search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/1.9/callsite.c

@@ -0,0 +1,234 @@
+#include <ruby.h>
+#include <ruby/st.h>
+#include <stdlib.h>
+
+#define DEBUG 0
+
+static char callsite_hook_set_p;
+
+typedef struct {
+  const char *sourcefile;
+  unsigned int sourceline;
+  VALUE curr_meth;
+} type_def_site;       
+
+static VALUE caller_info = 0;
+static VALUE method_def_site_info = 0;
+
+static int caller_stack_len = 1;
+
+static VALUE record_callsite_info(VALUE args) {
+  VALUE caller_ary;
+  VALUE curr_meth;
+  VALUE count_hash;
+  VALUE count;
+  VALUE *pargs = (VALUE *)args;
+
+  caller_ary = pargs[0];
+  curr_meth = pargs[1];
+  count_hash = rb_hash_aref(caller_info, curr_meth);
+  
+  if(TYPE(count_hash) != T_HASH) { 
+    /* Qnil, anything else should be impossible unless somebody's been
+     * messing with ObjectSpace */
+    count_hash = rb_hash_new();
+    rb_hash_aset(caller_info, curr_meth, count_hash);
+  }
+  
+  count = rb_hash_aref(count_hash, caller_ary);
+  
+  if(count == Qnil) 
+    count = INT2FIX(0);
+  
+  count = INT2FIX(FIX2UINT(count) + 1);
+  rb_hash_aset(count_hash, caller_ary, count);
+
+  if(DEBUG == 1)
+    printf("CALLSITE: %s -> %s   %d\n", RSTRING_PTR(rb_inspect(curr_meth)), RSTRING_PTR(rb_inspect(caller_ary)), FIX2INT(count));
+
+  return Qnil;
+}
+
+static VALUE record_method_def_site(VALUE args) {
+  type_def_site *pargs = (type_def_site *)args;
+  VALUE def_site_info;
+
+  if( RTEST(rb_hash_aref(method_def_site_info, pargs->curr_meth)) )
+    return Qnil;
+  
+  def_site_info = rb_ary_new();
+  rb_ary_push(def_site_info, rb_str_new2(pargs->sourcefile));
+  rb_ary_push(def_site_info, INT2NUM(pargs->sourceline+1));
+  rb_hash_aset(method_def_site_info, pargs->curr_meth, def_site_info);
+
+  if(DEBUG == 1)
+    printf("DEFSITE: %s:%d  for %s\n", pargs->sourcefile, pargs->sourceline+1, RSTRING_PTR(rb_inspect(pargs->curr_meth)));
+  
+  return Qnil;
+}
+
+static VALUE callsite_custom_backtrace(int lev) {
+  ID id;
+  VALUE klass;
+  VALUE klass_path;
+  VALUE eval_string;
+  
+  rb_frame_method_id_and_class(&id, &klass);
+  
+  if (id == ID_ALLOCATOR)
+    return Qnil;
+  
+  if (klass) {
+    if (TYPE(klass) == T_ICLASS) {
+      klass = RBASIC(klass)->klass;
+    }
+    else if (FL_TEST(klass, FL_SINGLETON)) {
+      klass = rb_iv_get(klass, "__attached__");
+    }
+  }
+  // rb_sprintf("\"#<Class:%s>\"", RSTRING_PTR(klass_path))
+  
+  /*
+  klass = class << klass; self end unless klass === eval("self", binding)
+  */
+  
+  klass_path = rb_class_path(klass);
+  VALUE reciever = rb_funcall(rb_binding_new(), rb_intern("eval"), 1, rb_str_new2("self"));
+  
+  if (rb_funcall(klass, rb_intern("=="), 1, reciever) == Qtrue) {
+    klass_path = rb_sprintf("\"#<Class:%s>\"", RSTRING_PTR(klass_path));
+    OBJ_FREEZE(klass_path);
+  }
+  
+  eval_string = rb_sprintf("caller[%d, 1].map do |line|\nmd = /^([^:]*)(?::(\\d+)(?::in `(?:block in )?(.*)'))?/.match(line)\nraise \"Bad backtrace format\" unless md\n[%s, md[3] ? md[3].to_sym : nil, md[1], (md[2] || '').to_i]\nend", lev, RSTRING_PTR(klass_path));
+  return rb_eval_string(RSTRING_PTR(eval_string));
+}
+
+static void coverage_event_callsite_hook(rb_event_flag_t event, VALUE node,  VALUE self, ID mid, VALUE klass) {
+  VALUE caller_ary;
+  VALUE curr_meth;
+  VALUE args[2];
+  int status;
+
+  caller_ary = callsite_custom_backtrace(caller_stack_len);
+
+  VALUE klass_path;
+  curr_meth = rb_ary_new();
+   
+  rb_frame_method_id_and_class(&mid, &klass);
+  
+  if (mid == ID_ALLOCATOR)
