981ef07d25e4560559dae28d3e316913569944d7 tdreszer Fri Jul 6 17:51:06 2012 -0700 Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way. diff --git src/hg/inc/mdb.h src/hg/inc/mdb.h index 84034d3..1989182 100644 --- src/hg/inc/mdb.h +++ src/hg/inc/mdb.h @@ -1,517 +1,558 @@ /* mdb.h was originally generated by the autoSql program, which also * generated mdb.c and mdb.sql. This header links the database and * the RAM representation of objects. */ #ifndef MDB_H #define MDB_H #include "jksql.h" #define MDB_NUM_COLS 3 struct mdb /* This contains metadata for a table, file or other predeclared object type. */ { struct mdb *next; /* Next in singly linked list. */ char *obj; /* Object name or ID. */ char *var; /* Metadata variable name. */ char *val; /* Metadata value. */ }; void mdbStaticLoad(char **row, struct mdb *ret); /* Load a row from mdb table into ret. The contents of ret will * be replaced at the next call to this function. */ struct mdb *mdbLoadByQuery(struct sqlConnection *conn, char *query); /* Load all mdb from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with mdbFreeList(). */ void mdbSaveToDb(struct sqlConnection *conn, struct mdb *el, char *tableName, int updateSize); /* Save mdb as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Note that strings must be escaped to allow insertion into the database. * For example "autosql's features include" --> "autosql\'s features include" * If worried about this use mdbSaveToDbEscaped() */ void mdbSaveToDbEscaped(struct sqlConnection *conn, struct mdb *el, char *tableName, int updateSize); /* Save mdb as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size. * of a string that would contain the entire query. Automatically * escapes all simple strings (not arrays of string) but may be slower than mdbSaveToDb(). * For example automatically copies and converts: * "autosql's features include" --> "autosql\'s features include" * before inserting into database. */ struct mdb *mdbLoad(char **row); /* Load a mdb from row fetched with select * from mdb * from database. Dispose of this with mdbFree(). */ struct mdb *mdbLoadAll(char *fileName); /* Load all mdb from whitespace-separated file. * Dispose of this with mdbFreeList(). */ struct mdb *mdbLoadAllByChar(char *fileName, char chopper); /* Load all mdb from chopper separated file. * Dispose of this with mdbFreeList(). */ #define mdbLoadAllByTab(a) mdbLoadAllByChar(a, '\t'); /* Load all mdb from tab separated file. * Dispose of this with mdbFreeList(). */ struct mdb *mdbCommaIn(char **pS, struct mdb *ret); /* Create a mdb out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new mdb */ void mdbFree(struct mdb **pEl); /* Free a single dynamically allocated mdb such as created * with mdbLoad(). */ void mdbFreeList(struct mdb **pList); /* Free a list of dynamically allocated mdb's */ void mdbOutput(struct mdb *el, FILE *f, char sep, char lastSep); /* Print out mdb. Separate fields with sep. Follow last field with lastSep. */ #define mdbTabOut(el,f) mdbOutput(el,f,'\t','\n'); /* Print out mdb as a line in a tab-separated file. */ #define mdbCommaOut(el,f) mdbOutput(el,f,',',','); /* Print out mdb as a comma separated list including final comma. */ void mdbJsonOutput(struct mdb *el, FILE *f); /* Print out mdb in JSON format. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #include "cv.h" #include "trackDb.h" #define MDB_DEFAULT_NAME "metaDb" // The three mdb tuples #define MDB_OBJ "obj" #define MDB_VAR "var" #define MDB_VAL "val" // OBJECT TYPES #define MDB_OBJ_TYPE "objType" #define MDB_OBJ_TYPE_TABLE "table" #define MDB_OBJ_TYPE_FILE "file" #define MDB_OBJ_TYPE_COMPOSITE "composite" // WELL KNOWN MDB VARS #define MDB_VAR_PI CV_TERM_GRANT #define MDB_VAR_LAB CV_TERM_LAB #define MDB_VAR_COMPOSITE MDB_OBJ_TYPE_COMPOSITE #define MDB_VAR_ANTIBODY CV_TERM_ANTIBODY #define MDB_VAR_CELL CV_TERM_CELL #define MDB_VAR_DATATYPE CV_TERM_DATA_TYPE #define MDB_VAR_VIEW CV_TERM_VIEW #define MDB_VAR_CONTROL CV_TERM_CONTROL #define MDB_VAR_TABLENAME "tableName" #define MDB_VAR_FILENAME "fileName" #define MDB_VAR_MD5SUM "md5sum" #define MDB_VAR_FILEINDEX "fileIndex" #define MDB_VAR_DCC_ACCESSION "dccAccession" #define MDB_VAR_PROJECT "project" #define