Tests: update single trial upload tests

update row indices
add csv files to tests

t/data/trial/trial_layout_bad_accessions.csv

@@ -0,0 +1,9 @@
+plot_name,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number
+ba_plot_01,bad_accession1,1,1,0,1,1,1,1
+ba_plot_02,bad_accession2,2,1,0,2,1,2,1
+ba_plot_03,bad_accession3,3,1,0,1,1,3,1
+ba_plot_04,bad_accession4,4,1,1,2,1,4,1
+ba_plot_05,bad_accession5,5,2,1,1,2,1,2
+ba_plot_06,bad_accession6,6,2,0,2,2,2,2
+ba_plot_07,bad_accession7,7,2,0,1,2,3,2
+ba_plot_08,bad_accession8,8,2,0,2,2,4,2

t/data/trial/trial_layout_example.csv

@@ -0,0 +1,9 @@
+plot_name,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number,seedlot_name,num_seed_per_plot,weight_gram_seed_per_plot
+plot_name1,test_accession1,1,1,0,1,1,1,1,,,
+plot_name2,test_accession1,2,1,0,2,1,2,1,,,
+plot_name3,test_accession2,3,1,0,1,1,3,1,,,
+plot_name4,test_accession2,4,1,0,2,1,4,1,,,
+plot_name5,test_accession3,5,2,0,1,2,1,2,,,
+plot_name6,test_accession3,6,2,0,2,2,2,2,,,
+plot_name7,test_accession4,7,2,0,1,2,3,2,,,
+plot_name8,test_accession4,8,2,0,2,2,4,2,,,

t/data/trial/trial_layout_example_flexible.csv

@@ -0,0 +1,9 @@
+entry_number,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number
+1,test_accession1,1,1,0,1,1,1,1
+1,test_accession1,2,1,0,2,1,2,1
+2,test_accession2,3,1,0,1,1,3,1
+2,test_accession2,4,1,0,2,1,4,1
+3,test_accession3,5,2,0,1,2,1,2
+3,test_accession3,6,2,0,2,2,2,2
+4,test_accession4,7,2,0,1,2,3,2
+4,test_accession4,8,2,0,2,2,4,2

t/data/trial/trial_layout_example_with_management_factor.csv

@@ -0,0 +1,9 @@
+plot_name,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number,seedlot_name,num_seed_per_plot,weight_gram_seed_per_plot,fert_factor1,manage_factor2
+trial_management_factor_plot_name1,test_accession1,1,1,0,1,1,1,1,,,,1,
+trial_management_factor_plot_name2,test_accession1,2,1,0,2,1,2,1,,,,1,
+trial_management_factor_plot_name3,test_accession2,3,1,0,1,1,3,1,,,,1,1
+trial_management_factor_plot_name4,test_accession2,4,1,0,2,1,4,1,,,,,1
+trial_management_factor_plot_name5,test_accession3,5,2,0,1,2,1,2,,,,,1
+trial_management_factor_plot_name6,test_accession3,6,2,0,2,2,2,2,,,,1,
+trial_management_factor_plot_name7,test_accession4,7,2,0,1,2,3,2,,,,1,
+trial_management_factor_plot_name8,test_accession4,8,2,0,2,2,4,2,,,,1,

t/data/trial/trial_layout_with_seedlot_example.csv

@@ -0,0 +1,9 @@
+plot_name,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number,seedlot_name,num_seed_per_plot,weight_gram_seed_per_plot
+plot_with_seedlot_name1,test_accession1,1,1,0,1,1,1,1,test_accession1_001,12,
+plot_with_seedlot_name2,test_accession1,2,1,0,2,1,2,1,test_accession1_001,12,
+plot_with_seedlot_name3,test_accession2,3,1,0,1,1,3,1,test_accession2_001,12,4
+plot_with_seedlot_name4,test_accession2,4,1,0,2,1,4,1,test_accession2_001,12,5
+plot_with_seedlot_name5,test_accession3,5,2,0,1,2,1,2,test_accession3_001,12,
+plot_with_seedlot_name6,test_accession3,6,2,0,2,2,2,2,test_accession3_001,12,
+plot_with_seedlot_name7,test_accession4,7,2,0,1,2,3,2,test_accession4_001,12,
+plot_with_seedlot_name8,test_accession4,8,2,0,2,2,4,2,test_accession4_001,12,

t/unit_fixture/CXGN/Trial/ParseUpload.t

@@ -9,7 +9,7 @@ use Data::Dumper;
 
 my $f = SGN::Test::Fixture->new();
 
-for my $extension ("xls", "xlsx") {
+for my $extension ("xls", "xlsx", "csv") {
 
     my $p = CXGN::Trial::ParseUpload->new({ filename => "t/data/genotype_trial_upload/CASSAVA_GS_74Template.csv", chado_schema => $f->bcs_schema() });
     $p->load_plugin("ParseIGDFile");
@@ -54,7 +54,14 @@ for my $extension ("xls", "xlsx") {
 
     $results = $p->parse();
     $errors = $p->get_parse_errors();
-    ok($errors->{'error_messages'}->[0] eq "No Excel data found in file", 'check that accessions not in db');
+    my $expected = {
+        'error_messages' => [
+            'Required column stock_name is missing',
+            'Required column plot_number is missing',
+            'Required column block_number is missing'
+        ]
+    };
+    is_deeply($errors, $expected, 'check file format errors');
 
     $f->clean_up_db();
 }