4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/visiGene/visiGeneSearch/visiGeneSearch.c src/hg/visiGene/visiGeneSearch/visiGeneSearch.c index fdf8c9e..2891ef7 100644 --- src/hg/visiGene/visiGeneSearch/visiGeneSearch.c +++ src/hg/visiGene/visiGeneSearch/visiGeneSearch.c @@ -1,560 +1,560 @@ /* visiGeneSearch - Test out search routines for VisiGene. */ /* Copyright (C) 2013 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "dystring.h" #include "obscure.h" #include "rbTree.h" #include "jksql.h" #include "visiGene.h" char *database = "visiGene"; void usage() /* Explain usage and exit. */ { errAbort( "visiGeneSearch - Test out search routines for VisiGene\n" "usage:\n" " visiGeneSearch searchTerm\n" "options:\n" " -db=XXX set another database (default visiGene)\n" ); } static struct optionSpec options[] = { {"db", OPTION_STRING}, {NULL, 0}, }; struct visiMatch /* Info on a score of an image in free format search. */ { struct visiMatch *next; int imageId; /* Image ID associated with search. */ double weight; /* The higher the weight the better the match */ }; static int visiMatchCmpImageId(void *va, void *vb) /* rbTree comparison function to tree on imageId. */ { struct visiMatch *a = va, *b = vb; return a->imageId - b->imageId; } static int visiMatchCmpWeight(const void *va, const void *vb) /* Compare to sort based on match. */ { const struct visiMatch *a = *((struct visiMatch **)va); const struct visiMatch *b = *((struct visiMatch **)vb); double dif = b->weight - a->weight; if (dif > 0) return 1; else if (dif < 0) return -1; else return 0; } struct visiSearcher /* This collects together information for free format searches. */ { struct visiSearcher *next; /* Next search */ struct visiMatch *matchList; /* List of matching images. */ struct rbTree *tree; /* Tree for near random access. */ }; static struct visiSearcher *visiSearcherNew() /* Create a new, empty search structure. */ { struct visiSearcher *searcher; AllocVar(searcher); searcher->tree = rbTreeNew(visiMatchCmpImageId); return searcher; } static void visiSearcherFree(struct visiSearcher **pSearcher) /* Free up memory associated with *pSearcher */ { struct visiSearcher *searcher = *pSearcher; if (searcher != NULL) { slFreeList(&searcher->matchList); rbTreeFree(&searcher->tree); freez(pSearcher); } } static struct visiMatch *visiSearcherAdd(struct visiSearcher *searcher, int imageId, double weight) /* Add given weight to match involving imageId, creating * a fresh match if necessary for imageId. */ { struct visiMatch key, *match; key.imageId = imageId; match = rbTreeFind(searcher->tree, &key); if (match == NULL) { AllocVar(match); match->imageId = imageId; slAddHead(&searcher->matchList, match); rbTreeAdd(searcher->tree, match); } match->weight += weight; return match; } static struct visiMatch *visiSearcherSortResults(struct visiSearcher *searcher) /* Get sorted list of match results from searcher. * You don't own the list returned though. It will evaporate * with visiSearcherFree. */ { slSort(&searcher->matchList, visiMatchCmpWeight); return searcher->matchList; } static char *stripSpacesEtc(char *s) /* Return a copy of s with spaces, periods, and dashes removed */ { char *d = cloneString(s); stripChar(d, ' '); stripChar(d, '.'); stripChar(d, '-'); touppers(d); return d; } static int countPartsUsedInName(char *name, struct slName *wordList) /* The name here is last name followed by initials with a * period after each initial and no space between initials. * The last name may contain multiple words. Some complex * examples are "van den Eijnden-van Raaij A.J." and * "Van De Water T." A typical example "Kwong W.H." * The word list is just space separated words. We'd * Want the last example to be matched by "Kwong" "W.H." * as well as "Kwong WH" as well as "Kwong W H". */ { int count = 0; struct slName *word; char *stripped = stripSpacesEtc(name); char *pt = stripped; for (word = wordList; word != NULL; word = word->next) { char *w = stripSpacesEtc(word->name); if (startsWith(w, pt)) { count += 1; pt += strlen(w); freeMem(w); } else { freeMem(w); break; } } freeMem(stripped); return count; } static int countWordsUsedInPhrase(char *phrase, struct slName *wordList) /* Count the number of words in wordList that are used in phrase. * The words are in order and space-separated in phrase. */ { int count = 0; struct slName *word; char *dupe = cloneString(phrase); char *s = dupe, *w; for (word = wordList; word != NULL; word = word->next) { w = nextWord(&s); if (w == NULL) break; if (sameWord(w, word->name)) count += 1; else break; } freeMem(dupe); return count; } typedef void AdderFunc(struct visiSearcher *searcher, struct sqlConnection *conn, struct dyString *dy, char *exactMatch); /* Typedef of function to add things that are exact matches of * some type to searcher. This is broken out separately * so that the visiGeneMatchMultiWord function below can be * used in many contexts. */ static void visiGeneMatchMultiWord(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList, char *table, AdderFunc adder) /* This helps cope with matches that may involve more than * one word. It will preferentially match as many words * as possible, and if there is a multiple-word match it * will take that over a single-word match. */ { struct slName *word; struct dyString *query = dyStringNew(0); struct sqlResult *sr; char **row; for (word = wordList; word != NULL; ) { struct slName *nameList, *name; int maxWordsUsed = 0; dyStringClear(query); sqlDyStringPrintf(query, "select name from %s where name like \"", table); dyStringAppend(query, word->name); dyStringAppend(query, "%\""); nameList = sqlQuickList(conn, query->string); if (nameList != NULL) { for (name = nameList; name != NULL; name = name->next) { int wordsUsed = countWordsUsedInPhrase(name->name, word); if (wordsUsed > maxWordsUsed) maxWordsUsed = wordsUsed; } } if (maxWordsUsed > 0) { for (name = nameList; name != NULL; name = name->next) { if (countWordsUsedInPhrase(name->name, word) == maxWordsUsed) (*adder)(searcher, conn, query, name->name); } while (--maxWordsUsed >= 0) word = word->next; } else word = word->next; slFreeList(&nameList); } dyStringFree(&query); } static void addImagesMatchingQuery(struct visiSearcher *searcher, struct sqlConnection *conn, char *query) /* Add images that match query */ { struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) visiSearcherAdd(searcher, sqlUnsigned(row[0]), 1.0); sqlFreeResult(&sr); } static void addImagesMatchingName(struct visiSearcher *searcher, struct sqlConnection *conn, struct dyString *dy, char *contributor) /* Add images that are contributed by given contributor to * searcher with a weight of one. Use dy for scratch space for * the query. */ { int contributorId; dyStringClear(dy); sqlDyStringPrintf(dy, "select image.id from " "contributor,submissionContributor,imageFile,image " "where contributor.name = \"%s\" " "and contributor.id = submissionContributor.contributor " "and submissionContributor.submissionSet = imageFile.submissionSet " "and imageFile.id = image.imageFile" , contributor); addImagesMatchingQuery(searcher, conn, dy->string); } static void visiGeneMatchContributor(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Put images from contributors in wordList into searcher. * We want the behavior to be such that if you give it two names * say "Smith Mahoney" it will weigh those that match both * names. We also want it so that if you include the initials * after the last name either with or without periods that will * set those matching the last name and initials. For * instance "Smith JJ" or "Smith J.J." or "Smith J. J." all would * match a particular John Jacob Smith, but not Francis K. Smith. * Making this a little more interesting is a case like * "smith li" which could either be two last names, or a last * name followed by initials. We would want to match both * cases. Finally, making it even more interesting, is the * case