| 1 | // ================================================================ // |
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| 2 | // // |
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| 3 | // File : GenomeImport.cxx // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Coded by Ralf Westram (coder@reallysoft.de) in November 2006 // |
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| 7 | // Institute of Microbiology (Technical University Munich) // |
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| 8 | // http://www.arb-home.de/ // |
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| 9 | // // |
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| 10 | // ================================================================ // |
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| 11 | |
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| 12 | #include "tools.h" |
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| 13 | #include "DBwriter.h" |
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| 14 | |
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| 15 | #include <cerrno> |
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| 16 | #define AW_RENAME_SKIP_GUI |
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| 17 | #include <AW_rename.hxx> |
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| 18 | #include <aw_question.hxx> |
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| 19 | #include <arb_stdstr.h> |
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| 20 | #include <arb_file.h> |
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| 21 | #include <arb_diff.h> |
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| 22 | |
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| 23 | using namespace std; |
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| 24 | |
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| 25 | GB_ERROR GI_importGenomeFile(ImportSession& session, const char *file_name, const char *ali_name) { |
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| 26 | GB_ERROR error = NULp; |
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| 27 | try { |
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| 28 | if (strcmp(ali_name, "ali_genom") != 0) throw "Alignment has to be 'ali_genom'"; |
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| 29 | |
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| 30 | FILE *in = fopen(file_name, "rb"); |
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| 31 | if (!in) throw GBS_global_string("Can't read file '%s' (Reason: %s)", file_name, strerror(errno)); |
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| 32 | |
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| 33 | BufferedFileReader flatfile(file_name, in); |
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| 34 | flatfile.showFilenameInLineError(false); |
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| 35 | |
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| 36 | DBwriter db_writer(session, ali_name); |
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| 37 | |
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| 38 | SmartPtr<Importer> importer; |
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| 39 | { |
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| 40 | string line; |
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| 41 | if (!flatfile.getLine(line)) throw flatfile.lineError("File is empty"); |
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| 42 | |
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| 43 | if (beginsWith(line, "LOCUS")) importer = new GenebankImporter(flatfile, db_writer); |
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| 44 | else if (beginsWith(line, "ID")) importer = new EmblImporter (flatfile, db_writer); |
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| 45 | else throw flatfile.lineError("Wrong format. Expected 'LOCUS' or 'ID'"); |
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| 46 | |
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| 47 | flatfile.backLine(line); |
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| 48 | } |
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| 49 | |
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| 50 | importer->import(); |
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| 51 | } |
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| 52 | catch (const string &err) { error = GBS_static_string(err.c_str()); } |
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| 53 | catch (const char *err) { error = err; } |
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| 54 | catch (...) { error = "Unknown exception during import (program error)"; } |
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| 55 | return error; |
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| 56 | } |
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| 57 | |
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| 58 | |
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| 59 | |
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| 60 | |
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| 61 | ImportSession::ImportSession(GBDATA *gb_species_data_, int estimated_genomes_count) |
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| 62 | : gb_species_data(gb_species_data_) |
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| 63 | { |
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| 64 | und_species = new UniqueNameDetector(gb_species_data, estimated_genomes_count); |
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| 65 | ok_to_ignore_wrong_start_codon = new AW_repeated_question; |
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| 66 | } |
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| 67 | |
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| 68 | ImportSession::~ImportSession() { |
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| 69 | delete ok_to_ignore_wrong_start_codon; |
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| 70 | delete und_species; |
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| 71 | DBwriter::deleteStaticData(); |
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| 72 | } |
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| 73 | |
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| 74 | // -------------------------------------------------------------------------------- |
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| 75 | |
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| 76 | #ifdef UNIT_TESTS |
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| 77 | #ifndef TEST_UNIT_H |
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| 78 | #include <test_unit.h> |
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| 79 | #endif |
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| 80 | |
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| 81 | // #define TEST_AUTO_UPDATE // uncomment to auto-update expected result-database |
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| 82 | |
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| 83 | void TEST_SLOW_import_genome_flatfile() { |
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| 84 | GB_shell shell; |
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| 85 | GBDATA *gb_main = GB_open("nosuch.arb", "wc"); |
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| 86 | |
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| 87 | // import flatfile |
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| 88 | { |
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| 89 | GB_transaction ta(gb_main); |
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| 90 | GBDATA *gb_species_data = GBT_find_or_create(gb_main, "species_data", 7); |
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| 91 | |
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| 92 | ImportSession isess(gb_species_data, 1); |
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| 93 | TEST_EXPECT_NO_ERROR(GI_importGenomeFile(isess, "AB735678.txt", "ali_genom")); |
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| 94 | } |
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| 95 | |
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| 96 | // save database and compare with expectation |
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| 97 | { |
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| 98 | const char *savename = "AB735678.arb"; |
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| 99 | const char *expected = "AB735678_expected.arb"; |
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| 100 | |
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| 101 | TEST_EXPECT_NO_ERROR(GB_save_as(gb_main, savename, "a")); |
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| 102 | #if defined(TEST_AUTO_UPDATE) |
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| 103 | TEST_COPY_FILE(savename, expected); |
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| 104 | #else |
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| 105 | TEST_EXPECT_TEXTFILES_EQUAL(savename, expected); |
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| 106 | #endif // TEST_AUTO_UPDATE |
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| 107 | TEST_EXPECT_ZERO_OR_SHOW_ERRNO(GB_unlink(savename)); |
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| 108 | } |
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| 109 | |
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| 110 | GB_close(gb_main); |
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| 111 | } |
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| 112 | |
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| 113 | #endif // UNIT_TESTS |
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| 114 | |
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| 115 | // -------------------------------------------------------------------------------- |
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