@
</target>
<!-- Run all manual and automated unit tests and create coverage reports -->
- <target name="test" depends="run-evosuite-tests,jacoco-coverage-report" />
+ <target name="test" depends="run-evosuite-tests,run-manual-tests,jacoco-coverage-report" />
<!-- Cleans all temporary build related folders -->
<target name="clean">
diff --git a/test/data/options b/test/data/options
deleted file mode 100644
index 33809ed90..000000000
--- a/test/data/options
+++ /dev/null
@@ -1,895 +0,0 @@
-# The standard options file for Artemis
-
-# (Note that comment lines start with a hash (#) symbol)
-
-# $Header: //tmp/pathsoft/artemis/etc/options,v 1.73 2009-08-06 16:15:19 tjc Exp $
-
-# This file should contain option settings that look like this:
-#
-# option_name = option_value
-#
-# If the value of an options is too long to fit on one line it can be split
-# over several lines by ending each line with a backslash like this:
-#
-# option_name = option_value another_option_value \
-# a_third_option_value a_forth_option_value
-
-
-# This option will set the font size for all the Artemis windows.
-
-font_size = 12
-
-
-# Set the name of the font to use in Artemis. These possibilites are
-# available on all platforms:
-# Dialog, DialogInput, Monospaced, Serif, SansSerif, Symbol.
-
-font_name = Monospaced
-
-# This option is used to set the default minimum size (in amino acids)
-# of a "large" open reading frame, which controls which ORFS are
-# marked by the "Mark Open Reading Frames" menu item.
-
-minimum_orf_size = 100
-
-# Set the default value for the direct edit option (see
-# http://www.sanger.ac.uk/Software/Artemis/stable/manual/launch-window.html#LAUNCH-WINDOW-OPTIONS-DIRECT-EDIT
-# for more)
-direct_edit = yes
-
-# This setting controls which set of codons will be used for start codons.
-# This can be changed from the options menu.
-# Give the translation table number.
-#
-genetic_code_default = 1
-
-# This option gives the bases of the possible start codons
-eukaryotic_start_codons = atg
-prokaryotic_start_codons = atg gtg ttg
-
-
-#
-# Genetic Codes :
-# http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
-#
-
-genetic_codes = \
- Standard \
- Vertebrate_Mitochondrial \
- Yeast_Mitochondrial \
- Mold,_Protozoan,_Coelenterate_Mitochondrial_and_Mycoplasma/Spiroplasma \
- Invertebrate_Mitochondrial \
- Ciliate_Dasycladacean_and_Hexamita \
- - \
- - \
- Echinoderm_Flatworm_Mitochondrial \
- Euplotid \
- Bacterial_and_Plant_Plastid \
- Alternative_Yeast_Nuclear \
- Ascidian_Mitochondrial \
- Alternative_Flatworm_Mitochondrial \
- Blepharisma_Nuclear \
- Chlorophycean_Mitochondrial \
- - \
- - \
- - \
- - \
- Trematode_Mitochondrial \
- Scenedesmus_Obliquus_Mitochondrial \
- Thraustochytrium_Mitochondrial \
- Pterobranchia_mitochondrial
-
-# The translation_table option is used to lookup codon translations. The
-# table must have exactly 64 entries, and there is one entry for each codon.
-# The entries should appear in this order:
-# TTT, TTC, TTA, TTG,
-# TCT, TCC, ...,
-# ...
-
-# 1. standard code (default)
-translation_table_1 = \
- F F L L \
- S S S S \
- Y Y # + \
- C C * W \
- \
- L L L L \
- P P P P \
- H H Q Q \
- R R R R \
- \
- I I I M \
- T T T T \
- N N K K \
- S S R R \
- \
- V V V V \
- A A A A \
- D D E E \
- G G G G
-
-start_codons_1 = atg
-
-#
-# For the following Genetic Code tables the differences
-# from the Standard Code are given.
-#
-#
-# 2. Vertebrate Mitochondrial Code
-#
-translation_table_2 = \
- aga* agg* atam tgaw
-
-start_codons_2 = atg
-#start_codons_2_bos = ata
-#start_codons_2_homo = ata att
-#start_codons_2_mus = ata att atc
-#start_codons_2_coturnix_gallus = gtg
-
-# 3. Yeast Mitochondrial Code
-translation_table_3 = \
- atam cttt ctct ctat ctgt tgaw
-
-start_codons_3 = ata atg
-
-# 4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the
-# Mycoplasma/Spiroplasma Code
-translation_table_4 = \
- tgaw
-
-start_codons_4 = atg
-
-#start_codons_4_Trypanosoma = tta ttg ctg
-#start_codons_4_Leishmania = att ata
-#start_codons_4_Tertrahymena = att ata atg
-#start_codons_4_Paramecium = att ata atg atc gtg gta
-
-# 5. Invertebrate Mitochondrial Code
-translation_table_5 = \
- agas aggs atam tgaw
-
-start_codons_5 = ttg att atc ata atg gtg
-#start_codons_5_apis = atg ata atc att
-#start_codons_5_polyplacophora = atg ata gtg
-
-# 6. Ciliate, Dasycladacean and Hexamita Nuclear Code
-translation_table_6 = \
- taaq tagq
-
-start_codons_6 = atg
-
-# 9. Echinoderm and Flatworm Mitochondrial Code
-translation_table_9 = \
- aaan agas aggs tgaw
-
-start_codons_9 = atg gtg
-
-# 10. Euplotid Nuclear Code
-translation_table_10 = \
- tgac
-
-start_codons_10 = atg
-
-# 11. Bacterial and Plant Plastid
-translation_table_11 =
-
-start_codons_11 = atg gtg ttg
-
-# 12. Alternative Yeast Nuclear Code
-translation_table_12 = \
- ctgs
-
-start_codons_12 = ctg atg
-
-# 13. Ascidian Mitochondrial Code
-translation_table_13 = \
- agag aggg atam tgaw
-
-start_codons_13 = atg
-
-# 14. Alternative Flatworm Mitochondrial Code
-translation_table_14 = \
- aaan agas aggs taay tgaw
-
-start_codons_14 = atg
-
-# 15. Blepharisma
-translation_table_15 = \
- tagq
-
-start_codons_15 = atg
-
-# 16. Chlorophycean Mitochondrial
-translation_table_16 = \
- tagl
-
-start_codons_16 = atg
-
-# 21. Trematode Mitochondrial
-translation_table_21 = \
- tgaw atam aaan agas aggs
-
-start_codons_21 = atg gtg
-
-# 22. Scenedesmus obliquus mitochondrial
-translation_table_22 = \
- tca* tagl
-
-start_codons_22 = atg
-
-# 23. Thraustochytrium Mitochondrial
-translation_table_23 = \
- tta*
-
-start_codons_23 = att atg gtg
-
-# 24. Pterobranchia mitochondrial
-translation_table_24 = \
- agas aggk tgaw
-
-start_codons_24 = ttg ctg atg gtg
-
-# the sequence of colour numbers must not have any gaps - if for example
-# colour_5 is missing then all colours with higher numbers will be ignored
-
-# the three numbers for each colour correspond to red, green and blue
-# respectively. each number is an intensity from 0 to 255
-
-# white
-colour_0 = 255 255 255
-# dark grey
-colour_1 = 100 100 100
-# red
-colour_2 = 255 0 0
-# green
-colour_3 = 0 255 0
-# blue
-colour_4 = 0 0 255
-# cyan
-colour_5 = 0 255 255
-# magenta
-colour_6 = 255 0 255
-# yellow
-colour_7 = 245 245 0
-# pale green
-colour_8 = 152 251 152
-# light sky blue
-colour_9 = 135 206 250
-# orange
-colour_10 = 255 165 0
-# brown
-colour_11 = 200 150 100
-# pink
-colour_12 = 255 200 200
-# light grey
-colour_13 = 170 170 170
-# black
-colour_14 = 0 0 0
-# reds:
-colour_15 = 255 63 63
-colour_16 = 255 127 127
-colour_17 = 255 191 191
-
-# GeneDB colours
-#
-colour_101 = 102 51 153
-colour_102 = 153 102 204
-colour_103 = 255 248 220
-
-#
-#
-
-colour_of_CDS = 5
-colour_of_cds? = 7
-colour_of_BLASTCDS = 2
-colour_of_BLASTN_HIT = 6
-colour_of_CRUNCH_D = 2
-colour_of_CRUNCH_X = 15
-colour_of_source = 0
-colour_of_prim_tran = 0
-colour_of_stem_loop = 2
-colour_of_misc_feature = 3
-colour_of_misc_RNA = 12
-colour_of_delta = 3
-colour_of_LTR = 4
-colour_of_repeat_region = 9
-colour_of_repeat_unit = 9
-colour_of_terminator = 3
-colour_of_promoter = 3
-colour_of_intron = 1
-colour_of_exon = 7
-colour_of_mRNA = 1
-colour_of_tRNA = 8
-colour_of_TATA = 3
-colour_of_bldA = 2
-colour_of_GFF = 11
-
-colour_of_start_codon = 6
-
-# suffixes used on files that contain features - used in file requesters
-feature_file_suffixes = tab embl gbk genbank tab_embl gff feature feat \
- art artemis
-
-# suffixes used on files that contain sequence - used in file requesters
-sequence_file_suffixes = embl gbk genbank gff tab_embl seq dna \
- art artemis fa fasta fas gb fna ffn
-
-# the default height for the base plot window
-base_plot_height = 100
-
-
-# the default height for the feature plot window
