t/CXGN/Metadata/dbversion.t

   1 #!/usr/bin/perl
   2
   3 =head1 NAME
   4
   5   dbversion.t
   6   A piece of code to test the CXGN::Metadata::Dbversion module
   7
   8 =cut
   9
  10 =head1 SYNOPSIS
  11
  12  perl Dbversion.t
  13
  14  Note: To run the complete test the database connection should be done as
  15        postgres user
  16  (web_usr have not privileges to insert new data into the sed tables)
  17
  18  prove Dbversion.t
  19
  20  this test need some environment variables:
  21
  22    export METADATA_TEST_METALOADER='metaloader user'
  23    export METADATA_TEST_DBDSN='database dsn as:
  24     dbi:DriverName:database=database_name;host=hostname;port=port'
  25
  26    example:
  27     export METADATA_TEST_DBDSN='dbi:Pg:database=sandbox;host=localhost;'
  28
  29    export METADATA_TEST_DBUSER='database user with insert permissions'
  30    export METADATA_TEST_DBPASS='database password'
  31
  32 =head1 DESCRIPTION
  33
  34  This script check 33 variables to test the right operation of the
  35  CXGN::Metadata::DBipath module:
  36
  37  + Test from 1 to 3 - use modules.
  38  + Test from 4 to 6 - BASIC SET/GET FUNCTIONS.
  39  + Test from 7 to 14 - STORE FUNCTION.
  40  + Test from 15 to 18 - OBSOLETE FUNCTION.
  41  + Test 19 and 20 - GET PATCH NUMBER METHOD.
  42  + Test 21 and 22 - EXISTS DBPATCH METHOD.
  43  + Test from 23 to 29 - CHECKING PREVIOUS DBPATCHES METHOD.
  44
  45 =cut
  46
  47 =head1 AUTHORS
  48
  49  Aureliano Bombarely Gomez
  50  (ab782@cornell.edu)
  51
  52 =cut
  53
  54
  55 use strict;
  56 use warnings;
  57
  58 use Data::Dumper;
  59 use Test::More; #qw | no_plan |; # while developing the tests
  60 use Test::Exception;
  61
  62 use CXGN::DB::Connection;
  63
  64 ## The tests still need search_path
  65
  66 my @schema_list = ('metadata', 'public');
  67 my $schema_list = join(',', @schema_list);
  68 my $set_path = "SET search_path TO $schema_list";
  69
  70 ## First check env. variables and connection
  71
  72 BEGIN {
  73
  74     ## Env. variables have been changed to use biosource specific ones
  75
  76     my @env_variables = qw/METADATA_TEST_METALOADER METADATA_TEST_DBDSN METADATA_TEST_DBUSER METADATA_TEST_DBPASS/;
  77
  78     ## RESET_DBSEQ is an optional env. variable, it doesn't need to check it
  79
  80     for my $env (@env_variables) {
  81         unless (defined $ENV{$env}) {
  82             plan skip_all => "Environment variable $env not set, aborting";
  83         }
  84     }
  85
  86     eval {
  87         CXGN::DB::Connection->new(
  88                                    $ENV{METADATA_TEST_DBDSN},
  89                                    $ENV{METADATA_TEST_DBUSER},
  90                                    $ENV{METADATA_TEST_DBPASS},
  91                                    {on_connect_do => $set_path}
  92                                  );
  93     };
  94
  95     if ($@ =~ m/DBI connect/) {
  96
  97         plan skip_all => "Could not connect to database";
  98     }
  99
 100     plan tests => 23;
 101 }
 102
 103 BEGIN {
 104     use_ok('CXGN::Metadata::Schema');               ## TEST1
 105     use_ok('CXGN::Metadata::Dbversion');            ## TEST2
 106     use_ok('CXGN::Metadata::Metadbdata');           ## TEST3
 107 }
 108
 109
 110 #if we cannot load the CXGN::Metadata::Schema module, no point in continuing
 111 CXGN::Metadata::Schema->can('connect')
 112     or BAIL_OUT('could not load the CXGN::Metadata::Schema module');
 113
 114 ## Prespecified variable
 115
 116 my $metadata_creation_user = $ENV{METADATA_TEST_METALOADER};
 117
 118 ## The biosource schema contain all the metadata classes so don't need to create another Metadata schema
 119 ## CXGN::DB::DBICFactory is obsolete, it has been replaced by CXGN::Metadata::Schema
 120
 121 my $schema = CXGN::Metadata::Schema->connect( $ENV{METADATA_TEST_DBDSN},
 122                                                $ENV{METADATA_TEST_DBUSER},
 123                                                $ENV{METADATA_TEST_DBPASS},
 124                                                {on_connect_do => $set_path});
 125
 126
 127 $schema->txn_begin();
 128
 129
 130 ## Get the last values
 131 my %nextvals = $schema->get_nextval();
 132 my $last_metadata_id = $nextvals{'md_metadata'};
 133 my $last_dbversion_id = $nextvals{'md_dbversion'};
 134
 135 ## Create a empty metadata object to use in the database store functions
 136 my $metadbdata = CXGN::Metadata::Metadbdata->new($schema, $metadata_creation_user);
 137 my $creation_date = $metadbdata->get_object_creation_date();
 138 my $creation_user_id = $metadbdata->get_object_creation_user_by_id();
 139
 140 ## FIRST TEST BLOCK (TEST FROM 4 TO 6)
