From 52bd3ac07d2ce11421512e80cb7ac8877e738d24 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Fri, 21 Feb 2025 22:14:07 +0000
Subject: [PATCH] Added a second test

---
 .vscode/tasks.json                 |   6 ++
 Jenkinsfile                        |   4 +-
 autobigs-cli.xml                   |  32 +++----
 test-data/databases-2025-02-21.csv | 146 +++++++++++++++++++++++++++++
 test-data/schemas-2025-02-21.csv   |  11 +++
 5 files changed, 182 insertions(+), 17 deletions(-)
 create mode 100644 test-data/databases-2025-02-21.csv
 create mode 100644 test-data/schemas-2025-02-21.csv

diff --git a/.vscode/tasks.json b/.vscode/tasks.json
index dbb3a29..29bd266 100644
--- a/.vscode/tasks.json
+++ b/.vscode/tasks.json
@@ -14,6 +14,12 @@
             "type": "shell",
             "command": "planemo serve",
             "problemMatcher": []
+        },
+        {
+            "label": "run tests",
+            "type": "shell",
+            "command": "planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html",
+            "problemMatcher": []
         }
     ]
 }
\ No newline at end of file
diff --git a/Jenkinsfile b/Jenkinsfile
index 9a0c436..2cac2ed 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -2,7 +2,7 @@ pipeline {
     agent {
         kubernetes {
             cloud 'rsys-devel'
-            defaultContainer 'pip'
+            defaultContainer 'rootless-pip'
             inheritFrom 'pip'
         }
     }
@@ -11,6 +11,8 @@ pipeline {
         stage ("install") {
             steps {
                 sh 'pip install -r requirements.txt'
+                sh 'pip install standard-imghdr'
+                sh 'useradd galaxy -m'
             }
         }
         stage ("lint") {
diff --git a/autobigs-cli.xml b/autobigs-cli.xml
index 5598a5b..4f6865a 100644
--- a/autobigs-cli.xml
+++ b/autobigs-cli.xml
@@ -1,4 +1,4 @@
-<tool id="autobigs-cli" name="AutoBIGS.CLI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+<tool id="autobigs-cli" name="autoBIGS.cli" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
 	<description>Automated MLST typing from PubMLST and InstitutPasteur.</description>
 	<macros>
 		<token name="@TOOL_VERSION@">0.5.0</token>
@@ -12,14 +12,14 @@
 	</requirements>
 
 	<command detect_errors="exit_code"><![CDATA[
-			#if $mode.operation == "info":
-				#if $select_info.retrieved == "schema":
+			#if $mode['operation'] == "info":
+				#if $select_info['retrieved'] == "schemas":
 					autoBIGS info $selected_schema --csv $info_out
-				#else if $select_info.retrieved == "databases":
+				#else if $select_info['retrieved'] == "databases":
 					autoBIGS info --retrieve-bigsdbs --csv $info_out
 				#end if
-			#else if $mode.operation == "st":
-				autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output"
+			#else if $mode['operation'] == "st":
+				autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
 			#end if
 	]]></command>
 	<inputs>
@@ -30,13 +30,13 @@
 			</param>
 			<when value="info">
 				<conditional name="select_info">
-					<param name="retrieved" label="Schema or Database List" type="select">
-						<option value="schema">Available Schemas for Database</option>
+					<param name="retrieved" label="Schemas or Database List" type="select">
+						<option value="schemas">Available Schemas for Database</option>
 						<option value="databases">Available Databases</option>
