PluginSpec ModulesPluginDatabase::lookupProvides (std::string const & which) const
{
// check if plugin itself exists:
if (status (PluginSpec (which)) == real)
{
return PluginSpec (which);
}
std::string errors;
std::vector<std::string> allPlugins = listAllPlugins ();
std::map<int, PluginSpec> foundPlugins;
for (auto const & plugin : allPlugins)
{
// TODO: make sure (non)-equal plugins (i.e. with same/different contract) are handled correctly
try
{
// TODO: support for generic plugins with config
std::istringstream ss (
lookupInfo (PluginSpec (plugin, KeySet (5, *Key ("system/module", KEY_VALUE,
"this plugin was loaded without a config", KEY_END),
KS_END)),
"provides"));
std::string provide;
while (ss >> provide)
{
if (provide == which)
{
int s = calculateStatus (lookupInfo (
PluginSpec (plugin, KeySet (5, *Key ("system/module", KEY_VALUE,
"this plugin was loaded without a config", KEY_END),
KS_END)),
"status"));
foundPlugins.insert (std::make_pair (s, PluginSpec (plugin)));
}
}
}
catch (std::exception const & e)
{
errors += e.what ();
errors += ",";
} // assume not loaded
}
if (foundPlugins.empty ())
{
if (!errors.empty ())
throw NoPlugin ("No plugin that provides " + which + " could be found, got errors: " + errors);
else
throw NoPlugin ("No plugin that provides " + which + " could be found");
}
// the largest element of the map contains the best-suited plugin:
return foundPlugins.rbegin ()->second;
}
std::map<int, PluginSpec> ModulesPluginDatabase::lookupAllProvidesWithStatus (std::string const & which) const
{
std::string errors;
std::vector<std::string> allPlugins = listAllPlugins ();
std::map<int, PluginSpec> foundPlugins;
for (auto const & plugin : allPlugins)
{
// TODO: make sure (non)-equal plugins (i.e. with same/different contract) are handled correctly
try
{
PluginSpec spec = PluginSpec (
plugin,
KeySet (5, *Key ("system/module", KEY_VALUE, "this plugin was loaded without a config", KEY_END), KS_END));
// lets see if there is a plugin named after the required provider
if (plugin == which)
{
int s = calculateStatus (lookupInfo (spec, "status"));
foundPlugins.insert (std::make_pair (s, PluginSpec (plugin)));
continue; // we are done with this plugin
}
// TODO: support for generic plugins with config
std::istringstream ss (lookupInfo (spec, "provides"));
std::string provide;
while (ss >> provide)
{
if (provide == which)
{
int s = calculateStatus (lookupInfo (spec, "status"));
foundPlugins.insert (std::make_pair (s, PluginSpec (plugin)));
}
}
}
catch (std::exception const & e)
{
errors += e.what ();
errors += ",";
} // assume not loaded
}
if (foundPlugins.empty ())
{
if (!errors.empty ())
throw NoPlugin ("No plugin that provides " + which + " could be found, got errors: " + errors);
else
throw NoPlugin ("No plugin that provides " + which + " could be found");
}
return foundPlugins;
}
PluginSpec ModulesPluginDatabase::lookupMetadata (std::string const & which) const
{
std::vector<std::string> allPlugins = listAllPlugins ();
std::map<int, PluginSpec> foundPlugins;
std::string errors;
// collect possible plugins
for (auto const & plugin : allPlugins)
{
try
{
// TODO remove /module hack
std::istringstream ss (
lookupInfo (PluginSpec (plugin, KeySet (5, *Key ("system/module", KEY_VALUE,
"this plugin was loaded without a config", KEY_END),
KS_END)),
"metadata"));
std::string metadata;
while (ss >> metadata)
{
if (metadata == which)
{
int s = calculateStatus (lookupInfo (
PluginSpec (plugin, KeySet (5, *Key ("system/module", KEY_VALUE,