+    return; //Qnil;
+  if (klass) {
+    if (TYPE(klass) == T_ICLASS) {
+      klass = RBASIC(klass)->klass;
+    }
+    else if (FL_TEST(klass, FL_SINGLETON)) {
+      klass = rb_iv_get(klass, "__attached__");
+    }
+  }
+  
+  /*
+  klass = class << klass; self end unless klass === eval("self", binding)
+  */
+  
+  klass_path = rb_class_path(klass);
+  VALUE reciever = rb_funcall(rb_binding_new(), rb_intern("eval"), 1, rb_str_new2("self"));
+
+  if (rb_funcall(klass, rb_intern("=="), 1, reciever) == Qtrue) {
+    klass_path = rb_sprintf("#<Class:%s>", RSTRING_PTR(klass_path));
+    OBJ_FREEZE(klass_path);
+  }
+    
+  rb_ary_push(curr_meth, klass_path);
+  rb_ary_push(curr_meth, ID2SYM(mid));
+
+  args[0] = caller_ary;
+  args[1] = curr_meth;
+  rb_protect(record_callsite_info, (VALUE)args, &status);
+
+  if(!status) {
+    type_def_site args;
+
+    args.sourcefile = rb_sourcefile();
+    args.sourceline = rb_sourceline();
+    args.curr_meth = curr_meth;
+    rb_protect(record_method_def_site, (VALUE)&args, NULL);
+  }
+
+  if(status)
+    rb_gv_set("$!", Qnil);
+}
+
+static VALUE cov_install_callsite_hook(VALUE self) {
+  if(!callsite_hook_set_p) {
+    if(TYPE(caller_info) != T_HASH)
+      caller_info = rb_hash_new();
+    callsite_hook_set_p = 1;
+    VALUE something = 0;
+    rb_add_event_hook(coverage_event_callsite_hook, 
+                      RUBY_EVENT_CALL, something);
+    return Qtrue;
+  } 
+  else
+    return Qfalse;
+}
+
+static VALUE cov_remove_callsite_hook(VALUE self) {
+  if(!callsite_hook_set_p) 
+    return Qfalse;
+  else {
+    rb_remove_event_hook(coverage_event_callsite_hook);
+    callsite_hook_set_p = 0;
+    return Qtrue;
+  }
+}
+
+static VALUE cov_generate_callsite_info(VALUE self) {
+  VALUE ret;
+
+  ret = rb_ary_new();
+  rb_ary_push(ret, caller_info);
+  rb_ary_push(ret, method_def_site_info);
+  return ret;
+}
+
+static VALUE cov_reset_callsite(VALUE self) {
+  if(callsite_hook_set_p) {
+    rb_raise(rb_eRuntimeError, "Cannot reset the callsite info in the middle of a traced run.");
+    return Qnil;
+  }
+  
+  caller_info = rb_hash_new();
+  method_def_site_info = rb_hash_new();
+  return Qnil;
+}
+
+void Init_rcov_callsite() {
+  VALUE mRcov;
+  VALUE mRCOV__;
+  ID id_rcov = rb_intern("Rcov");
+  ID id_coverage__ = rb_intern("RCOV__");
+  // ID id_script_lines__ = rb_intern("SCRIPT_LINES__");
+  
+  if(rb_const_defined(rb_cObject, id_rcov)) 
+    mRcov = rb_const_get(rb_cObject, id_rcov);
+  else
+    mRcov = rb_define_module("Rcov");
+  
+  if(rb_const_defined(mRcov, id_coverage__))
+    mRCOV__ = rb_const_get_at(mRcov, id_coverage__);
+  else
+    mRCOV__ = rb_define_module_under(mRcov, "RCOV__");
+
+  callsite_hook_set_p = 0;
+  caller_info = rb_hash_new();
+  method_def_site_info = rb_hash_new();
+  rb_gc_register_address(&caller_info);
+  rb_gc_register_address(&method_def_site_info);
+  
+  rb_define_singleton_method(mRCOV__, "install_callsite_hook", cov_install_callsite_hook, 0);
+  rb_define_singleton_method(mRCOV__, "remove_callsite_hook", cov_remove_callsite_hook, 0);
+  rb_define_singleton_method(mRCOV__, "generate_callsite_info", cov_generate_callsite_info, 0);
+  rb_define_singleton_method(mRCOV__, "reset_callsite", cov_reset_callsite, 0);
+}

data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/1.9/rcovrt.c

@@ -0,0 +1,264 @@
+#include <ruby.h>
+#include <ruby/st.h>
+#include <stdlib.h>
+#include <assert.h>
+
+#define COVERAGE_DEBUG_EVENTS 0
+
+#define RCOVRT_VERSION_MAJOR 2
+#define RCOVRT_VERSION_MINOR 0