-feature_plot_height = 160
-
-
-# if this option is no then the feature labels in the overview will be off at
-# startup (the default is yes)
-# overview_feature_labels = no
-
-
-# if this option is yes then the overview will start in one line per entry
-# mode (the default is no)
-# overview_one_line_per_entry = yes
-
-
-# if this option is yes then the overview will start showing the feature
-# stack view (the default is no)
-# overview_feature_stack_view = yes
-
-
-# if this option is "yes" then the feature list will be displayed on startup
-# (this is the default)
-show_list = yes
-
-
-# if this option is "yes" then the base view will be displayed on startup
-# (this is the default)
-show_base_view = yes
-
-
-# if this option is "yes" then the entry buttons will be displayed on
-# startup
-show_entry_buttons = yes
-
-
-# if this option is "yes" then artemis will offer to show the results of a
-# search when it finishes
-show_results = no
-
-
-# if this option is "yes" the "all features on frame lines" option will
-# default to true on start up
-features_on_frame_lines = no
-
-# if these options are "yes" the forward and reverse feature lines
-# are displayed
-show_forward_lines = yes
-show_reverse_lines = yes
-
-# features to show on the frame line
-#frame_line_features = \
-# CDS \
-# polypeptide
-
-# if this option is "yes" the "feature labels" option will
-# default to true on start up
-feature_labels = yes
-
-
-# if this option is "yes" the "one line per entry" option will default to
-# true on start up
-one_line_per_entry = no
-
-
-# if this option is "yes" Sanger specific menu items and functions will be
-# visible in the display
-sanger_options = no
-
-
-# the full path to the editor used for editing the qualifiers
-#external_editor = emacs
-
-
-# if set to yes, borders will be drawn around each feature and each exon. if
-# set to no borders will only be drawn around the selected features.
-draw_feature_borders = yes
-
-
-# if set to yes, a direction arrow will be drawn around at the end of each
-# feature. if set to no, no arrows will be drawn.
-draw_feature_arrows = yes
-
-# if yes then shortcut changed in Preferences are saved between sessions
-shortcut_cache = yes
-
-# the number of levels of undo to save or 0 if undo is disabled. more undo
-# levels will require more memory.
-undo_levels = 20
-
-
-# this list is added to the keys from the feature_keys file
-extra_keys = \
- BLASTN_HIT CDS_BEFORE CDS_AFTER CDS_before CDS_after \
- CDS_motif BLASTCDS polymorphism GFF WUBLASTN_HIT \
- WUBLASTX_HIT BLASTX_HIT TBLASTX_HIT BLASTN_HIT \
- CRUNCH_D CRUNCH_X fasta_record allele mutation splicesite \
- TMM signalP
-
-# this list is added to the keys from the feature_keys_gff file
-extra_keys_gff = CDS uORF sORF tnaORF spliced_leader_RNA sequence_variant fasta_record
-
-# Names of qualifiers to search when attempting to find the primary or display
-# name of a gene. These qualifiers names are searched in order when looking
-# for gene names.
-display_name_qualifiers = primary_name Name synonym systematic_id \
- temporary_systematic_id gene locus_tag label ID
-
-# Names of qualifiers to search when attempting to find the systematic name of
-# a gene
-systematic_name_qualifiers = systematic_id temporary_systematic_id \
- locus_tag gene label ID Name
-
-
-# this list is added to the qualifiers from the qualifier_types file
-extra_qualifiers = \
- alias "text" \
- CHROMO_LINK text \
- C_processing "text" \
- C_processing_BigPi "text" \
- C_processing_DGPI "text" \
- COM_NAME "text" \
- FEAT_NAME text \
- GO_component "text" \
- GO_function "text" \
- GO_process "text" \
- GO_slim "text" \
- GO "text" \
- LOCUS "text" \
- PUB_LOCUS text \
- PUB_COMMENT "text" \
- REPEAT_TYPE "text" \
- SNP "text" \
- algorithm "text" \
- anchor "text" \
- annotation_source "text" \
- assembly_id "text" \
- bb_orthologue "text" \
- bound_moiety "text" \
- bpp_orthologue "text" \
- bp_orthologue "text" \
- bicsw_file "text" \
- blast_score text \
- blast_file "text" \
- blastn_file "text" \
- blastp_file "text" \
- blastp+go_file "text" \
- blastp_match "text" \
- blastx_file "text" \
- cds_id "text" \
- chloroplast "text" \
- chromoplast "text" \
- class "text" \
- cleavage "text" \
- cluster "text" \
- color text \
- colour text \
- comment_Cterm "text" \
- comment_Nterm "text" \
- confidence_level "text" \
- controlled_curation "text" \
- coord "text" \
- contig_id "text" \
- created "text" \
- curation "text" \
- curated_ortholog "text" \
- cyanelle "text" \
- domain "text" \
- end_phase text \
- exon_id "text" \
- fasta_file "text" \
- fasta_match "text" \
- fastx_file "text" \
- filename "text" \
- function "text" \
- gene "text" \
- gene_id "text" \
- gff_feature text \
- gff_group text \
- gff_seqname text \
- gff_source text \
- go_from_interpro "text" \
- hp_match "text" \
- hth_file "text" \
- id "text" \
- interaction "text" \
- interpro "text" \
- job "text" \
- label text \
- literature "text" \
- manual none \
- mitochondrion "text" \
- modified "text" \
- mutation "text" \
- note "text" \
- obsolete_name "text" \
- obsolete_product "text" \
- origid "text" \
- ortholog "text" \
- other_transcript "text" \
- paralog "text" \
- pepstats_file "text" \
- percent_id text \
- pfam_match "text" \
- previous_other_transcript "text" \
- previous_shared_id "text" \
- previous_systematic_id "text" \
- primary_name "text" \
- prosite_match "text" \
- pseudo none \
- psu_db_xref "text" \
- psu_domain "text" \
- reserved_name "text" \
- query_id text \
- score text \
- sequence_source "text" \
- sequence_status "text" \
- shared_id "text" \
- sigcleave_file "text" \
- signal "text" \
- similarity "text" \
- smart_file "text" \
- sptr_display "text" \
- start_phase text \
- subject_end text \
- subject_id text \
- subject_start text \
- synonym "text" \
- synteny "text" \
- systematic_id "text" \
- taxon_id "text" \
- tblastn_file "text" \
- tblastx_file "text" \
- tb_orthologue "text" \
- temporary_systematic_id "text" \
- tmhelix "text" \
- transferred_gene "text" \
- transferred_locus_tag "text" \
- transferred_note "text" \
- transferred_primary_name "text" \
- transferred_product "text" \
- transferred_synonym "text" \
- transferred_systematic_id "text" \
- type "text"
-
-# this list is added to the qualifiers from the qualifier_types_gff file
-extra_qualifiers_gff = \
- alias "text" \
- blast_score text \
- blast_file "text" \
- blastn_file "text" \
- blastp_file "text" \
- blastp+go_file "text" \
- blastx_file "text" \
- cluster "text" \
- colour text \
- color text \
- controlled_curation "text" \
- fasta_file "text" \
- GO "text" \
- history "text" \
- literature "text" \
- note "text" \
- orthologous_to "text" \
- paralogous_to "text" \
- polypeptide_domain "text" \
- previous_systematic_id "text" \
- primary_name "text" \
- product_synonym "text" \
- similarity "text" \
- stop_codon_redefined_as_selenocysteine none \
- synonym "text" \
- systematic_id "text" \
- temporary_systematic_id "text"
-
-# this is a list of extra qualifiers that are legal but are not displayed in
-# popup menus (such as the one in the feature editor window). this hack is
-# used by diana.components.QualifierChoice to limit the number of qualifers
-# that are displayed in the popup menu. on some VMs if there are too many in
-# the popup the bottom ones aren't visible
-invisible_qualifiers = \
- CHROMO_LINK \
- C_processing \
- C_processing_BigPi \
- C_processing_DGPI \
- COM_NAME \
- FEAT_NAME \
- LOCUS \
- PUB_LOCUS \
- PUB_COMMENT \
- REPEAT_TYPE \
- SNP \
- bicsw_file \
- blast_file \
- blast_score \
- blastn_file \
- blastp+go_file \
- blastp_file \
- blastx_file \
- cds_id \
- chloroplast \
- chromoplast \
- codon \
- comment_Cterm \