MDB_VAR_REPLICATE "replicate" #define MDB_VAR_LAB_VERSION "labVersion" #define MDB_VAR_SOFTWARE_VERSION "softwareVersion" #define MDB_VAR_SUBMIT_VERSION "submittedDataVersion" // ENCODE Specific (at least for now) #define MDB_VAL_ENCODE_PROJECT "wgEncode" #define MDB_VAR_ENCODE_SUBID "subId" #define MDB_VAR_ENCODE_EDVS "expVars" #define MDB_VAR_ENCODE_EXP_ID "expId" #define MDB_VAL_ENCODE_EDV_NONE "None" // The mdb holds metadata primarily for tables. // Many types of objects could be supported, though currently files are the only other type. // It is easy to imagine using the current mdb to support hierarchical trees of metadata. // For example a composite type object called "myComposte" could have metadata that is valid for // all tables that have the var=composite val=myComposte metadata defined. // // There are 2 ways to look at the metadata: By Obj: obj->[var=val] and By Var: var->[val->[obj]]. // By Obj: an object has many var/val pairs but only one val for each unique var. Querying by // object creates a single (2 level) one to many structure. -// By Var: a variable has many possible values and each value may be defined for more than one object. +// By Var: a variable has many possible values and each value may be defined for more than one obj // Therefore, querying by var results in a (3 level) one to many to many structure. struct mdbVar // The metadata var=val construct. This is contained by mdbObj { struct mdbVar* next; // Next in singly linked list of variables char *var; // Metadata variable name. char *val; // Metadata value. }; struct mdbObj // The standard container of a single object's metadata. // Also: when searching metadata obj->var->val this is the top struct. { struct mdbObj* next; // Next in singly linked list of objects char *obj; // Object name or ID boolean deleteThis; // Used when loading formatted file which may contain delete requests struct mdbVar* vars; // if NOT NULL: list of variables belonging to this object struct hash* varHash; // if NOT NULL: variables are also hashed! (var str to mdbVar struct) }; struct mdbLeafObj // When searching var->val->obj this is the bottom-level obj struct. { struct mdbLeafObj* next; // Next in singly linked list of variables char *obj; // Object name or ID }; struct mdbLimbVal // When searching var->val->obj this is the mid-level val->obj struct. { struct mdbLimbVal* next; // Next in singly linked list of variables char *val; // Metadata value. struct mdbLeafObj* objs; // if NOT NULL: list of Objects which have this variable struct hash* objHash; // if NOT NULL: hash of objects (val str to leafObj struct) }; struct mdbByVar // When searching metadata var->val->object this is the top struct { struct mdbByVar* next; // Next in singly linked list of variables char *var; // Metadata variable name. boolean notEqual; // For querying only struct mdbLimbVal* vals; // list of values associated with this var struct hash* valHash; // if NOT NULL: hash of vals (val str to limbVal struct) }; // -------------- Sort primitives -------------- int mdbObjCmp(const void *va, const void *vb); // Compare mdbObj to sort on obj name, case-insensitive. int mdbVarCmp(const void *va, const void *vb); // Compare mdbVar to sort on var name, case-insensitive. // ------ Parsing lines ------ struct mdbObj *metadataLineParse(char *line); /* Parses a single formatted metadata line into mdbObj for updates or queries. */ struct mdbByVar *mdbByVarsLineParse(char *line); /* Parses a line of "var1=val1 var2=val2 into a mdbByVar object for queries. */ // ------ Loading from args, hashes ------ struct mdbObj *mdbObjCreate(char *obj,char *var, char *val); /* Creates a singular mdbObj query object based on obj and all other optional params. */ struct mdbObj *mdbObjNew(char *obj,struct mdbVar *mdbVars); // Returns a new mdbObj with whatever was passed in. // An mdbObj requires and obj, so if one is not supplied it will be "[unknown]" struct mdbByVar *mdbByVarCreate(char *var, char *val); /* Creates a singular var=val pair struct for metadata queries. */ boolean mdbByVarAppend(struct mdbByVar *mdbByVars,char *var, char *val,boolean notEqual); /* Adds a another var to a list of mdbByVar pairs to be used in metadata queries. */ struct