+#define RCOVRT_VERSION_REV   0
+
+static VALUE mRcov;
+static VALUE mRCOV__;
+static VALUE oSCRIPT_LINES__;
+static ID id_cover;
+static st_table* coverinfo = 0;
+static char coverage_hook_set_p;
+
+struct cov_array {
+  unsigned int len;
+  unsigned int *ptr;
+};
+
+static struct cov_array *cached_array = 0;
+static char *cached_file = 0; 
+
+static struct cov_array * coverage_increase_counter_uncached(char *sourcefile, unsigned int sourceline, char mark_only) {
+  struct cov_array *carray = NULL;
+ 
+  if(sourcefile == NULL) {
+    /* "can't happen", just ignore and avoid segfault */
+    return NULL;
+  } 
+  else if(!st_lookup(coverinfo, (st_data_t)sourcefile, (st_data_t*)&carray)) {
+    VALUE arr;
+
+    arr = rb_hash_aref(oSCRIPT_LINES__, rb_str_new2(sourcefile));
+    if(NIL_P(arr)) 
+      return 0;
+    rb_check_type(arr, T_ARRAY);
+    carray = calloc(1, sizeof(struct cov_array));
+    carray->ptr = calloc(RARRAY_LEN(arr), sizeof(unsigned int));
+    carray->len = RARRAY_LEN(arr);
+    st_insert(coverinfo, (st_data_t)strdup(sourcefile), (st_data_t) carray);
+  } 
+  else {
+    /* recovered carray, sanity check */
+    assert(carray && "failed to create valid carray");
+  }
+
+  if(mark_only) {
+    if(!carray->ptr[sourceline])
+      carray->ptr[sourceline] = 1;
+  } 
+  else {
+    if (carray && carray->len > sourceline) {
+      carray->ptr[sourceline]++;
+    }
+  }
+
+  return carray;
+}
+
+static void coverage_mark_caller() {
+  coverage_increase_counter_uncached(rb_sourcefile(), rb_sourceline(), 1);
+}
+
+static void coverage_increase_counter_cached(char *sourcefile, int sourceline) {
+  if(cached_file == sourcefile && cached_array && cached_array->len > sourceline) {
+    cached_array->ptr[sourceline]++;
+    return;
+  }
+  cached_file = sourcefile;
+  cached_array = coverage_increase_counter_uncached(sourcefile, sourceline, 0);
+}
+
+static void coverage_event_coverage_hook(rb_event_flag_t event, VALUE node, VALUE self, ID mid, VALUE klass) {
+  char *sourcefile;
+  unsigned int sourceline;
+  static unsigned int in_hook = 0;
+ 
+  if(in_hook) {
+    return;
+  }
+
+  in_hook++;
+
+  #if COVERAGE_DEBUG_EVENTS
+  do {
+    int status;
+    VALUE old_exception;
+    old_exception = rb_gv_get("$!");
+    rb_protect(rb_inspect, klass, &status);
+    if(!status) {
+      printf("EVENT: %d %s %s %s %d\n", event,
+             klass ? RSTRING(rb_inspect(klass))->ptr : "", 
+             mid ? (mid == ID_ALLOCATOR ? "ID_ALLOCATOR" : rb_id2name(mid))
+             : "unknown",
+             node ? node->nd_file : "", node ? nd_line(node) : 0);
+    } 
+    else {
+      printf("EVENT: %d %s %s %d\n", event,
+             mid ? (mid == ID_ALLOCATOR ? "ID_ALLOCATOR" : rb_id2name(mid)) 
+             : "unknown",
+             node ? node->nd_file : "", node ? nd_line(node) : 0);
+    }
+    rb_gv_set("$!", old_exception);
+  } while (0); 
+  #endif
+
+  if(event & RUBY_EVENT_C_CALL) {
+    coverage_mark_caller();
+  }
+  if(event & (RUBY_EVENT_C_CALL | RUBY_EVENT_C_RETURN | RUBY_EVENT_CLASS)) {
+    in_hook--;
+    return;
+  }
+  
+  sourcefile = rb_sourcefile();
+  sourceline = rb_sourceline();
+  
+  if (0 == sourceline || 0 == sourcefile) {
+    in_hook--;
+    return;
+  }
+  
+  coverage_increase_counter_cached(sourcefile, sourceline);
+  if(event & RUBY_EVENT_CALL)
+    coverage_mark_caller();
+  in_hook--;
+}
+
+static VALUE cov_install_coverage_hook(VALUE self) {
+  if(!coverage_hook_set_p) {
+    if(!coverinfo)
+      coverinfo = st_init_strtable();
+    coverage_hook_set_p = 1;