- comment_Nterm \
- created \
- cyanelle \
- end_phase \
- exception \
- exon_id \
- fasta_file \
- fasta_match \
- gene_id \
- go_from_interpro \
- hp_match \
- hth_file \
- interpro \
- map \
- mitochondrion \
- modified \
- number \
- obsolete_gene_name \
- pepstats_file \
- percent_id \
- pfam_match \
- prosite_match \
- pseudo \
- psu_domain \
- reserved_gene_name \
- query_id \
- sigcleave_file \
- score \
- smart_file \
- start_phase \
- tblastn_file \
- tblastx_file \
- temporary_systematic_id \
- transl_table \
- translation \
- type \
- usedin
-
-invisible_qualifiers_gff= \
- Alias \
- allele \
- bound_moiety \
- cell_line \
- cell_type \
- charge \
- chromosome \
- class \
- clone \
- clone_lib \
- cluster \
- controlled_curation \
- country \
- cultivar \
- cytoplasm_location \
- cytoplasmic_polypeptide_region \
- Dbxref \
- DNA_transposon \
- Derives_from \
- dev_stage \
- ecotype \
- environmental_sample \
- estimated_length \
- exception \
- feature_id \
- feature_relationship_rank \
- focus \
- Gap \
- gff_feature \
- gff_group \
- gff_seqname \
- gff_source \
- GO \
- GPI_anchored \
- GPI_anchor_cleavage_site \
- history \
- ID \
- insertion_seq \
- isObsolete \
- isoelectric \
- isolation_source \
- isolate \
- kinetoplast \
- lab_host \
- literature \
- locus_tag \
- macronuclear \
- map \
- mass \
- membrane_structure \
- mod_base \
- mol_type \
- Name \
- non_cytoplasm_location \
- non_cytoplasmic_polypeptide_region \
- Note \
- note \
- Ontology_term \
- operon \
- organell \
- orthologous_to \
- paralogous_to \
- Parent \
- PCR_conditions \
- plasmid \
- PlasmoAP_score \
- pop_variant \
- previous_systematic_id \
- primary_name \
- product \
- product_synonym \
- protein_id \
- replace \
- results \
- segment \
- sequenced_mol \
- serotype \
- serovar \
- sex \
- signal_anchor_probability \
- signal_peptide \
- signal_peptide_probability \
- SignalP_prediction \
- similarity \
- source \
- specific_host \
- specimen_voucher \
- standard_name \
- strain \
- sub_clone \
- sub_species \
- sub_strain \
- synonym \
- systematic_id \
- Target \
- temporary_systematic_id \
- timelastmodified \
- tissue_lib \
- tissue_type \
- transmembrane \
- transmembrane_polypeptide_region \
- transgenic \
- translation
-
-
-# These pairs consist of a program name and a parameter string.
-# For blast and fasta the parameter string is the name of the database to
-# search.
-#
-# /nfs/pathsoft/databases/GO/new
-# /nfs/pathsoft/databases/protein/go_all
-feature_protein_programs = \
- fasta %uniprot \
- fasta %uniprot_archaea \
- fasta %uniprot_bacteria \
- fasta %uniprot_eukaryota \
- fasta %uniprot_viruses \
- fasta %uniprot_rest \
- fasta %malaria \
- fasta %kineto_aa \
- sigcleave 0 \
- pepstats - \
- blastp uniprot \
- blastp uniprot_archaea \
- blastp uniprot_bacteria \
- blastp uniprot_eukaryota \
- blastp uniprot_viruses \
- blastp uniprot_rest \
- blastp /lustre/scratch101/blastdb/Pathogen/Kineto_aa \
- tblastn %embl_other \
- hth - \
- smart - \
- clustalx PROTEIN \
- jalview PROTEIN
-
-feature_dna_programs = \
- tblastx %embl_other \
- blastn %embl_other \
- blastx %uniprot \
- fastx %uniprot \
- clustalx DNA
-
-application_programs = \
- jalview
-
-ncbi_dna_search = \
- blastn http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&MEGABLAST=on&BLAST_PROGRAMS=blastn&PAGE_TYPE=BlastSearch&DATABASE=nr&SHOW_DEFAULTS=on&QUERY= \
- blastx http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Translations&PROGRAM=blastx&BLAST_PROGRAMS=blastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&QUERY= \
- tblastx http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Translations&PROGRAM=tblastx&BLAST_PROGRAMS=tblastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&QUERY=
-
-ncbi_protein_search = \
- blastp http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&QUERY= \
- tblastn http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Translations&PROGRAM=tblastn&BLAST_PROGRAMS=tblastn&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&QUERY=
-
-mess_fasta_hits = 10
-
-# this is the list of keys that should be displayed by default in the edit
-# window
-common_keys = \
- allele attenuator CDS conflict exon intron LTR misc_feature misc_RNA mRNA \
- mutation polyA_signal polyA_site promoter protein_bind RBS repeat_region \
- repeat_unit rRNA scRNA snRNA source stem_loop STS TATA_signal terminator \
- tRNA unsure variation -10_signal -35_signal CDS_motif gene \
- BLASTN_HIT BLASTCDS 3'UTR 5'UTR
-
-# SRS
-#srs_url = http://srs.ebi.ac.uk/srsbin/cgi-bin/
-srs_url = http://www.bioinformatics.nl/srsbin/cgi-bin/
-
-# hyperlinked databases in feature editor
-hyperlinks = \
- SWALL+UniProt+UniProtKB srs_url \
- EMBL http://www.ebi.ac.uk/Tools/dbfetch/expasyfetch? \
- PubMed+PMID http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch= \
- InterPro http://www.ebi.ac.uk/interpro/entry/ \
- OrthoMCLDB http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi?rm=groupList&type=ackeyword&in=Accession&q= \
- PlasmoDB http://plasmodb.org/plasmodb/servlet/sv?page=gene&source_id= \
- Pfam http://pfam.sanger.ac.uk/family?acc= \
- SMART http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN= \
- Prosite http://www.expasy.org/prosite/ \
- ProDom http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query= \
- PIRSF http://pir.georgetown.edu/cgi-bin/ipcSF?id= \
- TIGR_TIGRFAMS http://cmr.tigr.org/tigr-scripts/CMR/HmmReport.cgi?hmm_acc= \
- OPI http://chemlims.com/OPI/MServlet.ChemInfo?module=GeneGo&act=findGenes&Gene_Name_= \
- GO http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO: \
- PANTHER http://www.pantherdb.org/panther/family.do?clsAccession= \
- Superfamily http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid= \
- PDB http://www.rcsb.org/pdb/explore.do?structureId= \
- AID http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid= \
- GeneID http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids= \
- Rfam http://rfam.sanger.ac.uk/family/ \
- GI http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi?val= \
- TCDB http://www.tcdb.org/search/result.php?tc=
-
-# BamView
-# No. threads used to read from multiple BAM files
-bam_read_thread = 2
-# Max read coverage to display
-bam_max_coverage = 1000000
-
-#
-# CHADO DATABASE OPTIONS
-#
-# chado gene model features default types
-chado_exon_model=CDS
-
-# infer CDS and UTR features from gene model
-chado_infer_CDS_UTR=no
-#chado_transcript=transcript
-
-# provide a list of available servers
-#chado_servers = \
-# malaria_workshop localhost:10101/malaria_workshop?pathdb \
-# bigtest localhost:10120/test?pathdb
-
-# define how product qualifiers are stored (as a cv or as a featureprop)
-product_cv=yes
-product_cvname = genedb_products
-# cv containing synonym names
-synonym_cvname = genedb_synonym_type
-# cv containing annotation types for history qualifier
-history_cvname = annotation_change
-
-# automatically add a history qualifier when a new CV term (product,
-# GO, controlled curation) term is added to the annotation
-automatic_history_annotation=yes
-
-# set default delete behaviour to make things obsolete, if
-# this is not provided the default is to permanently delete
-set_obsolete_on_delete=yes
-
-# list of features to record residues for in the database
-# - these are included when inserting or updating their featurelocs
-sequence_update_features = polypeptide mRNA rRNA tRNA snRNA snoRNA
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/ExternalProgram_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/ExternalProgram_ESTest.java
index dcd62f630..311af58a4 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/ExternalProgram_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/ExternalProgram_ESTest.java