where the last name is compound, like "Van Koppen" or * "de la Cruz" and the like. Also don't forget the apostrophe * containing names like O'Shea. */ { struct slName *word; struct dyString *query = dyStringNew(0); struct sqlResult *sr; char **row; for (word = wordList; word != NULL; ) { struct slName *nameList, *name; int maxWordsUsed = 0; dyStringClear(query); sqlDyStringPrintf(query, "select name from contributor where name like \""); dyStringAppend(query, word->name); dyStringAppend(query, " %\""); nameList = sqlQuickList(conn, query->string); if (nameList != NULL) { for (name = nameList; name != NULL; name = name->next) { int wordsUsed = countPartsUsedInName(name->name, word); if (wordsUsed > maxWordsUsed) maxWordsUsed = wordsUsed; } for (name = nameList; name != NULL; name = name->next) { if (countPartsUsedInName(name->name, word) == maxWordsUsed) addImagesMatchingName(searcher, conn, query, name->name); } while (--maxWordsUsed >= 0) word = word->next; } else word = word->next; slFreeList(&nameList); } dyStringFree(&query); } static void addImageListAndFree(struct visiSearcher *searcher, struct slInt *imageList) /* Add images in list to searcher with weight one. * Then free imageList */ { struct slInt *image; for (image = imageList; image != NULL; image = image->next) visiSearcherAdd(searcher, image->val, 1.0); slFreeList(&imageList); } static void visiGeneMatchGene(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Add images matching genes in wordList to searcher. * The wordList can include wildcards. */ { struct slName *word; for (word = wordList; word != NULL; word = word->next) { char *sqlPat = sqlLikeFromWild(word->name); struct slInt *imageList, *image; if (sqlWildcardIn(sqlPat)) imageList = visiGeneSelectNamed(conn, sqlPat, vgsLike); else imageList = visiGeneSelectNamed(conn, sqlPat, vgsExact); addImageListAndFree(searcher, imageList); freez(&sqlPat); } } static void visiGeneMatchAccession(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Add images matching RefSeq, LocusLink, GenBank, or UniProt * accessions to searcher. */ { struct slName *word; for (word = wordList; word != NULL; word = word->next) { addImageListAndFree(searcher, visiGeneSelectRefSeq(conn, word->name)); addImageListAndFree(searcher, visiGeneSelectLocusLink(conn, word->name)); addImageListAndFree(searcher, visiGeneSelectGenbank(conn, word->name)); addImageListAndFree(searcher, visiGeneSelectUniProt(conn, word->name)); } } static void addImagesMatchingBodyPart(struct visiSearcher *searcher, struct sqlConnection *conn, struct dyString *dy, char *bodyPart) /* Add images that are contributed by given contributor to * searcher with a weight of one. Use dy for scratch space for * the query. */ { dyStringClear(dy); sqlDyStringPrintf(dy, "select imageProbe.image from " "bodyPart,expressionLevel,imageProbe " "where bodyPart.name = \"%s\" " "and bodyPart.id = expressionLevel.bodyPart " "and expressionLevel.imageProbe = imageProbe.id" , bodyPart); addImagesMatchingQuery(searcher, conn, dy->string); dyStringClear(dy); sqlDyStringPrintf(dy, "select image.id from bodyPart,specimen,image " "where bodyPart.name = \"%s\" " "and bodyPart.id = specimen.bodyPart " "and specimen.id = image.specimen"); addImagesMatchingQuery(searcher, conn, dy->string); } static void visiGeneMatchBodyPart(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Add images matching bodyPart to searcher. * This is a little complicated by some body parts containing * multiple words, like "choroid plexus". */ { visiGeneMatchMultiWord(searcher, conn, wordList, "bodyPart", addImagesMatchingBodyPart); } void addImagesMatchingStage(struct visiSearcher *searcher, struct sqlConnection *conn, int schemeId, int taxon, char *minAge) /* Given a developmental stage scheme (schemeId) and a specific * stage, return all images that match stage */ { struct dyString *dy = dyStringNew(0); char *maxAge; struct sqlResult *sr; char **row; dyStringClear(dy); sqlDyStringPrintf(dy, "select