"this plugin was loaded without a config", KEY_END),
KS_END)),
"status"));
foundPlugins.insert (std::make_pair (s, PluginSpec (plugin)));
break;
}
}
}
catch (std::exception const & e)
{
errors += e.what ();
errors += ",";
} // assume not loaded
}
if (foundPlugins.empty ())
{
if (!errors.empty ())
throw NoPlugin ("No plugin that provides " + which + " could be found, got errors: " + errors);
else
throw NoPlugin ("No plugin that provides " + which + " could be found");
}
// the largest element of the map contains the best-suited plugin:
return foundPlugins.rbegin ()->second;
}
void analyse(int start, int stop)
{
struct hash *hash;
char line[512];
int lineCount = 0;
char *words[32];
int wordCount;
struct cdnaInfo *cdnaList = NULL;
struct cdnaInfo *ci = NULL;
int cdnaCount;
int maxCdnaCount = stop - start;
cdnaCount = 1;
if (start > 1)
{
for (;;)
{
if (!fgets(line, sizeof(line), inFile))
errAbort("Not %d cDNAs in file, only %d\n", start, cdnaCount);
++lineCount;
if (line[0] == '#') /* Skip comments. */
continue;
wordCount = chopString(line, whiteSpaceChopper, words, ArraySize(words));
if (wordCount <= 0) /* Skip empty lines. */
continue;
if (!differentWord(words[1], "alignments"))
{
++cdnaCount;
if (cdnaCount >= start)
break;
}
}
}
cdnaCount = 0;
hash = newHash(14); /* Hash table with 16k entries. */
for (;;)
{
if (!fgets(line, sizeof(line), inFile))
break;
++lineCount;
if (line[0] == '#') /* Skip comments. */
continue;
wordCount = chopString(line, whiteSpaceChopper, words, ArraySize(words));
if (wordCount <= 0) /* Skip empty lines. */
continue;
if (wordCount < 4) /* Everyone else has at least four words. */
{
errAbort("Short line %d:\n", lineCount);
}
if (sameWord(words[1], "Blasting"))
{
char *cdnaName = words[2];
if ((ci = lookupInfo(hash, cdnaName)) == NULL)
{
struct hashEl *hel;
ci = needMem(sizeof(*ci));
hel = hashAdd(hash, cdnaName, ci);
ci->next = cdnaList;
cdnaList = ci;
ci->ix = atoi(words[0]);
ci->name = hel->name;
}
}
else if (sameWord(words[2], "hits"))
{
/* Newer style - includes cDNA matching range. */
if (ci == NULL)
continue;
hitLine(ci, lineCount, words[0], words[1], words[3], words[4], words[5], words[9]);
}
else if (sameWord(words[1], "hits"))
/* Older style - no cDNA matching range. */
{
if (ci == NULL)
continue;
hitLine(ci, lineCount, words[0], NULL, words[2], words[3], words[4], words[8]);
}
else if (sameWord(words[1], "alignments"))
{
struct dnaSeq *cdnaSeq;
struct wormCdnaInfo info;
if (ci == NULL)
continue;
if (differentWord(ci->name, words[3]))
errAbort("Line %d - %s is not %s", lineCount, words[3], ci->name);
if (!ci->finished)
{
if (!anyCdnaSeq(ci->name, &cdnaSeq, &info))
{
warn("Can't find cDNA %s", ci->name);
ci->isDupe = TRUE;
}
else
{
ci->baseCount = cdnaSeq->size;
ci->baseCrc = dnaCrc(cdnaSeq->dna, cdnaSeq->size);
slReverse(&ci->roughAli);
ci->roughScore = bestRoughScore(ci->roughAli);
filterDupeCdna(ci, cdnaSeq);
ci->isBackwards = (info.orientation == '-');
refineAlis(ci, cdnaSeq);
ci->fineScore = bestFineScore(ci->fineAli);
ci->isEmbryonic = info.isEmbryonic;
ci->finished = TRUE;
freeDnaSeq(&cdnaSeq);
++cdnaCount;
if (cdnaCount >= maxCdnaCount)
break;
}
}
}
else
{
errAbort("Can't deal with line %d\n", lineCount);
}
}
slReverse(&cdnaList);
doGoodBad(cdnaList);
doUnusual(cdnaList);
//makeCdnaToGene(cdnaList);
/* Clean up. */
/* These two are slow and not really necessary. */
#ifdef FASTIDIOUS
slFreeList(&cdnaList);
freeHash(&hash);
#endif
uglyf("Done analyse\n");
}