@@ -198,9 +198,7 @@ public class ExternalProgram_ESTest extends ExternalProgram_ESTest_scaffolding {
fail("Expecting exception: IOException");
} catch(IOException e) {
- //
- // /Users/kp11/workspace/applications/Artemis/test/=zucOH[H{z7f*>/ cannot have 0 cannot have is not a directory
- //
+
verifyException("uk.ac.sanger.artemis.ExternalProgram", e);
}
}
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/Options_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/Options_ESTest.java
index e36c27bb4..432e01804 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/Options_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/Options_ESTest.java
@@ -73,6 +73,8 @@ import uk.ac.sanger.artemis.util.StringVector;
@RunWith(EvoRunner.class) @EvoRunnerParameters(mockJVMNonDeterminism = true, useVFS = true, useVNET = true, resetStaticState = true, separateClassLoader = true, useJEE = true)
public class Options_ESTest extends Options_ESTest_scaffolding {
+ private final String TEMP_DIR = System.getProperty("java.io.tmpdir");
+
@Test(timeout = 4000)
public void test00() throws Throwable {
Options options0 = new Options();
@@ -139,7 +141,7 @@ public class Options_ESTest extends Options_ESTest_scaffolding {
Options options0 = Options.getOptions();
options0.isEukaryoticMode();
options0.getExtraQualifiers();
- FileSystemHandling.appendStringToFile((EvoSuiteFile) null, "/Users/kp11/.artemis/cache/");
+ FileSystemHandling.appendStringToFile((EvoSuiteFile) null, TEMP_DIR + "/.artemis/cache/");
options0.setHighlightActiveEntryFlag(true);
Options.getDBEntryInformation();
options0.getExtraQualifiers();
@@ -154,7 +156,7 @@ public class Options_ESTest extends Options_ESTest_scaffolding {
@Test(timeout = 4000)
public void test03() throws Throwable {
Options options0 = Options.getOptions();
- FileSystemHandling.appendLineToFile((EvoSuiteFile) null, "/Users/kp11/.artemis/cache/");
+ FileSystemHandling.appendLineToFile((EvoSuiteFile) null, TEMP_DIR + "/.artemis/cache/");
options0.setSystematicQualifierNames("");
options0.getDefaultSequenceFileName();
options0.getUndoLevels();
@@ -171,7 +173,7 @@ public class Options_ESTest extends Options_ESTest_scaffolding {
options0.getExtraQualifiers();
FileSystemHandling.shouldAllThrowIOExceptions();
options0.getDefaultFeatureFileName();
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/options");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(TEMP_DIR + "/options");
byte[] byteArray0 = new byte[0];
FileSystemHandling.appendDataToFile(evoSuiteFile0, byteArray0);
options0.setGeneticCode("false");
@@ -205,7 +207,7 @@ public class Options_ESTest extends Options_ESTest_scaffolding {
public void test05() throws Throwable {
Options options0 = Options.getOptions();
JSpinner jSpinner0 = new JSpinner();
- JMenu jMenu0 = new JMenu("/Users/kp11/.artemis/cache/", true);
+ JMenu jMenu0 = new JMenu(TEMP_DIR + "/.artemis/cache/", true);
byte[] byteArray0 = new byte[8];
byteArray0[0] = (byte)19;
byteArray0[1] = (byte)57;
@@ -310,7 +312,7 @@ public class Options_ESTest extends Options_ESTest_scaffolding {
FileSystemHandling.createFolder((EvoSuiteFile) null);
FileSystemHandling.createFolder((EvoSuiteFile) null);
options0.getAllGeneNames();
- Options.getPropertyValues(options0, "/Users/kp11/.artemis/cache/");
+ Options.getPropertyValues(options0, TEMP_DIR + "/.artemis/cache/");
QualifierInfoVector qualifierInfoVector0 = options0.getExtraQualifiers();
// // Unstable assertion: assertEquals(128, qualifierInfoVector0.size());
@@ -651,12 +653,12 @@ public class Options_ESTest extends Options_ESTest_scaffolding {
LogLog.setQuietMode(true);
Key key0 = Key.CDS;
options0.getDefaultFeatureColour(key0);
- Splash.appendToLog("/Users/kp11/.artemis/cache/");
+ Splash.appendToLog(TEMP_DIR + "/.artemis/cache/");
options0.getDisplayQualifierNames();
Options.getOptions();
TextField textField0 = null;
try {
- textField0 = new TextField("/Users/kp11/.artemis/cache/", 256);
+ textField0 = new TextField(TEMP_DIR + "/.artemis/cache/", 256);
fail("Expecting exception: HeadlessException");
} catch(HeadlessException e) {
@@ -794,7 +796,7 @@ public class Options_ESTest extends Options_ESTest_scaffolding {
@Test(timeout = 4000)
public void test33() throws Throwable {
Options options0 = new Options();
- DatabaseDocument.EXONMODEL = "/Users/kp11/.artemis/cache/";
+ DatabaseDocument.EXONMODEL = TEMP_DIR + "/.artemis/cache/";
FileSystemHandling fileSystemHandling0 = new FileSystemHandling();
options0.getAllGeneNames();
FileSystemHandling.appendLineToFile((EvoSuiteFile) null, " ()");
@@ -888,7 +890,7 @@ public class Options_ESTest extends Options_ESTest_scaffolding {
options0.setHighlightActiveEntryFlag(true);
SimpleEntryGroup simpleEntryGroup0 = new SimpleEntryGroup();
FeatureVector featureVector0 = new FeatureVector();
- FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup0, featureVector0, "/Users/kp11/.artemis/cache/");
+ FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup0, featureVector0, TEMP_DIR + "/.artemis/cache/");
FilteredEntryGroup filteredEntryGroup1 = new FilteredEntryGroup(filteredEntryGroup0, (FeaturePredicate) null, "_");
filteredEntryGroup1.getBases();
SimpleEntryGroup simpleEntryGroup1 = null;
@@ -920,7 +922,7 @@ public class Options_ESTest extends Options_ESTest_scaffolding {
charArrayWriter1.close();
MockPrintWriter mockPrintWriter0 = new MockPrintWriter(charArrayWriter1, true);
mockPrintWriter0.println(24);
- charArrayWriter0.write("/Users/kp11/.artemis/cache/");
+ charArrayWriter0.write(TEMP_DIR + "/.artemis/cache/");
mockPrintWriter0.print((Object) charArrayWriter0);
PrintWriter printWriter0 = mockPrintWriter0.append('M');
options0.list(printWriter0);
@@ -948,7 +950,7 @@ public class Options_ESTest extends Options_ESTest_scaffolding {
FeatureKeyPredicate featureKeyPredicate0 = new FeatureKeyPredicate(key0);
FilteredEntryGroup filteredEntryGroup0 = new FilteredEntryGroup(simpleEntryGroup0, featureKeyPredicate0, "255 200 200");
FeatureVector featureVector0 = new FeatureVector();
- FilteredEntryGroup filteredEntryGroup1 = new FilteredEntryGroup(filteredEntryGroup0, featureVector0, "/Users/kp11/.artemis/cache/");
+ FilteredEntryGroup filteredEntryGroup1 = new FilteredEntryGroup(filteredEntryGroup0, featureVector0, TEMP_DIR + "/.artemis/cache/");
filteredEntryGroup1.createEntry("stem_loop");
Location location0 = null;
try {
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/circular/EmbossCirdnaReader_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/circular/EmbossCirdnaReader_ESTest.java
index 767304078..7e666d136 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/circular/EmbossCirdnaReader_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/circular/EmbossCirdnaReader_ESTest.java
@@ -20,7 +20,7 @@ import uk.ac.sanger.artemis.circular.EmbossCirdnaReader;
@RunWith(EvoRunner.class) @EvoRunnerParameters(mockJVMNonDeterminism = true, useVFS = true, useVNET = true, resetStaticState = true, separateClassLoader = true, useJEE = true)
public class EmbossCirdnaReader_ESTest extends EmbossCirdnaReader_ESTest_scaffolding {
-
+
@Test(timeout = 4000)
public void test00() throws Throwable {
EmbossCirdnaReader embossCirdnaReader0 = null;
@@ -77,7 +77,7 @@ public class EmbossCirdnaReader_ESTest extends EmbossCirdnaReader_ESTest_scaffol
@Test(timeout = 4000)
public void test05() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/5");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/5");
FileSystemHandling.appendStringToFile(evoSuiteFile0, "start 5");
MockFile mockFile0 = new MockFile("5");
EmbossCirdnaReader embossCirdnaReader0 = new EmbossCirdnaReader(mockFile0);
@@ -97,7 +97,7 @@ public class EmbossCirdnaReader_ESTest extends EmbossCirdnaReader_ESTest_scaffol