 					</param>
-					<when value="schema">
-						<repeat name="schemas" title="Schemas" min="1">
-							<param name="selected_schema" argument="--retrieve-bigsdb-schemas" label="Retrieve schemas for" type="integer" min="0"/>
+					<when value="schemas">
+						<repeat name="schemas_list" title="Schemas" min="1">
+							<param name="selected_schema" argument="--retrieve-bigsdb-schemas" label="Retrieve schemas for" type="text"/>
 						</repeat>
 					</when>
 					<when value="databases">
@@ -48,7 +48,7 @@
 				<param name="fastas" label="FASTA files" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
 				<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text" optional="false"/>
 				<param name="schema" label="BIGSdb SeqDef Schema ID" type="integer" min="0"/>
-				<param name="stop_on_fail" argument="--sof" label="Stop on failure to match" value="false" type="boolean"/>
+				<param name="stop_on_fail" label="Stop on failure to match" truevalue="--sof" falsevalue="" value="false" type="boolean"/>
 			</when>
 		</conditional>
 	</inputs>
@@ -56,8 +56,8 @@
 		<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
 			<filter>mode['operation'] == "st"</filter>
 		</data>
-		<data name="info_out" label="${tool.name} supported databases/schemas" format="csv">
-			<filter>mode['operation'] == "info"</filter>
+		<data name="info_out" label="${tool.name} supported Databases" format="csv">
+			<filter>mode['operation'] == "info" and select_info['retrieved'] == 'databases'</filter>
 		</data>
 	</outputs>
     <tests>
@@ -73,8 +73,8 @@
             <param name="retrieved" value="databases" />
             <output name="info_out">
 				<assert_contents>
-					<has_line line="BIGSdb Names,Source"/>
-					<has_line line="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>
+					<has_text text="BIGSdb Names,Source"/>
+					<has_text text="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>
 				</assert_contents>
 			</output>
         </test>
diff --git a/test-data/databases-2025-02-21.csv b/test-data/databases-2025-02-21.csv
new file mode 100644
index 0000000..b3c7ad7
--- /dev/null
+++ b/test-data/databases-2025-02-21.csv
@@ -0,0 +1,146 @@
+BIGSdb Names,Source
+pubmlst_aactinomycetemcomitans_seqdef,https://rest.pubmlst.org
+pubmlst_abaumannii_seqdef,https://rest.pubmlst.org
+pubmlst_achromobacter_seqdef,https://rest.pubmlst.org
+pubmlst_aeromonas_seqdef,https://rest.pubmlst.org
+pubmlst_afumigatus_seqdef,https://rest.pubmlst.org
+pubmlst_aparagallinarum_seqdef,https://rest.pubmlst.org
+pubmlst_aphagocytophilum_seqdef,https://rest.pubmlst.org
+pubmlst_arcobacter_seqdef,https://rest.pubmlst.org
+pubmlst_bbacilliformis_seqdef,https://rest.pubmlst.org
+pubmlst_bcc_seqdef,https://rest.pubmlst.org
+pubmlst_bcereus_seqdef,https://rest.pubmlst.org
+pubmlst_bfragilis_seqdef,https://rest.pubmlst.org
+pubmlst_bhenselae_seqdef,https://rest.pubmlst.org
+pubmlst_blastocystis_seqdef,https://rest.pubmlst.org
+pubmlst_blicheniformis_seqdef,https://rest.pubmlst.org
+pubmlst_bmallei_seqdef,https://rest.pubmlst.org
+pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api
+pubmlst_borrelia_seqdef,https://rest.pubmlst.org
+pubmlst_bpseudomallei_seqdef,https://rest.pubmlst.org
+pubmlst_brachyspira_seqdef,https://rest.pubmlst.org
+pubmlst_brucella_seqdef,https://rest.pubmlst.org
+pubmlst_bsubtilis_seqdef,https://rest.pubmlst.org
