ARB
ptclean.cxx
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1 // ================================================================= //
2 // //
3 // File : ptclean.cxx //
4 // Purpose : prepare db for ptserver/ptpan //
5 // //
6 // Coded by Ralf Westram (coder@reallysoft.de) in September 2011 //
7 // Institute of Microbiology (Technical University Munich) //
8 // http://www.arb-home.de/ //
9 // //
10 // ================================================================= //
11 
12 #include "ptclean.h"
13 #include <arbdbt.h>
14 #include <arb_progress.h>
15 #include <arb_diff.h>
16 
17 #define pt_assert(cond) arb_assert(cond)
18 
19 class EntryRemover : virtual Noncopyable {
20  // deletes all entries from DB, which are of no use for PTSERVER
21 
22  GBDATA *gb_main;
23  GB_transaction ta;
24  char *ali_name;
25 
26  mutable arb_progress progress;
27 
28  enum Need {
29  NONE,
30  ALL,
31  SOME_OF_ROOT,
32  SOME_OF_SPECIES_DATA,
33  SOME_OF_EXTENDED_DATA,
34  SOME_OF_SPECIES,
35  SOME_OF_EXTENDED,
36  SOME_OF_ALI_CONTAINER, // below species or SAI
37  };
38 
39  Need data_needed(GBDATA *gbd, const char *keyname, Need from) const {
40  switch (from) {
41  case SOME_OF_ROOT:
42  if (strcmp(keyname, GB_SYSTEM_FOLDER)== 0) return ALL;
43  if (strcmp(keyname, "genom_db") == 0) return ALL;
44  if (strcmp(keyname, "gene_map") == 0) return ALL;
45  if (strcmp(keyname, "species_data") == 0) return SOME_OF_SPECIES_DATA;
46  if (strcmp(keyname, "extended_data") == 0) return SOME_OF_EXTENDED_DATA;
47  if (strcmp(keyname, "presets") == 0) return ALL;
48  break;
49 
50  case SOME_OF_SPECIES_DATA:
51  if (strcmp(keyname, "species") == 0) {
52  progress.inc();
53  return SOME_OF_SPECIES;
54  }
55  break;
56 
57  case SOME_OF_EXTENDED_DATA:
58  if (strcmp(keyname, "extended") == 0) {
59  const char *sainame = GBT_get_name_or_description(gbd);
60  if (strcmp(sainame, "ECOLI") == 0) return SOME_OF_EXTENDED;
61  if (strcmp(sainame, "HELIX") == 0) return SOME_OF_EXTENDED;
62  if (strcmp(sainame, "HELIX_NR") == 0) return SOME_OF_EXTENDED;
63  }
64  break;
65 
66  case SOME_OF_SPECIES:
67  if (strcmp(keyname, "abspos") == 0) return ALL;
68  if (strcmp(keyname, "start") == 0) return ALL;
69  if (strcmp(keyname, "stop") == 0) return ALL;
71 
72  case SOME_OF_EXTENDED:
73  if (strcmp(keyname, "name") == 0) return ALL;
74  if (strcmp(keyname, "acc") == 0) return ALL;
75  if (strcmp(keyname, "full_name") == 0) return ALL;
76  if (strcmp(keyname, ali_name) == 0) return SOME_OF_ALI_CONTAINER;
77  break;
78 
79  case SOME_OF_ALI_CONTAINER:
80  if (strcmp(keyname, "data") == 0) return ALL;
81  break;
82 
83  case NONE: pt_assert(0); break;
84  case ALL: pt_assert(0); break;
85  }
86 
87  return NONE;
88  }
89 
90  GB_ERROR del_child(GBDATA *gb_entry, const char *keyname, Need from) {
92  Need need = data_needed(gb_entry, keyname, from);
93  switch (need) {
94  case NONE: error = GB_delete(gb_entry); break;
95  case ALL: break;
96  default: error = del_subentries(gb_entry, need); break;
97  }
98  return error;
99  }
100  GB_ERROR del_subentries(GBDATA *gb_father, Need from) {
101  GB_ERROR error = NULp;
102  if (!GB_is_temporary(gb_father)) {
103  GBDATA *gb_next_child = NULp;
104  for (GBDATA *gb_child = GB_child(gb_father); gb_child && !error; gb_child = gb_next_child) {
105  gb_next_child = GB_nextChild(gb_child);
106  const char *key = GB_read_key_pntr(gb_child);
107  error = del_child(gb_child, key, from);