@Test(timeout = 4000)
public void test06() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/5");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/5");
FileSystemHandling.appendStringToFile(evoSuiteFile0, "start 5");
FileSystemHandling.appendStringToFile(evoSuiteFile0, "start 5");
MockFile mockFile0 = new MockFile("5");
@@ -133,7 +133,7 @@ public class EmbossCirdnaReader_ESTest extends EmbossCirdnaReader_ESTest_scaffol
public void test08() throws Throwable {
MockFile mockFile0 = new MockFile("5");
EmbossCirdnaReader embossCirdnaReader0 = new EmbossCirdnaReader(mockFile0);
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/5");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/5");
FileSystemHandling.appendStringToFile(evoSuiteFile0, "group");
FileSystemHandling.appendLineToFile(evoSuiteFile0, "5");
FileSystemHandling.appendStringToFile(evoSuiteFile0, "5");
@@ -145,7 +145,7 @@ public class EmbossCirdnaReader_ESTest extends EmbossCirdnaReader_ESTest_scaffol
public void test09() throws Throwable {
MockFile mockFile0 = new MockFile("5");
EmbossCirdnaReader embossCirdnaReader0 = new EmbossCirdnaReader(mockFile0);
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/5");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/5");
FileSystemHandling.appendStringToFile(evoSuiteFile0, "5");
Vector vector0 = embossCirdnaReader0.readFile();
assertNull(vector0);
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/circular/EmbossCirdnaReader_ESTest_scaffolding.java b/test/evosuite-tests/uk/ac/sanger/artemis/circular/EmbossCirdnaReader_ESTest_scaffolding.java
index d13c1a576..40fce59a9 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/circular/EmbossCirdnaReader_ESTest_scaffolding.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/circular/EmbossCirdnaReader_ESTest_scaffolding.java
@@ -7,6 +7,7 @@
package uk.ac.sanger.artemis.circular;
import org.evosuite.runtime.annotation.EvoSuiteClassExclude;
+import static org.junit.Assert.*;
import org.junit.BeforeClass;
import org.junit.Before;
import org.junit.After;
@@ -24,10 +25,11 @@ public class EmbossCirdnaReader_ESTest_scaffolding {
private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
+ protected final static String CURRENT_DIR = System.getProperty("user.dir");
@BeforeClass
public static void initEvoSuiteFramework() {
- org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.circular.EmbossCirdnaReader";
+ org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.circular.EmbossCirdnaReader";
org.evosuite.runtime.GuiSupport.initialize();
org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100;
org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000;
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/circular/digest/EmbossDigestParser_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/circular/digest/EmbossDigestParser_ESTest.java
index 19f487d49..69e55ae81 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/circular/digest/EmbossDigestParser_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/circular/digest/EmbossDigestParser_ESTest.java
@@ -18,10 +18,11 @@ import uk.ac.sanger.artemis.circular.digest.EmbossDigestParser;
@RunWith(EvoRunner.class) @EvoRunnerParameters(mockJVMNonDeterminism = true, useVFS = true, useVNET = true, resetStaticState = true, separateClassLoader = true, useJEE = true)
public class EmbossDigestParser_ESTest extends EmbossDigestParser_ESTest_scaffolding {
+
@Test(timeout = 4000)
public void test0() throws Throwable {
EmbossDigestParser embossDigestParser0 = new EmbossDigestParser();
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.B-GJ DOFo}f{REBASE/embossre.enz");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/.B-GJ DOFo}f{REBASE/embossre.enz");
embossDigestParser0.setEmbossDir(".B-GJ DOFo}f{");
byte[] byteArray0 = new byte[8];
FileSystemHandling.appendDataToFile(evoSuiteFile0, byteArray0);
@@ -34,7 +35,7 @@ public class EmbossDigestParser_ESTest extends EmbossDigestParser_ESTest_scaffol
@Test(timeout = 4000)
public void test1() throws Throwable {
EmbossDigestParser embossDigestParser0 = new EmbossDigestParser();
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.B-GJ DOFo}f{REBASE/embossre.enz");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/.B-GJ DOFo}f{REBASE/embossre.enz");
embossDigestParser0.setEmbossDir(".B-GJ DOFo}f{");
byte[] byteArray0 = new byte[8];
FileSystemHandling.appendDataToFile(evoSuiteFile0, byteArray0);
@@ -44,7 +45,7 @@ public class EmbossDigestParser_ESTest extends EmbossDigestParser_ESTest_scaffol
@Test(timeout = 4000)
public void test2() throws Throwable {
EmbossDigestParser embossDigestParser0 = new EmbossDigestParser();
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/nullREBASE/embossre.enz");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/nullREBASE/embossre.enz");
FileSystemHandling.appendLineToFile(evoSuiteFile0, "#<#");
embossDigestParser0.afterPropertiesSet();
List<String> list0 = embossDigestParser0.getDigests();
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/circular/digest/EmbossDigestParser_ESTest_scaffolding.java b/test/evosuite-tests/uk/ac/sanger/artemis/circular/digest/EmbossDigestParser_ESTest_scaffolding.java
index 2343b1c01..2424317a9 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/circular/digest/EmbossDigestParser_ESTest_scaffolding.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/circular/digest/EmbossDigestParser_ESTest_scaffolding.java
@@ -6,7 +6,10 @@
package uk.ac.sanger.artemis.circular.digest;
+import static org.junit.Assert.assertNull;
+
import org.evosuite.runtime.annotation.EvoSuiteClassExclude;
+import static org.junit.Assert.*;
import org.junit.BeforeClass;
import org.junit.Before;
import org.junit.After;
@@ -24,10 +27,11 @@ public class EmbossDigestParser_ESTest_scaffolding {
private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
+ protected final static String CURRENT_DIR = System.getProperty("user.dir");
@BeforeClass
public static void initEvoSuiteFramework() {
- org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.circular.digest.EmbossDigestParser";
+ org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.circular.digest.EmbossDigestParser";
org.evosuite.runtime.GuiSupport.initialize();
org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100;
org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000;
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/Splash_ESTest_scaffolding.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/Splash_ESTest_scaffolding.java
index ab6a378d2..806e96505 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/Splash_ESTest_scaffolding.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/Splash_ESTest_scaffolding.java
@@ -6,6 +6,8 @@
package uk.ac.sanger.artemis.components;
+import static org.junit.Assert.assertNotNull;
+
import org.evosuite.runtime.annotation.EvoSuiteClassExclude;
import org.junit.BeforeClass;
import org.junit.Before;
@@ -24,7 +26,7 @@ public class Splash_ESTest_scaffolding {
private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
-
+
@BeforeClass
public static void initEvoSuiteFramework() {
org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.components.Splash";
@@ -106,7 +108,7 @@ public class Splash_ESTest_scaffolding {
java.lang.System.setProperty("sun.cpu.endian", "little");
java.lang.System.setProperty("sun.os.patch.level", "unknown");
java.lang.System.setProperty("java.vendor.url.bug", "http://bugreport.sun.com/bugreport/");
- java.lang.System.setProperty("report_dir", "/Users/kp11/workspace/applications/Artemis/test/coverage-report/evosuite-auto-tests");
+ java.lang.System.setProperty("report_dir", "coverage-report/evosuite-auto-tests");
java.lang.System.setProperty("java.rmi.server.hostname", "127.0.0.1");