 141 ## This is the first group of tests, to check if an empty object can store and after can return the data
 142 ## Create a new empty object;
 143
 144 my $dbversion = CXGN::Metadata::Dbversion->new($schema, undef);
 145
 146 ## Load of the eight different parameters for an empty object using a hash with keys=root name for tha function and
 147  ## values=value to test
 148
 149 my %test_values_for_empty_object=( dbversion_id       => $last_dbversion_id+1,
 150                                    patch_name         => '9999_patch_test',
 151                                    patch_description  => 'this is a test for description',
 152                                   );
 153
 154 ## Load the data in the empty object
 155 my @function_keys = sort keys %test_values_for_empty_object;
 156 foreach my $rootfunction (@function_keys) {
 157     my $setfunction = 'set_' . $rootfunction;
 158     if ($rootfunction eq 'dbversion_id') {
 159         $setfunction = 'force_set_' . $rootfunction;
 160     }
 161     $dbversion->$setfunction($test_values_for_empty_object{$rootfunction});
 162 }
 163 ## Get the data from the object and store in two hashes. The first %getdata with keys=root_function_name and
 164  ## value=value_get_from_object and the second, %testname with keys=root_function_name and values=name for the test.
 165
 166 my (%getdata, %testnames);
 167 foreach my $rootfunction (@function_keys) {
 168     my $getfunction = 'get_'.$rootfunction;
 169     my $data = $dbversion->$getfunction();
 170     $getdata{$rootfunction} = $data;
 171     my $testname = 'BASIC SET/GET FUNCTION for ' . $rootfunction.' test';
 172     $testnames{$rootfunction} = $testname;
 173 }
 174
 175 ## And now run the test for each function and value
 176
 177 foreach my $rootfunction (@function_keys) {
 178     is($getdata{$rootfunction}, $test_values_for_empty_object{$rootfunction}, $testnames{$rootfunction})
 179         or diag "Looks like this failed.";
 180 }
 181
 182 ### SECOND TEST BLOCK
 183 ### Use of store functions.
 184
 185 eval {
 186
 187     ### It will create a new object based in dbipath and it will store (TEST 7 to 9)
 188     my $dbversion2 = CXGN::Metadata::Dbversion->new($schema);
 189     $dbversion2->set_patch_name('9998_patch_test');
 190     $dbversion2->set_patch_description('This is a description test');
 191     $dbversion2->store($metadbdata);
 192
 193     is($dbversion2->get_dbversion_id(), $last_dbversion_id+1, 'STORE FUNCTION test, checking dbversion_id')
 194         or diag "Looks like this failed";
 195     is($dbversion2->get_patch_name(), '9998_patch_test', 'STORE FUNCTION test, checking patch_name')
 196         or diag "Looks like this failed";
 197     is($dbversion2->get_patch_description(), 'This is a description test', 'STORE FUNCTION test, checking patch_description')
 198         or diag "Looks like this failed";
 199
 200     ## Get the metadbdata and test obsolete (TEST 10 and 11)
 201
 202     my $dbv_md = $dbversion2->get_metadbdata();
 203     is($dbv_md->get_metadata_id(), $last_metadata_id+1, 'STORE FUNCTION (as insert) and GET METADATA test, checking metadata_id')
 204         or diag "Looks like this failed";
 205
 206     is($dbversion2->is_obsolete(), 0, 'IS OBSOLETE FUNCTION test, checking boolean false')
 207         or diag "Looks like this failed";
 208
 209     ## Testing new object based in path_name (TEST 12)
 210     my $dbversion3 = CXGN::Metadata::Dbversion->new($schema);
 211     $dbversion3->set_patch_name('9999_patch_test');
 212     $dbversion3->set_patch_description('This is a description test');
 213     $dbversion3->store($metadbdata);
 214
 215     my $dbversion4 = CXGN::Metadata::Dbversion->new_by_patch_name($schema, '9999_patch_test');
 216     is($dbversion4->get_dbversion_id(), $last_dbversion_id+2, 'CONTRUCTOR new_by_patch_name TEST, checking dbversion_id')
 217         or diag "Looks like this failed";
 218
 219     ## Testing modification and storing (TEST 13 and 14)
 220     $dbversion4->set_patch_description('This is another description test');
 221     $dbversion4->store($metadbdata);
 222
 223     my $dbversion5 = CXGN::Metadata::Dbversion->new($schema, $dbversion4->get_dbversion_id() );
 224     is($dbversion5->get_patch_description(), 'This is another description test', 'STORE FUNCTION (as update) test, checking patch_descr')
 225         or diag "Looks like this failed";
 226
 227     my $dbv_md2 = $dbversion4->get_metadbdata();
 228     is($dbv_md2->get_metadata_id(), $last_metadata_id+2, 'STORE FUNCTION (as update) and GET METADATA test, checking metadata_id')
 229         or diag "Looks like this failed";
 230
 231     ## Testing obsolete and revert obsolete something (TEST 15 to 18)