+pubmlst_bwashoensis_seqdef,https://rest.pubmlst.org
+pubmlst_calbicans_seqdef,https://rest.pubmlst.org
+pubmlst_campylobacter_nonjejuni_seqdef,https://rest.pubmlst.org
+pubmlst_campylobacter_seqdef,https://rest.pubmlst.org
+pubmlst_cbotulinum_seqdef,https://rest.pubmlst.org
+pubmlst_cchauvoei_seqdef,https://rest.pubmlst.org
+pubmlst_cdifficile_seqdef,https://rest.pubmlst.org
+pubmlst_cfreundii_seqdef,https://rest.pubmlst.org
+pubmlst_cglabrata_seqdef,https://rest.pubmlst.org
+pubmlst_chlamydiales_seqdef,https://rest.pubmlst.org
+pubmlst_ckrusei_seqdef,https://rest.pubmlst.org
+pubmlst_cmaltaromaticum_seqdef,https://rest.pubmlst.org
+pubmlst_cperfringens_seqdef,https://rest.pubmlst.org
+pubmlst_cronobacter_seqdef,https://rest.pubmlst.org
+pubmlst_csepticum_seqdef,https://rest.pubmlst.org
+pubmlst_csinensis_seqdef,https://rest.pubmlst.org
+pubmlst_ctropicalis_seqdef,https://rest.pubmlst.org
+pubmlst_diphtheria_seqdef,https://bigsdb.pasteur.fr/api
+pubmlst_dnodosus_seqdef,https://rest.pubmlst.org
+pubmlst_ecloacae_seqdef,https://rest.pubmlst.org
+pubmlst_edwardsiella_seqdef,https://rest.pubmlst.org
+pubmlst_efaecalis_seqdef,https://rest.pubmlst.org
+pubmlst_efaecium_seqdef,https://rest.pubmlst.org
+pubmlst_escherichia_seqdef,https://rest.pubmlst.org
+pubmlst_fpsychrophilum_seqdef,https://rest.pubmlst.org
+pubmlst_gallibacterium_seqdef,https://rest.pubmlst.org
+pubmlst_geotrichum_seqdef,https://rest.pubmlst.org
+pubmlst_hcinaedi_seqdef,https://rest.pubmlst.org
+pubmlst_helicobacter_seqdef,https://rest.pubmlst.org
+pubmlst_hinfluenzae_seqdef,https://rest.pubmlst.org
+pubmlst_hparasuis_seqdef,https://rest.pubmlst.org
+pubmlst_hsuis_seqdef,https://rest.pubmlst.org
+pubmlst_kaerogenes_seqdef,https://rest.pubmlst.org
+pubmlst_klebsiella_seqdef,https://bigsdb.pasteur.fr/api
+pubmlst_koxytoca_seqdef,https://rest.pubmlst.org
+pubmlst_kseptempunctata_seqdef,https://rest.pubmlst.org
+pubmlst_leptospira_seqdef,https://rest.pubmlst.org
+pubmlst_lgarvieae_seqdef,https://rest.pubmlst.org
+pubmlst_liberibacter_seqdef,https://rest.pubmlst.org
+pubmlst_listeria_seqdef,https://bigsdb.pasteur.fr/api
+pubmlst_llactis_phage_seqdef,https://rest.pubmlst.org
+pubmlst_lsalivarius_seqdef,https://rest.pubmlst.org
+pubmlst_mabscessus_seqdef,https://rest.pubmlst.org
+pubmlst_magalactiae_seqdef,https://rest.pubmlst.org
+pubmlst_manserisalpingitidis_seqdef,https://rest.pubmlst.org
+pubmlst_mbovis_seqdef,https://rest.pubmlst.org
+pubmlst_mcanis_seqdef,https://rest.pubmlst.org
+pubmlst_mcaseolyticus_seqdef,https://rest.pubmlst.org
+pubmlst_mflocculare_seqdef,https://rest.pubmlst.org
+pubmlst_mgallisepticum_seqdef,https://rest.pubmlst.org
+pubmlst_mgenitalium_seqdef,https://rest.pubmlst.org
+pubmlst_mhaemolytica_seqdef,https://rest.pubmlst.org
+pubmlst_mhominis_seqdef,https://rest.pubmlst.org
+pubmlst_mhyopneumoniae_seqdef,https://rest.pubmlst.org
+pubmlst_mhyorhinis_seqdef,https://rest.pubmlst.org
+pubmlst_mhyosynoviae_seqdef,https://rest.pubmlst.org
+pubmlst_miowae_seqdef,https://rest.pubmlst.org
+pubmlst_mplutonius_seqdef,https://rest.pubmlst.org
+pubmlst_mpneumoniae_seqdef,https://rest.pubmlst.org
+pubmlst_msciuri_seqdef,https://rest.pubmlst.org
+pubmlst_msynoviae_seqdef,https://rest.pubmlst.org
+pubmlst_mycobacteria_seqdef,https://rest.pubmlst.org
+pubmlst_neisseria_seqdef,https://rest.pubmlst.org
+pubmlst_oralstrep_seqdef,https://rest.pubmlst.org
+pubmlst_orhinotracheale_seqdef,https://rest.pubmlst.org