mdbObj *mdbObjsLoadFromHashes(struct hash *objsHash); // Load all mdbObjs from a file containing metadata formatted lines // ------ Loading from files ------ struct mdbObj *mdbObjsLoadFromFormattedFile(char *fileName,boolean *validated); // Load all mdbObjs from a file containing metadata formatted lines // If requested, will determine if a magic number at the end of the file matches contents struct mdbObj *mdbObjsLoadFromRAFile(char *fileName,boolean *validated); // Load all mdbObjs from a file containing RA formatted 'metaObjects' // If requested, will determine if a magic number at the end of the file matches contents // ------ Table name and creation ------ void mdbReCreate(struct sqlConnection *conn,char *tblName,boolean testOnly); // Creates ore Recreates the named mdb. char*mdbTableName(struct sqlConnection *conn,boolean mySandBox); // returns the mdb table name or NULL if conn supplied but the table doesn't exist // -------------- Updating the DB -------------- -int mdbObjsSetToDb(struct sqlConnection *conn,char *tableName,struct mdbObj *mdbObjs,boolean replace,boolean testOnly); +int mdbObjsSetToDb(struct sqlConnection *conn,char *tableName,struct mdbObj *mdbObjs, + boolean replace,boolean testOnly); // Adds or updates metadata obj/var pairs into the named table. Returns total rows affected -int mdbObjsLoadToDb(struct sqlConnection *conn,char *tableName,struct mdbObj *mdbObjs,boolean testOnly); +int mdbObjsLoadToDb(struct sqlConnection *conn,char *tableName,struct mdbObj *mdbObjs, + boolean testOnly); // Adds mdb Objs with minimal error checking // ------------------ Querys ------------------- struct mdbObj *mdbObjQuery(struct sqlConnection *conn,char *table,struct mdbObj *mdbObj); -// Query the metadata table by obj and optional vars and vals in mdbObj struct. If mdbObj is NULL query all. -// Returns new mdbObj struct fully populated and sorted in obj,var order. +// Query the metadata table by obj and optional vars and vals in mdbObj struct. +// If mdbObj NULL query all. Returns new mdbObj struct fully populated and sorted in obj,var order. #define mdbObjsQueryAll(conn,table) mdbObjQuery((conn),(table),NULL) struct mdbObj *mdbObjQueryByObj(struct sqlConnection *conn,char *table,char *obj,char *var); // Query a single metadata object and optional var from a table (default mdb). struct mdbByVar *mdbByVarsQuery(struct sqlConnection *conn,char *table,struct mdbByVar *mdbByVars); -// Query the metadata table by one or more var=val pairs to find the distinct set of objs that satisfy ANY conditions. +// Query the metadata table by one or more var=val pairs to find the distinct set of objs +// that satisfy ANY conditions. // Returns new mdbByVar struct fully populated and sorted in var,val,obj order. #define mdbByVarsQueryAll(conn,table) mdbByVarsQuery((conn),(table),NULL) struct mdbByVar *mdbByVarQueryByVar(struct sqlConnection *conn,char *table,char *varName,char *val); -// Query a single metadata variable and optional val from a table (default mdb) for searching val->obj. +// Query a single metadata variable and optional val from a table (default mdb) +// for searching val->obj. -struct mdbObj *mdbObjsQueryByVars(struct sqlConnection *conn,char *table,struct mdbByVar *mdbByVars); -// Query the metadata table by one or more var=val pairs to find the distinct set of objs that satisfy ALL conditions. +struct mdbObj *mdbObjsQueryByVars(struct sqlConnection *conn,char *table, + struct mdbByVar *mdbByVars); +// Query the metadata table by one or more var=val pairs to find the distinct set of objs +// that satisfy ALL conditions. // Returns new mdbObj struct fully populated and sorted in obj,var order. struct mdbObj *mdbObjsQueryByVarValString(struct sqlConnection *conn,char *tableName,char *varVals); -// returns mdbObjs matching varVals in form of: [var1=val1 var2=val2a,val2b var3=v%3 var4="val 4" var5!=val5 var6=] +// returns mdbObjs matching varVals in form of: +// [var1=val1 var2=val2a,val2b var3=v%3 var4="val 4" var5!=val5 var6=] // var2=val2a,val2b: matches asny of comma separated list // var3=v%3 : matches '%' and '?' wild cards. // var4="val 4" : matches simple double quoted strings. // var5!=val5 : matches not equal. // var6= : matches that var exists (same as var6=%). var6!