age from lifeStage where lifeStageScheme = %d ", schemeId); dyStringPrintf(dy, "and age > %s order by age", minAge); maxAge = sqlQuickString(conn, dy->string); dyStringClear(dy); sqlDyStringPrintf(dy, "select image.id from specimen,image "); dyStringPrintf(dy, "where specimen.age >= %s ", minAge); if (maxAge != NULL) dyStringPrintf(dy, "and specimen.age < %s ", maxAge); dyStringPrintf(dy, "and specimen.taxon = %d ", taxon); dyStringPrintf(dy, "and specimen.id = image.specimen"); addImagesMatchingQuery(searcher, conn, dy->string); dyStringFree(&dy); } static void visiGeneMatchStage(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Add images matching Theiler or other developmental stage */ { struct slName *word; struct dyString *dy = dyStringNew(0); struct sqlResult *sr; char **row; for (word = wordList; word != NULL && word->next != NULL; word = word->next) { int schemeId = 0,taxon=0; dyStringClear(dy); sqlDyStringPrintf(dy, "select id,taxon from lifeStageScheme where name = \"%s\"", word->name); sr = sqlGetResult(conn, dy->string); if ((row = sqlNextRow(sr)) != NULL) { schemeId = sqlUnsigned(row[0]); taxon = sqlUnsigned(row[1]); } sqlFreeResult(&sr); if (schemeId > 0) { char *specificStage = word->next->name; char *minAge; dyStringClear(dy); sqlDyStringPrintf(dy, "select age from lifeStage where name = \"%s\" ", specificStage); dyStringPrintf(dy, "and lifeStageScheme = %d\n", schemeId); minAge = sqlQuickString(conn, dy->string); if (minAge != NULL) addImagesMatchingStage(searcher, conn, schemeId, taxon, minAge); freez(&minAge); } } dyStringFree(&dy); } static void addImagesMatchingYears(struct visiSearcher *searcher, struct sqlConnection *conn, int minYear, int maxYear) /* Fold in images that are published between given years */ { struct dyString *dy = dyStringNew(0); sqlDyStringPrintf(dy, "select image.id from submissionSet,imageFile,image " "where submissionSet.year >= %d and submissionSet.year <= %d " "and submissionSet.id = imageFile.submissionSet " "and imageFile.id = image.imageFile" , minYear, maxYear); addImagesMatchingQuery(searcher, conn, dy->string); dyStringFree(&dy); } static void visiGeneMatchYear(struct visiSearcher *searcher, struct sqlConnection *conn, struct slName *wordList) /* Fold in matches to a year. */ { struct slName *word; char *now = sqlQuickString(conn, NOSQLINJ "select now()"); int currentYear = atoi(now); int maxYear = currentYear+1; /* May be slightly ahead of publication */ int minYear = 1988; /* Oldest record in Jackson Labs database. */ for (word = wordList; word != NULL; word = word->next) { char *name = word->name; if (strlen(name) == 4 && isdigit(name[0])) { int year = atoi(name); if (year >= minYear && year <= maxYear) addImagesMatchingYears(searcher, conn, year, year); } } } struct slInt *visiGeneSearch(char *searchString) /* visiGeneSearch - Test out search routines for VisiGene. */ { struct sqlConnection *conn = sqlConnect(database); struct visiMatch *matchList, *match; struct slInt *imageList = NULL, *image; struct visiSearcher *searcher = visiSearcherNew(); struct slName *wordList = stringToSlNames(searchString); uglyf("Searching %s for \"%s\"\n", database, searchString); visiGeneMatchContributor(searcher, conn, wordList); visiGeneMatchYear(searcher, conn, wordList); visiGeneMatchGene(searcher, conn, wordList); visiGeneMatchAccession(searcher, conn, wordList); visiGeneMatchBodyPart(searcher, conn, wordList); #ifdef SOON visiGeneMatchStage(searcher, conn, wordList); #endif /* SOON */ matchList = visiSearcherSortResults(searcher); for (match = matchList; match != NULL; match = match->next) { uglyf("%f %d\n", match->weight, match->imageId); image = slIntNew(match->imageId); slAddHead(&imageList, image); } slFreeList(&matchList); slFreeList(&wordList); slReverse(&imageList); return imageList; } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); database = optionVal("db", database); if (argc != 2) usage(); visiGeneSearch(argv[1]); return 0; }