 232     $dbversion5->obsolete($metadbdata, 'Obsolete test');
 233     is($dbversion5->is_obsolete(), 1, 'OBSOLETE FUNCTION test, checking boolean with is_obsolete() method')
 234         or diag "Looks like this failed";
 235
 236     is($dbversion5->get_metadbdata()->get_metadata_id(), $last_metadata_id+3, 'OBSOLETE FUNTION test, checking new metadata_id')
 237         or diag "Looks like this failed";
 238
 239     $dbversion5->obsolete($metadbdata, 'Obsolete test', 'REVERT');
 240     is($dbversion5->is_obsolete(), 0, 'REVERT OBSOLETE FUNCTION test, checking boolean with is_obsolete() method')
 241         or diag "Looks like this failed";
 242
 243     is($dbversion5->get_metadbdata()->get_metadata_id(), $last_metadata_id+4, 'REVERT OBSOLETE FUNTION test, checking new metadata_id')
 244         or diag "Looks like this failed";
 245
 246     ##############################################################################
 247     ## DEPRECATED METHODS (get_patch_number and check_previous_dbpatches)      ###
 248     ##############################################################################
 249
 250     #### Cheking a get_patch_number (TEST 19 and 20)
 251     ## my $patch_number = $dbversion5->get_patch_number();
 252     ## is ($patch_number, 9999, 'GET PATCH NUMBER METHOD, checking patch number')
 253     ##  or diag "Looks like this failed";
 254
 255     #### It will test too with a patch name with zeros
 256
 257     my $dbversion6 = CXGN::Metadata::Dbversion->new($schema);
 258     $dbversion6->set_patch_name('00023_patch_test');
 259
 260     ## is($dbversion6->get_patch_number(), 23, 'GET PATCH NUMBER METHOD, cheking patch number with zeros')
 261     ##  or diag "Looks like this failed";
 262
 263     ## Using exists dbpatches (TEST 19 and 20)
 264
 265     is($dbversion6->exists_dbpatch('9999_patch_test'), 1, 'EXISTS DBPATCH METHOD, checking boolean for a true value')
 266         or diag "Looks like this failed";
 267     is($dbversion6->exists_dbpatch('0023_patch_test'), 0, 'EXISTS DBPATCH METHOD, cheking boolean for a false value')
 268         or diag "Looks like this failed";
 269
 270     ## DEPRECATED METHOD
 271     #### Using checking previous dbpatches. It will check this function in three different ways:
 272
 273     ## ## 1-With a specific value, 9999_patch_test. It should return 9998 keys into the hash, perhaps more if exists
 274     ## ## patch names with the same patch number, for example if during this test exists an original 9998_something
 275
 276     ## ## (TEST 23 to 26)
 277
 278     ## my %check_previous1 = $dbversion6->check_previous_dbpatches('9999_patch_test');
 279     ## my $key_n1 = scalar(keys %check_previous1);
 280
 281     ## It can have more than one patch with the same number, to fix that.
 282
 283     ## my %rep;
 284     ## my $same_c = 0;
 285     ## foreach my $p (keys %check_previous1) {
 286     ##  if ($p =~ m/^(\d+)/) {
 287     ##     my $number = $1;
 288
 289     ##     if (exists $rep{$number}) {
 290     ##        $same_c++;
 291     ##     }
 292     ##     else {
 293     ##       $rep{$number} = 1;
 294     ##     }
 295     ##   }
 296     ## }
 297
 298     ## my $expected_key_n = 9998;
 299     ## if ($last_dbversion_id > 9998) {
 300     ##  $expected_key_n = 9999;
 301     ## }
 302     ## $expected_key_n += $same_c;
 303
 304     ## is($key_n1, $expected_key_n, 'CHECKING PREVIOUS DBPATCHES METHOD, checking number of previous patch numbers (for 9999_patch_test)')
 305     ##  or diag "Looks like this failed";
 306
 307     ## is($check_previous1{'9998_patch_test'}, 1, 'CHECKING PREVIOUS DBPATCHES METHOD, checking boolean for a known patch name (9998)')
 308     ## or diag "Looks like this failed";
 309
 310     ## is($check_previous1{'0000_patch_test'}, undef, 'CHECKING PREVIOUS DBPATCHES METHOD, checking boolean for a unknown patch name (0000)')
 311     ## or diag "Looks like this failed";
 312
 313     ## if ($last_dbversion_id < 9997) {
 314
 315         ## 9997 should be a unknown number only if last_dbversion_id < 9997
 316         ## is($check_previous1{'9997'}, 0, 'CHEKING PREVIOUS DBPATCHES METHOD, checking boolean for a unknown patch number (9997)')
 317         ##    or diag "Looks like this failed";
 318
 319     ##   }
 320     ## else {
 321
 322         ## It still should do the same number of test.. so
 323     ##  is($check_previous1{'9997'}, undef, 'CHEKING PREVIOUS DBPATCHES METHOD, checking boolean for a unknown patch name (9997)')
 324     ##      or diag "Looks like this failed";
 325     ##  }
 326
 327      ## 2- Without any specific value, in this case should take the $patch_name for $dbversion6.