+    /* TODO: allow C_CALL too, since it's supported already
+     * the overhead is around ~30%, tested on typo */
+    VALUE holder = 0;
+    rb_add_event_hook(coverage_event_coverage_hook, 
+                      RUBY_EVENT_ALL & ~RUBY_EVENT_C_CALL &
+                      ~RUBY_EVENT_C_RETURN & ~RUBY_EVENT_CLASS, holder);
+    return Qtrue;
+  }
+  else
+    return Qfalse;
+}
+
+static int populate_cover(st_data_t key, st_data_t value, st_data_t cover) {
+  VALUE rcover;
+  VALUE rkey;
+  VALUE rval;
+  struct cov_array *carray;
+  unsigned int i;
+  
+  rcover = (VALUE)cover;
+  carray = (struct cov_array *) value;
+  rkey = rb_str_new2((char*) key);
+  rval = rb_ary_new2(carray->len);
+  for(i = 0; i < carray->len; i++)
+    rb_ary_push(rval, UINT2NUM(carray->ptr[i]));
+  
+  rb_hash_aset(rcover, rkey, rval);
+  
+  return ST_CONTINUE;
+}
+
+static int free_table(st_data_t key, st_data_t value, st_data_t ignored) {
+  struct cov_array *carray;
+  
+  carray = (struct cov_array *) value;
+  free((char *)key);
+  free(carray->ptr);
+  free(carray);
+  
+  return ST_CONTINUE;
+}
+
+static VALUE cov_remove_coverage_hook(VALUE self) {
+  if(!coverage_hook_set_p) 
+    return Qfalse;
+  else {
+    rb_remove_event_hook(coverage_event_coverage_hook);
+    coverage_hook_set_p = 0;
+    return Qtrue;
+  }
+}
+
+static VALUE cov_generate_coverage_info(VALUE self) {
+  VALUE cover;
+
+  if(rb_const_defined_at(mRCOV__, id_cover)) {
+    rb_mod_remove_const(mRCOV__, ID2SYM(id_cover));
+  }
+
+  cover = rb_hash_new();
+  if(coverinfo)
+    st_foreach(coverinfo, populate_cover, cover);
+  rb_define_const(mRCOV__, "COVER", cover);
+
+  return cover;
+}
+
+static VALUE cov_reset_coverage(VALUE self) {
+  if(coverage_hook_set_p) {
+    rb_raise(rb_eRuntimeError, "Cannot reset the coverage info in the middle of a traced run.");
+    return Qnil;
+  }
+
+  cached_array = 0;
+  cached_file = 0;
+  st_foreach(coverinfo, free_table, Qnil); 
+  st_free_table(coverinfo);
+  coverinfo = 0;
+
+  return Qnil;
+}
+
+static VALUE cov_ABI(VALUE self) {
+  VALUE ret;
+
+  ret = rb_ary_new();
+  rb_ary_push(ret, INT2FIX(RCOVRT_VERSION_MAJOR));
+  rb_ary_push(ret, INT2FIX(RCOVRT_VERSION_MINOR));
+  rb_ary_push(ret, INT2FIX(RCOVRT_VERSION_REV));
+
+  return ret;
+}
+
+void Init_rcovrt() {
+  ID id_rcov = rb_intern("Rcov");
+  ID id_coverage__ = rb_intern("RCOV__");
+  ID id_script_lines__ = rb_intern("SCRIPT_LINES__");
+  
+  id_cover = rb_intern("COVER");
+  
+  if(rb_const_defined(rb_cObject, id_rcov)) 
+    mRcov = rb_const_get(rb_cObject, id_rcov);
+  else
+    mRcov = rb_define_module("Rcov");
+  
+  if(rb_const_defined(mRcov, id_coverage__))
+    mRCOV__ = rb_const_get_at(mRcov, id_coverage__);
+  else
+    mRCOV__ = rb_define_module_under(mRcov, "RCOV__");
+  
+  if(rb_const_defined(rb_cObject, id_script_lines__))
+    oSCRIPT_LINES__ = rb_const_get(rb_cObject, rb_intern("SCRIPT_LINES__"));
+  else {
+    oSCRIPT_LINES__ = rb_hash_new();
+    rb_const_set(rb_cObject, id_script_lines__, oSCRIPT_LINES__);
+  }
+  
+  coverage_hook_set_p = 0;
+  
+  rb_define_singleton_method(mRCOV__, "install_coverage_hook", cov_install_coverage_hook, 0);
+  rb_define_singleton_method(mRCOV__, "remove_coverage_hook", cov_remove_coverage_hook, 0);
+  rb_define_singleton_method(mRCOV__, "generate_coverage_info", cov_generate_coverage_info, 0);
+  rb_define_singleton_method(mRCOV__, "reset_coverage", cov_reset_coverage, 0);
+  rb_define_singleton_method(mRCOV__, "ABI", cov_ABI, 0);
+  
+  Init_rcov_callsite();
+}