108  }
109  }
110  return error;
111  }
112 
113 public:
114  EntryRemover(GBDATA *gb_main_)
115  : gb_main(gb_main_),
116  ta(gb_main),
117  ali_name(GBT_get_default_alignment(gb_main)),
118  progress("Remove unused database entries", GBT_get_species_count(gb_main))
119  {}
121  free(ali_name);
122  progress.done();
123  }
124 
125  GB_ERROR del_unwanted_entries() { return del_subentries(gb_main, SOME_OF_ROOT); }
126 };
127 
129  return EntryRemover(gb_main).del_unwanted_entries();
130 }
131 
134  if (!error) {
135  GB_topSecurityLevel unsecured(gb_main);
136  error = clean_ptserver_database(gb_main);
137  }
138  return error;
139 }
140 // --------------------------------------------------------------------------------
141 
142 #ifdef UNIT_TESTS
143 #ifndef TEST_UNIT_H
144 #include <test_unit.h>
145 #endif
146 #include <arb_file.h>
147 
148 void TEST_SLOW_ptclean() {
149  GB_shell shell;
150  GBDATA *gb_main = GB_open("TEST_pt_src.arb", "rw");
151  const char *saveas = "TEST_pt_cleaned.arb";
152 
153  TEST_REJECT_NULL(gb_main);
155  TEST_EXPECT_NO_ERROR(GB_save_as(gb_main, saveas, "a"));
156  GB_close(gb_main);
157 
158 // #define TEST_AUTO_UPDATE
159 #if defined(TEST_AUTO_UPDATE)
160  TEST_COPY_FILE("TEST_pt_cleaned.arb", "TEST_pt_cleaned_expected.arb");
161 #else
162  TEST_EXPECT_TEXTFILES_EQUAL("TEST_pt_cleaned.arb", "TEST_pt_cleaned_expected.arb");
163 #endif
165 }
166 TEST_PUBLISH(TEST_SLOW_ptclean);
167 
168 #endif // UNIT_TESTS
169 
170 // --------------------------------------------------------------------------------
171 
const char * GB_ERROR
Definition: arb_core.h:25
#define GB_SYSTEM_FOLDER
Definition: arbdb.h:27
GBDATA * GB_open(const char *path, const char *opent)
Definition: ad_load.cxx:1363
GBDATA * GB_child(GBDATA *father)
Definition: adquery.cxx:322
bool GB_is_temporary(GBDATA *gbd)
Definition: arbdb.cxx:2277
GB_ERROR del_unwanted_entries()
Definition: ptclean.cxx:125
#define pt_assert(cond)
Definition: ptclean.cxx:17
int GB_unlink(const char *path)
Definition: arb_file.cxx:188
GB_ERROR GB_delete(GBDATA *&source)
Definition: arbdb.cxx:1880
#define TEST_PUBLISH(testfunction)
Definition: test_unit.h:1484
GB_CSTR GB_read_key_pntr(GBDATA *gbd)
Definition: arbdb.cxx:1630
GB_ERROR GB_save_as(GBDATA *gbd, const char *path, const char *savetype)
#define TEST_REJECT_NULL(n)
Definition: test_unit.h:1309
static void error(const char *msg)
Definition: mkptypes.cxx:96
#define TEST_EXPECT_ZERO_OR_SHOW_ERRNO(iocond)
Definition: test_unit.h:1079
EntryRemover(GBDATA *gb_main_)
Definition: ptclean.cxx:114
GB_ERROR cleanup_ptserver_database(GBDATA *gb_main)
Definition: ptclean.cxx:132
GB_ERROR clean_ptserver_database(GBDATA *gb_main)
Definition: ptclean.cxx:128
#define TEST_EXPECT_NO_ERROR(call)
Definition: test_unit.h:1107
#define NULp
Definition: cxxforward.h:97
char * GBT_get_default_alignment(GBDATA *gb_main)
Definition: adali.cxx:675
GB_ERROR GB_request_undo_type(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT_TODO
Definition: adindex.cxx:718
GBDATA * GB_nextChild(GBDATA *child)
Definition: adquery.cxx:326
#define FALLTHROUGH
Definition: cxxforward.h:107
long GBT_get_species_count(GBDATA *gb_main)
Definition: aditem.cxx:203
GBDATA * gb_main
Definition: adname.cxx:33
GB_CSTR GBT_get_name_or_description(GBDATA *gb_item)
Definition: aditem.cxx:437
#define TEST_EXPECT_TEXTFILES_EQUAL(fgot, fwant)
Definition: test_unit.h:1395
void GB_close(GBDATA *gbd)
Definition: arbdb.cxx:625