 328      ## We don't know how many of the db_patches exists from 22 to 1 but we know that there are 22 patch numbers
 329
 330      ## TEST 27
 331
 332     ## my %check_previous2 = $dbversion6->check_previous_dbpatches();
 333     ## is(scalar( keys %check_previous2), 22, 'CHECKING PREVIOUS DBPATCHES METHOD, checking previous patch n for patch 0023_patch_test')
 334     ##  or diag "Looks like this failed";
 335
 336
 337     ## 3- In an object without any patch_name, it should take the last_dbversion_id (9999_test_patch for this case)
 338
 339     ## TEST 28 and 29
 340
 341     ## my $empty_dbversion = CXGN::Metadata::Dbversion->new($schema);
 342     ## my %check_previous3 = $empty_dbversion->check_previous_dbpatches();
 343
 344     ## is($key_n1, $expected_key_n, 'CHECKING PREVIOUS DBPATCHES METHOD, checking number of previous patch numbers in EMPTY OBJ')
 345     ##  or diag "Looks like this failed";
 346
 347     ## is($check_previous1{'9998_patch_test'}, 1, 'CHECKING PREVIOUS DBPATCHES METHOD, checking boolean for a known patch name in EMPTY OBJ')
 348     ##  or diag "Looks like this failed";
 349
 350     ## Testing the complete checking
 351
 352     my $dbversion7 = CXGN::Metadata::Dbversion->new($schema);
 353
 354     ## Check that this patch has been executed before (test 30)
 355
 356     throws_ok { $dbversion7->complete_checking({ patch_name => '9998_patch_test'}) } qr/DBPATCH EXECUTION ERROR/,
 357                 "TESTING DIE for complete_checking when use patch_name";
 358
 359     ## Check that other previous patches by default (using patch number) has not been runned (TEST 31) ## DEPRECATED ##
 360
 361     ## throws_ok { $dbversion7->complete_checking({ patch_name => '9999_other_test'}) } qr/PREVIOUS DB_PATCH by default ERROR/,
 362     ##          "TESTING DIE for complete_checking when previous patches that don't exists";
 363
 364     ## Check a list of previous patches using a list (TEST 32)
 365
 366     throws_ok { $dbversion7->complete_checking({ patch_name => '9999_other_test', prepatch => ['9998_alt_test'] }) }
 367                 qr/PREVIOUS DB_PATCH ERROR/,
 368                 "TESTING DIE for complete_checking when use patch_name";
 369
 370     ## Test when pass the complete_cheking (TEST 33)
 371
 372     lives_ok { $dbversion7->complete_checking({ patch_name => '9999_other_test', prepatch => ['9998_patch_test'] }) }
 373                "TESTING DON'T DIE for complete_checking when pass the check";
 374
 375
 376 };  ## End of the eval function
 377
 378 if ($@) {
 379     print "\nEVAL ERROR:\n\n$@\n";
 380 }
 381
 382 ## RESTORING THE ORIGINAL STATE IN THE DATABASE
 383 ## To restore the original state in the database, rollback (it is in a transaction) and set the table_sequence values.
 384
 385 $schema->txn_rollback();
 386
 387 ## The transaction change the values in the sequence, so if we want set the original value, before the changes
 388  ## we have two options:
 389   ##     1) SELECT setval (<sequence_name>, $last_value_before_change, true); that said, ok your last true value was...
 390    ##    2) SELECT setval (<sequence_name>, $last_value_before_change+1, false); It is false that your last value was ... so the
 391     ##      next time take the value before this.
 392      ##
 393       ##   The option 1 leave the seq information in a original state except if there aren't any value in the seq, that it is
 394        ##   more as the option 2
 395
 396 ## The test does not reset the db sequences anymore.
 397
 398 ####
 399 1; #
 400 ####