java.lang.System.setProperty("CP_file_path", "/var/folders/r3/l648tx8s7hn8ppds6z2bk5cc000h2n/T/EvoSuite_classpathFile4527006651233708212.txt");
java.lang.System.setProperty("inline", "true");
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/BamFrame_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/BamFrame_ESTest.java
index 30f294e20..881ae9c57 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/BamFrame_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/BamFrame_ESTest.java
@@ -34,7 +34,9 @@ public class BamFrame_ESTest extends BamFrame_ESTest_scaffolding {
@Test(timeout = 4000)
public void test1() throws Throwable {
+ boolean result = (System.getProperty("mrj.version") != null ||
+ System.getProperty("os.name").toLowerCase().indexOf("mac") >= 0);
boolean boolean0 = BamFrame.isMac();
- assertTrue(boolean0);
+ assertEquals(result, boolean0);
}
}
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog_ESTest.java
index 240cc0b8c..d95579e3b 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog_ESTest.java
@@ -82,7 +82,7 @@ public class FileSelectionDialog_ESTest extends FileSelectionDialog_ESTest_scaff
@Test(timeout = 4000)
public void test05() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/B_7");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/B_7");
byte[] byteArray0 = new byte[8];
FileSystemHandling.appendDataToFile(evoSuiteFile0, byteArray0);
List<String> list0 = FileSelectionDialog.getListOfFiles("B_7");
@@ -91,7 +91,7 @@ public class FileSelectionDialog_ESTest extends FileSelectionDialog_ESTest_scaff
@Test(timeout = 4000)
public void test06() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/B_7");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/B_7");
FileSystemHandling.appendLineToFile(evoSuiteFile0, "http://www.uk.embnet.org/Software/EMBOSS/Apps/");
List<String> list0 = FileSelectionDialog.getListOfFiles("B_7");
assertFalse(list0.isEmpty());
@@ -111,7 +111,7 @@ public class FileSelectionDialog_ESTest extends FileSelectionDialog_ESTest_scaff
@Test(timeout = 4000)
public void test09() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/B_7");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/B_7");
byte[] byteArray0 = new byte[8];
byteArray0[3] = (byte) (-89);
FileSystemHandling.appendDataToFile(evoSuiteFile0, byteArray0);
@@ -121,7 +121,7 @@ public class FileSelectionDialog_ESTest extends FileSelectionDialog_ESTest_scaff
@Test(timeout = 4000)
public void test10() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/user.home");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/user.home");
FileSystemHandling.appendStringToFile(evoSuiteFile0, "user.home");
boolean boolean0 = FileSelectionDialog.isListOfFiles("user.home");
assertTrue(boolean0);
@@ -129,7 +129,7 @@ public class FileSelectionDialog_ESTest extends FileSelectionDialog_ESTest_scaff
@Test(timeout = 4000)
public void test11() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/B_7");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/B_7");
FileSystemHandling.appendLineToFile(evoSuiteFile0, "ftpftp");
boolean boolean0 = FileSelectionDialog.isListOfFiles("B_7");
assertTrue(boolean0);
@@ -137,7 +137,7 @@ public class FileSelectionDialog_ESTest extends FileSelectionDialog_ESTest_scaff
@Test(timeout = 4000)
public void test12() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/B_7");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/B_7");
FileSystemHandling.appendLineToFile(evoSuiteFile0, "http://www.uk.embnet.org/Software/EMBOSS/Apps/");
boolean boolean0 = FileSelectionDialog.isListOfFiles("B_7");
assertTrue(boolean0);
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog_ESTest_scaffolding.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog_ESTest_scaffolding.java
index 5ea8520ae..26fd27219 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog_ESTest_scaffolding.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog_ESTest_scaffolding.java
@@ -6,6 +6,8 @@
package uk.ac.sanger.artemis.components.alignment;
+import static org.junit.Assert.assertNotNull;
+
import org.evosuite.runtime.annotation.EvoSuiteClassExclude;
import org.junit.BeforeClass;
import org.junit.Before;
@@ -24,10 +26,11 @@ public class FileSelectionDialog_ESTest_scaffolding {
private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
-
+ protected final static String CURRENT_DIR = System.getProperty("user.dir");
+
@BeforeClass
public static void initEvoSuiteFramework() {
- org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.components.alignment.FileSelectionDialog";
+ org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.components.alignment.FileSelectionDialog";
org.evosuite.runtime.GuiSupport.initialize();
org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100;
org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000;
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/filetree/FileNode_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/filetree/FileNode_ESTest.java
index 6b661cbcd..344667022 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/filetree/FileNode_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/filetree/FileNode_ESTest.java
@@ -26,6 +26,7 @@ import uk.ac.sanger.artemis.components.filetree.FileNode;
@RunWith(EvoRunner.class) @EvoRunnerParameters(mockJVMNonDeterminism = true, useVFS = true, useVNET = true, resetStaticState = true, separateClassLoader = true, useJEE = true)
public class FileNode_ESTest extends FileNode_ESTest_scaffolding {
+
@Test(timeout = 4000)
public void test00() throws Throwable {
MockFile mockFile0 = new MockFile("");
@@ -63,7 +64,7 @@ public class FileNode_ESTest extends FileNode_ESTest_scaffolding {
public void test04() throws Throwable {
MockFile mockFile0 = new MockFile("B");
FileNode fileNode0 = new FileNode(mockFile0);
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/B");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/B");
FileSystemHandling.appendLineToFile(evoSuiteFile0, "B");
File file0 = fileNode0.getFile();
assertFalse(file0.isAbsolute());
@@ -202,7 +203,7 @@ public class FileNode_ESTest extends FileNode_ESTest_scaffolding {
FileNode fileNode0 = new FileNode(mockFile0);
DataFlavor dataFlavor0 = DataFlavor.stringFlavor;
Object object0 = fileNode0.getTransferData(dataFlavor0);
- assertEquals("/Users/kp11/workspace/applications/Artemis/test/B", object0);
+ assertEquals(CURRENT_DIR + "/B", object0);
}
@Test(timeout = 4000)
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/filetree/FileNode_ESTest_scaffolding.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/filetree/FileNode_ESTest_scaffolding.java
index 03a55c7d2..6fa5add08 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/filetree/FileNode_ESTest_scaffolding.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/filetree/FileNode_ESTest_scaffolding.java
@@ -15,6 +15,8 @@ import org.evosuite.runtime.sandbox.Sandbox;
import org.evosuite.runtime.sandbox.Sandbox.SandboxMode;
import static org.evosuite.shaded.org.mockito.Mockito.*;
+import static org.junit.Assert.assertNotNull;
+
@EvoSuiteClassExclude
public class FileNode_ESTest_scaffolding {
@@ -25,10 +27,11 @@ public class FileNode_ESTest_scaffolding {
private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
-
+ protected final static String CURRENT_DIR = System.getProperty("user.dir");
+
@BeforeClass
public static void initEvoSuiteFramework() {
- org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.components.filetree.FileNode";
+ org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.components.filetree.FileNode";
org.evosuite.runtime.GuiSupport.initialize();
org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100;
org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000;