+pubmlst_otsutsugamushi_seqdef,https://rest.pubmlst.org
+pubmlst_pacnes_seqdef,https://rest.pubmlst.org
+pubmlst_paeruginosa_seqdef,https://rest.pubmlst.org
+pubmlst_pdamselae_seqdef,https://rest.pubmlst.org
+pubmlst_pfluorescens_seqdef,https://rest.pubmlst.org
+pubmlst_pgingivalis_seqdef,https://rest.pubmlst.org
+pubmlst_plarvae_seqdef,https://rest.pubmlst.org
+pubmlst_plasmid_seqdef,https://rest.pubmlst.org
+pubmlst_pmultocida_seqdef,https://rest.pubmlst.org
+pubmlst_ppentosaceus_seqdef,https://rest.pubmlst.org
+pubmlst_pputida_seqdef,https://rest.pubmlst.org
+pubmlst_proteus_seqdef,https://rest.pubmlst.org
+pubmlst_psalmonis_seqdef,https://rest.pubmlst.org
+pubmlst_ranatipestifer_seqdef,https://rest.pubmlst.org
+pubmlst_rhodococcus_seqdef,https://rest.pubmlst.org
+pubmlst_rmlst_seqdef,https://rest.pubmlst.org
+pubmlst_sagalactiae_seqdef,https://rest.pubmlst.org
+pubmlst_salmonella_seqdef,https://rest.pubmlst.org
+pubmlst_saureus_seqdef,https://rest.pubmlst.org
+pubmlst_sbsec_seqdef,https://rest.pubmlst.org
+pubmlst_scanis_seqdef,https://rest.pubmlst.org
+pubmlst_schromogenes_seqdef,https://rest.pubmlst.org
+pubmlst_sdysgalactiae_seqdef,https://rest.pubmlst.org
+pubmlst_sepidermidis_seqdef,https://rest.pubmlst.org
+pubmlst_serratia_seqdef,https://rest.pubmlst.org
+pubmlst_sgallolyticus_seqdef,https://rest.pubmlst.org
+pubmlst_shaemolyticus_seqdef,https://rest.pubmlst.org
+pubmlst_shewanella_seqdef,https://rest.pubmlst.org
+pubmlst_shominis_seqdef,https://rest.pubmlst.org
+pubmlst_siniae_seqdef,https://rest.pubmlst.org
+pubmlst_sinorhizobium_seqdef,https://rest.pubmlst.org
+pubmlst_smaltophilia_seqdef,https://rest.pubmlst.org
+pubmlst_smitis_seqdef,https://rest.pubmlst.org
+pubmlst_sparasitica_seqdef,https://rest.pubmlst.org
+pubmlst_spneumoniae_seqdef,https://rest.pubmlst.org
+pubmlst_spseudintermedius_seqdef,https://rest.pubmlst.org
+pubmlst_spyogenes_seqdef,https://rest.pubmlst.org
+pubmlst_ssuis_seqdef,https://rest.pubmlst.org
+pubmlst_sthermophilus_seqdef,https://rest.pubmlst.org
+pubmlst_streptomyces_seqdef,https://rest.pubmlst.org
+pubmlst_suberis_seqdef,https://rest.pubmlst.org
+pubmlst_szooepidemicus_seqdef,https://rest.pubmlst.org
+pubmlst_taylorella_seqdef,https://rest.pubmlst.org
+pubmlst_tenacibaculum_seqdef,https://rest.pubmlst.org
+pubmlst_test_seqdef,https://rest.pubmlst.org
+pubmlst_tpallidum_seqdef,https://rest.pubmlst.org
+pubmlst_tvaginalis_seqdef,https://rest.pubmlst.org
+pubmlst_ureaplasma_seqdef,https://rest.pubmlst.org
+pubmlst_vcholerae_seqdef,https://rest.pubmlst.org
+pubmlst_vibrio_seqdef,https://rest.pubmlst.org
+pubmlst_vparahaemolyticus_seqdef,https://rest.pubmlst.org
+pubmlst_vtapetis_seqdef,https://rest.pubmlst.org
+pubmlst_vvulnificus_seqdef,https://rest.pubmlst.org
+pubmlst_wolbachia_seqdef,https://rest.pubmlst.org
+pubmlst_xcitri_seqdef,https://rest.pubmlst.org
+pubmlst_xfastidiosa_seqdef,https://rest.pubmlst.org
+pubmlst_yersinia_seqdef,https://bigsdb.pasteur.fr/api
+pubmlst_yruckeri_seqdef,https://rest.pubmlst.org
diff --git a/test-data/schemas-2025-02-21.csv b/test-data/schemas-2025-02-21.csv
new file mode 100644
index 0000000..e28c230
--- /dev/null
+++ b/test-data/schemas-2025-02-21.csv
@@ -0,0 +1,11 @@
+Name,ID
+Autotransporters,11
+Bp_vaccine antigens,7
+MLST,3
+Other toxins,9
+PRN-test-Bp,5
+Phase,8
+T3SS,10
+cgMLST_genus,1
+cgMLST_pertussis,4
+macrolide resistance,6