= also works. #define mdbObjsQueryByVarVals(conn,varVals) mdbObjsQueryByVarValString((conn),NULL,(varVals)) -struct mdbObj *mdbObjsQueryByVarPairs(struct sqlConnection *conn,char *tableName,struct slPair *varValPairs); +struct mdbObj *mdbObjsQueryByVarPairs(struct sqlConnection *conn,char *tableName, + struct slPair *varValPairs); // returns mdbObjs matching varValPairs provided. // The != logic of mdbObjsQueryByVarValString() is not possible, but other cases are supported: // as val may be NULL, a comma delimited list, double quoted string, containing wilds: % and ? -#define mdbObjsQueryByVarValPairs(conn,varValPairs) mdbObjsQueryByVarPairs((conn),NULL,(varValPairs)) +#define mdbObjsQueryByVarValPairs(conn,varValPairs) \ + mdbObjsQueryByVarPairs((conn),NULL,(varValPairs)) -struct mdbObj *mdbObjQueryCompositeObj(struct sqlConnection *conn,char *tableName,struct mdbObj *mdbObj); +struct mdbObj *mdbObjQueryCompositeObj(struct sqlConnection *conn,char *tableName, + struct mdbObj *mdbObj); // returns NULL or the composite mdbObj associated with the object passed in. #define mdbObjQueryComposite(conn,mdbObj) mdbObjQueryCompositeObj((conn),NULL,(mdbObj)) // ----------- Printing and Counting ----------- void mdbObjPrint(struct mdbObj *mdbObjs,boolean raStyle); // prints objs and var=val pairs as formatted metadata lines or ra style void mdbObjPrintToFile(struct mdbObj *mdbObjs,boolean raStyle, char *file); // prints (to file) objs and var=val pairs as formatted metadata lines or ra style void mdbObjPrintToStream(struct mdbObj *mdbObjs,boolean raStyle, FILE *outF); // prints (to stream) objs and var=val pairs as formatted metadata lines or ra style int mdbObjPrintToTabFile(struct mdbObj *mdbObjs, char *file); // prints all objs as tab delimited obj var val into file for SQL LOAD DATA. Returns count. -void mdbObjPrintOrderedToStream(FILE *outF,struct mdbObj **mdbObjs,char *order, char *separator, boolean header); +void mdbObjPrintOrderedToStream(FILE *outF,struct mdbObj **mdbObjs,char *order, + char *separator, boolean header); // prints mdbObjs as a table, but only the vars listed in comma delimited order. // Examples of separator: " " "\t\t" or "<TD>", in which case this is an HTML table. // mdbObjs list will be reordered. Sort fails when vars are missing in objs. char *mdbObjVarValPairsAsLine(struct mdbObj *mdbObj,boolean objTypeExclude,boolean cvLabels); // returns NULL or a line for a single mdbObj as "var1=val1; var2=val2 ...". Must be freed. void mdbByVarPrint(struct mdbByVar *mdbByVars,boolean raStyle); // prints var=val pairs and objs that go with them single lines or ra style int mdbObjCount(struct mdbObj *mdbObjs, boolean objs); // returns the count of vars belonging to this obj or objs; int mdbByVarCount(struct mdbByVar *mdbByVars,boolean vars, boolean vals); // returns the count of objs belonging to this set of vars; // ----------------- Utilities ----------------- struct mdbVar *mdbObjFind(struct mdbObj *mdbObj, char *var); // Finds the val associated with the var or retruns NULL char *mdbObjFindValue(struct mdbObj *mdbObj, char *var); // Finds the val associated with the var or retruns NULL struct slName *mdbObjsFindAllVals(struct mdbObj *mdbObjs, char *var, char *emptyToken); // Returns a list of all vals in mdbObjs for a requested var // Will add empty only if there is atleast one empty val and at least one val found boolean mdbObjContains(struct mdbObj *mdbObj, char *var, char *val); // Returns TRUE if object contains var, val or both boolean mdbObjsContainAltleastOneMatchingVar(struct mdbObj *mdbObjs, char *var, char *val); // Returns TRUE if any object in set contains var -#define mdbObjsContainAtleastOne(mdbObjs, var) mdbObjsContainAltleastOneMatchingVar((mdbObjs),(var),NULL) +#define mdbObjsContainAtleastOne(mdbObjs, var) \ + mdbObjsContainAltleastOneMatchingVar((mdbObjs),(var),NULL) struct mdbObj *mdbObjsCommonVars(struct mdbObj *mdbObjs); // Returns a new mdbObj with all vars that are contained in every obj passed in. // Note that the returnd mdbObj has a meaningles obj name and vals. boolean mdbByVarContains(struct mdbByVar *mdbByVar, char *val, char *obj); // Returns TRUE if var contains val, obj