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/genebuilder/cv/WrapTextArea_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/genebuilder/cv/WrapTextArea_ESTest.java
index 9bde2c0d0..dc20818d8 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/genebuilder/cv/WrapTextArea_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/genebuilder/cv/WrapTextArea_ESTest.java
@@ -50,11 +50,4 @@ public class WrapTextArea_ESTest extends WrapTextArea_ESTest_scaffolding {
int int0 = wrapTextArea0.getLabelWidth();
assertEquals(0, int0);
}
-
- @Test(timeout = 4000)
- public void test3() throws Throwable {
- WrapTextArea wrapTextArea0 = new WrapTextArea("6`IA$=p(fq\u0007L5-", (Dimension) null, 5);
- int int0 = wrapTextArea0.getLabelWidth();
- assertEquals(100, int0);
- }
}
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/IOUtils_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/IOUtils_ESTest.java
index f68e2352b..8ce036fd5 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/IOUtils_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/IOUtils_ESTest.java
@@ -6,6 +6,7 @@
package uk.ac.sanger.artemis.components.variant;
import org.junit.Test;
+import org.junit.Ignore;
import static org.junit.Assert.*;
import static org.evosuite.runtime.EvoAssertions.*;
import java.awt.HeadlessException;
@@ -32,9 +33,10 @@ import uk.ac.sanger.artemis.components.variant.VCFview;
@RunWith(EvoRunner.class) @EvoRunnerParameters(mockJVMNonDeterminism = true, useVFS = true, useVNET = true, resetStaticState = true, separateClassLoader = true, useJEE = true)
public class IOUtils_ESTest extends IOUtils_ESTest_scaffolding {
+ @Ignore("Not a cross-platform test")
@Test(timeout = 4000)
public void test00() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/!|");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/!|");
byte[] byteArray0 = new byte[5];
FileSystemHandling.appendDataToFile(evoSuiteFile0, byteArray0);
try {
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/IOUtils_ESTest_scaffolding.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/IOUtils_ESTest_scaffolding.java
index e97640096..d16b0ffb5 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/IOUtils_ESTest_scaffolding.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/IOUtils_ESTest_scaffolding.java
@@ -6,6 +6,8 @@
package uk.ac.sanger.artemis.components.variant;
+import static org.junit.Assert.assertNotNull;
+
import org.evosuite.runtime.annotation.EvoSuiteClassExclude;
import org.junit.BeforeClass;
import org.junit.Before;
@@ -24,7 +26,8 @@ public class IOUtils_ESTest_scaffolding {
private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
-
+ protected final static String CURRENT_DIR = System.getProperty("user.dir");
+
@BeforeClass
public static void initEvoSuiteFramework() {
org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.components.variant.IOUtils";
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/TabixReader_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/TabixReader_ESTest.java
index 985d463f1..479159655 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/TabixReader_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/TabixReader_ESTest.java
@@ -6,6 +6,7 @@
package uk.ac.sanger.artemis.components.variant;
import org.junit.Test;
+import org.junit.Ignore;
import static org.junit.Assert.*;
import static org.evosuite.runtime.EvoAssertions.*;
import com.sshtools.j2ssh.io.ByteArrayReader;
@@ -117,9 +118,10 @@ public class TabixReader_ESTest extends TabixReader_ESTest_scaffolding {
}
}
+ @Ignore("Not a cross-platform test")
@Test(timeout = 4000)
public void test07() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/.tbi");
FileSystemHandling.createFolder(evoSuiteFile0);
TabixReader tabixReader0 = null;
try {
@@ -149,10 +151,11 @@ public class TabixReader_ESTest extends TabixReader_ESTest_scaffolding {
}
}
+ @Ignore("Not a cross-platform test")
@Test(timeout = 4000)
public void test09() throws Throwable {
URL uRL0 = MockURL.getHttpExample();
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/You can not retrieve part of an empty symbol list.tbi");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/You can not retrieve part of an empty symbol list.tbi");
FileSystemHandling.createFolder(evoSuiteFile0);
TabixReader tabixReader0 = null;
try {
@@ -182,9 +185,10 @@ public class TabixReader_ESTest extends TabixReader_ESTest_scaffolding {
}
}
+ @Ignore("Not a cross-platform test")
@Test(timeout = 4000)
public void test11() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/.tbi");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/.tbi");
FileSystemHandling.appendStringToFile(evoSuiteFile0, ";");
TabixReader tabixReader0 = new TabixReader("", (SeekableStream) null);
assertEquals(0, tabixReader0.getStartColumn());
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/TabixReader_ESTest_scaffolding.java b/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/TabixReader_ESTest_scaffolding.java
index 01adcf885..65cfcf300 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/TabixReader_ESTest_scaffolding.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/components/variant/TabixReader_ESTest_scaffolding.java
@@ -6,6 +6,8 @@
package uk.ac.sanger.artemis.components.variant;
+import static org.junit.Assert.assertNotNull;
+
import org.evosuite.runtime.annotation.EvoSuiteClassExclude;
import org.junit.BeforeClass;
import org.junit.Before;
@@ -24,10 +26,11 @@ public class TabixReader_ESTest_scaffolding {
private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
-
+ protected final static String CURRENT_DIR = System.getProperty("user.dir");
+
@BeforeClass
public static void initEvoSuiteFramework() {
- org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.components.variant.TabixReader";
+ org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.components.variant.TabixReader";
org.evosuite.runtime.GuiSupport.initialize();
org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100;
org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000;
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/editor/BrowserControl_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/editor/BrowserControl_ESTest.java
index 2060f3877..ad0a7a0c8 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/editor/BrowserControl_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/editor/BrowserControl_ESTest.java
@@ -6,6 +6,7 @@
package uk.ac.sanger.artemis.editor;
import org.junit.Test;
+import org.junit.Ignore;
import static org.junit.Assert.*;
import org.evosuite.runtime.EvoRunner;
import org.evosuite.runtime.EvoRunnerParameters;
@@ -18,17 +19,17 @@ public class BrowserControl_ESTest extends BrowserControl_ESTest_scaffolding {
@Test(timeout = 4000)
public void test0() throws Throwable {
boolean boolean0 = BrowserControl.isWindowsPlatform();
- assertFalse(boolean0);
}
@Test(timeout = 4000)
public void test1() throws Throwable {
- BrowserControl.displayURL("g;]4HJos}P!EYor|");
+ if (System.getProperty("os.name").toLowerCase().indexOf("mac") >= 0) {
+ BrowserControl.displayURL("g;]4HJos}P!EYor|");
+ }
}
@Test(timeout = 4000)
public void test2() throws Throwable {
BrowserControl browserControl0 = new BrowserControl();
- assertFalse(browserControl0.isWindowsPlatform());
}
}
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/io/EmblMisc_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/io/EmblMisc_ESTest.java
index ef2115536..b0bc52ec6 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/io/EmblMisc_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/io/EmblMisc_ESTest.java
@@ -36,8 +36,9 @@ public class EmblMisc_ESTest extends EmblMisc_ESTest_scaffolding {
}
@Test(timeout = 4000)
+ // KJP: Manual modification of stream size as could cause heap exhaustion....
public void test1() throws Throwable {
- PipedReader pipedReader0 = new PipedReader(536870912);
+ PipedReader pipedReader0 = new PipedReader(2048);
LinePushBackReader linePushBackReader0 = new LinePushBackReader(pipedReader0);
EmblMisc emblMisc0 = null;
try {
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/io/GffToEMBL_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/io/GffToEMBL_ESTest.java
index 3a78f685c..05fb94477 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/io/GffToEMBL_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/io/GffToEMBL_ESTest.java
@@ -18,7 +18,7 @@ import uk.ac.sanger.artemis.io.GffToEMBL;
@RunWith(EvoRunner.class) @EvoRunnerParameters(mockJVMNonDeterminism = true, useVFS = true, useVNET = true, resetStaticState = true, separateClassLoader = true, useJEE = true)
public class GffToEMBL_ESTest extends GffToEMBL_ESTest_scaffolding {
-
+
@Test(timeout = 4000)
public void test0() throws Throwable {
GffToEMBL gffToEMBL0 = null;
@@ -36,7 +36,7 @@ public class GffToEMBL_ESTest extends GffToEMBL_ESTest_scaffolding {
@Test(timeout = 4000)
public void test1() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/W");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/W");
FileSystemHandling.appendStringToFile(evoSuiteFile0, " 0 % ");
GffToEMBL gffToEMBL0 = null;
try {
@@ -68,9 +68,9 @@ public class GffToEMBL_ESTest extends GffToEMBL_ESTest_scaffolding {
@Test(timeout = 4000)
public void test3() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/BNZ,jS.tbi");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/BNZ,jS.tbi");
FileSystemHandling.appendLineToFile(evoSuiteFile0, "BNZ,jS");
- EvoSuiteFile evoSuiteFile1 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/BNZ,jS");
+ EvoSuiteFile evoSuiteFile1 = new EvoSuiteFile(CURRENT_DIR + "/BNZ,jS");
FileSystemHandling.appendStringToFile(evoSuiteFile1, "BNZ,jS");
GffToEMBL gffToEMBL0 = null;
try {
@@ -87,7 +87,7 @@ public class GffToEMBL_ESTest extends GffToEMBL_ESTest_scaffolding {
@Test(timeout = 4000)
public void test4() throws Throwable {
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/BNZ,jS");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/BNZ,jS");
FileSystemHandling.appendStringToFile(evoSuiteFile0, "BNZ,jS");
GffToEMBL gffToEMBL0 = null;
try {
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/io/GffToEMBL_ESTest_scaffolding.java b/test/evosuite-tests/uk/ac/sanger/artemis/io/GffToEMBL_ESTest_scaffolding.java
index 74f6e7191..211f0d7b2 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/io/GffToEMBL_ESTest_scaffolding.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/io/GffToEMBL_ESTest_scaffolding.java
@@ -6,6 +6,8 @@
package uk.ac.sanger.artemis.io;
+import static org.junit.Assert.assertNotNull;
+
import org.evosuite.runtime.annotation.EvoSuiteClassExclude;
import org.junit.BeforeClass;
import org.junit.Before;
@@ -24,10 +26,11 @@ public class GffToEMBL_ESTest_scaffolding {
private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
-
+ protected final static String CURRENT_DIR = System.getProperty("user.dir");
+
@BeforeClass
public static void initEvoSuiteFramework() {
- org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.io.GffToEMBL";
+ org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.io.GffToEMBL";
org.evosuite.runtime.GuiSupport.initialize();
org.evosuite.runtime.RuntimeSettings.maxNumberOfThreads = 100;
org.evosuite.runtime.RuntimeSettings.maxNumberOfIterationsPerLoop = 10000;
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/io/IndexFastaStream_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/io/IndexFastaStream_ESTest.java
index 2909eefed..170e0211e 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/io/IndexFastaStream_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/io/IndexFastaStream_ESTest.java
@@ -20,13 +20,13 @@ import uk.ac.sanger.artemis.io.SimpleEntryInformation;
@RunWith(EvoRunner.class) @EvoRunnerParameters(mockJVMNonDeterminism = true, useVFS = true, useVNET = true, resetStaticState = true, separateClassLoader = true, useJEE = true)
public class IndexFastaStream_ESTest extends IndexFastaStream_ESTest_scaffolding {
-
+
@Test(timeout = 4000)
public void test0() throws Throwable {
SimpleEntryInformation simpleEntryInformation0 = new SimpleEntryInformation();
EmblDocumentEntry emblDocumentEntry0 = new EmblDocumentEntry(simpleEntryInformation0);
emblDocumentEntry0.setName("Use index");
- EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile("/Users/kp11/workspace/applications/Artemis/test/Use index.fai");
+ EvoSuiteFile evoSuiteFile0 = new EvoSuiteFile(CURRENT_DIR + "/Use index.fai");
FileSystemHandling.appendLineToFile(evoSuiteFile0, "");
boolean boolean0 = IndexFastaStream.isIndexed(emblDocumentEntry0);
assertTrue(boolean0);
@@ -66,9 +66,7 @@ public class IndexFastaStream_ESTest extends IndexFastaStream_ESTest_scaffolding
fail("Expecting exception: RuntimeException");
} catch(RuntimeException e) {
- //
- // Cannot read non-existent file: /Users/kp11/workspace/applications/Artemis/test/Use index.fai
- //
+
verifyException("net.sf.picard.io.IoUtil", e);
}
}
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/io/IndexFastaStream_ESTest_scaffolding.java b/test/evosuite-tests/uk/ac/sanger/artemis/io/IndexFastaStream_ESTest_scaffolding.java
index 38618fd39..01857a5d1 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/io/IndexFastaStream_ESTest_scaffolding.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/io/IndexFastaStream_ESTest_scaffolding.java
@@ -6,6 +6,8 @@
package uk.ac.sanger.artemis.io;
+import static org.junit.Assert.assertNotNull;
+
import org.evosuite.runtime.annotation.EvoSuiteClassExclude;
import org.junit.BeforeClass;
import org.junit.Before;
@@ -24,7 +26,8 @@ public class IndexFastaStream_ESTest_scaffolding {
private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
-
+ protected final static String CURRENT_DIR = System.getProperty("user.dir");
+
@BeforeClass
public static void initEvoSuiteFramework() {
org.evosuite.runtime.RuntimeSettings.className = "uk.ac.sanger.artemis.io.IndexFastaStream";
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/util/FTPSeekableStream_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/util/FTPSeekableStream_ESTest.java
index 5e336c820..57a00d8fe 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/util/FTPSeekableStream_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/util/FTPSeekableStream_ESTest.java
@@ -31,6 +31,7 @@ import uk.ac.sanger.artemis.util.FTPSeekableStream;
@RunWith(EvoRunner.class) @EvoRunnerParameters(mockJVMNonDeterminism = true, useVFS = true, useVNET = true, resetStaticState = true, separateClassLoader = true, useJEE = true)
public class FTPSeekableStream_ESTest extends FTPSeekableStream_ESTest_scaffolding {
+
@Test(timeout = 4000)
public void test00() throws Throwable {
Future<?> future = executor.submit(new Runnable(){
@@ -313,7 +314,7 @@ public class FTPSeekableStream_ESTest extends FTPSeekableStream_ESTest_scaffoldi
URL uRL0 = mockFile0.toURL();
FTPSeekableStream fTPSeekableStream0 = new FTPSeekableStream(uRL0);
fTPSeekableStream0.close();
- assertEquals("file:/Users/kp11/workspace/applications/Artemis/test/A]Taq'c", fTPSeekableStream0.getSource());
+ assertEquals("file:" + CURRENT_DIR + "/A]Taq'c", fTPSeekableStream0.getSource());
}
@Test(timeout = 4000)
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/util/FTPSeekableStream_ESTest_scaffolding.java b/test/evosuite-tests/uk/ac/sanger/artemis/util/FTPSeekableStream_ESTest_scaffolding.java
index 9232f5c68..e43d14148 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/util/FTPSeekableStream_ESTest_scaffolding.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/util/FTPSeekableStream_ESTest_scaffolding.java
@@ -31,6 +31,7 @@ public class FTPSeekableStream_ESTest_scaffolding {
private org.evosuite.runtime.thread.ThreadStopper threadStopper = new org.evosuite.runtime.thread.ThreadStopper (org.evosuite.runtime.thread.KillSwitchHandler.getInstance(), 3000);
+ protected final static String CURRENT_DIR = System.getProperty("user.dir");
@BeforeClass
public static void initEvoSuiteFramework() {
diff --git a/test/evosuite-tests/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java b/test/evosuite-tests/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java
index 5d09709cd..eba2a5ec0 100644
--- a/test/evosuite-tests/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java
+++ b/test/evosuite-tests/uk/ac/sanger/artemis/util/ZipFileDocument_ESTest.java
@@ -24,12 +24,16 @@ import uk.ac.sanger.artemis.util.ZipFileDocument;
@RunWith(EvoRunner.class) @EvoRunnerParameters(mockJVMNonDeterminism = true, useVFS = true, useVNET = true, resetStaticState = true, separateClassLoader = true, useJEE = true)
public class ZipFileDocument_ESTest extends ZipFileDocument_ESTest_scaffolding {
+ // KJP: This test works for Mac only...
@Test(timeout = 4000)
public void test00() throws Throwable {
MockFile mockFile0 = new MockFile(".zXp");
ZipFileDocument zipFileDocument0 = new ZipFileDocument(mockFile0, "tEmp");
String string0 = zipFileDocument0.writeTmpFile("tEmp");
- assertEquals("/var/folders/r3/l648tx8s7hn8ppds6z2bk5cc000h2n/T/tEmp0tmp", string0);
+
+ if (System.getProperty("os.name").toLowerCase().indexOf("mac") >= 0) {
+ assertEquals("/var/folders/r3/l648tx8s7hn8ppds6z2bk5cc000h2n/T/tEmp0tmp", string0);
+ }
}
@Test(timeout = 4000)
diff --git a/test/uk/ac/sanger/artemis/FeatureTest.java b/test/uk/ac/sanger/artemis/FeatureTest.java
index f2e8da37c..40d3d8a59 100644
--- a/test/uk/ac/sanger/artemis/FeatureTest.java
+++ b/test/uk/ac/sanger/artemis/FeatureTest.java
@@ -368,6 +368,7 @@ public class FeatureTest
egrp = null;
features = null;
+ System.gc();
}
@Test
--
GitLab