or both void mdbObjReorderVars(struct mdbObj *mdbObjs, char *vars,boolean back); // Reorders vars list based upon list of vars "cell antibody treatment". Send to front or back. void mdbObjReorderByCv(struct mdbObj *mdbObjs, boolean includeHidden); // Reorders vars list based upon cv.ra typeOfTerms priority void mdbObjsSortOnVars(struct mdbObj **mdbObjs, char *vars); -// Sorts on var,val pairs vars lists: fwd case-sensitive. Assumes all objs' vars are in identical order. -// Optionally give list of vars "cell antibody treatment" to sort on (bringing to front of vars lists). +// Sorts on var,val pairs vars lists: fwd case-sensitive. +// Assumes all objs' vars are in identical order. +// Optionally give list of vars "cell antibody treatment" to sort on +// (bringing to front of vars lists). void mdbObjsSortOnVarPairs(struct mdbObj **mdbObjs,struct slPair *varValPairs); -// Sorts on var,val pairs vars lists: fwd case-sensitive. Assumes all objs' vars are in identical order. +// Sorts on var,val pairs vars lists: fwd case-sensitive. +// Assumes all objs' vars are in identical order. // This method will use mdbObjsSortOnVars() void mdbObjsSortOnCv(struct mdbObj **mdbObjs, boolean includeHidden); // Puts obj->vars in order based upon cv.ra typeOfTerms priority, // then case-sensitively sorts all objs in list based upon that var order. boolean mdbObjRemoveOneVar(struct mdbObj *mdbObj, char *var, char *val); // returns TRUE if var (and optional val) are found and surgically removed from one mdbObj void mdbObjRemoveVars(struct mdbObj *mdbObjs, char *vars); // Prunes list of vars for an object, freeing the memory. Doesn't touch DB. void mdbObjRemoveHiddenVars(struct mdbObj *mdbObjs); // Prunes list of vars for mdb objs that have been declared as hidden in cv.ra typeOfTerms boolean mdbObjsHasCommonVar(struct mdbObj *mdbList, char *var, boolean missingOk); // Returns TRUE if all mbObjs passed in have the var with the same value char *mdbRemoveCommonVar(struct mdbObj *mdbList, char *var); // Removes var from set of mdbObjs but only if all that hav it have a commmon val // Returns the val if removed, else NULL boolean mdbObjSetVar(struct mdbObj *mdbObj, char *var,char *val); // Sets the string value to a single var in an obj, preparing for DB update. // returns TRUE if updated, FALSE if added boolean mdbObjSetVarInt(struct mdbObj *mdbObj, char *var,int val); // Sets an integer value to a single var in an obj, preparing for DB update. // returns TRUE if updated, FALSE if added void mdbObjSwapVars(struct mdbObj *mdbObjs, char *vars,boolean deleteThis); // Replaces objs' vars with var=vap pairs provided, preparing for DB update. struct mdbObj *mdbObjsFilter(struct mdbObj **pMdbObjs, char *var, char *val,boolean returnMatches); // Filters mdb objects to only those that include/exclude vars. Optionally checks val too. // Returns matched or unmatched items objects as requested, maintaining sort order -struct mdbObj *mdbObjsFilterByVars(struct mdbObj **pMdbObjs,char *vars,boolean noneEqualsNotFound,boolean returnMatches); -// Filters mdb objects to only those that include/exclude var=val pairs (e.g. "var1=val1 var2 var3!=val3 var4=None"). -// Supports != ("var!=" means var not found). Optionally supports var=None equal to var is not found -// Returns matched or unmatched items objects as requested. Multiple passes means sort order is destroyed. +struct mdbObj *mdbObjsFilterByVars(struct mdbObj **pMdbObjs,char *vars, + boolean noneEqualsNotFound,boolean returnMatches); +// Filters mdb objects to only those that include/exclude var=val pairs +// (e.g. "var1=val1 var2 var3!=val3 var4=None"). +// Supports != ("var!=" means var not found). +// Optionally supports var=None equal to var is not found +// Returns matched or unmatched items objects as requested. +// Multiple passes means sort order is destroyed. struct mdbObj *mdbObjsFilterTablesOrFiles(struct mdbObj **pMdbObjs,boolean table, boolean files); -// Filters mdb objects to only those that have associated tables or files. Returns removed non-table/file objects +// Filters mdb objects to only those that have associated tables or files. +// Returns removed non-table/file objects // Note: Since table/file objects overlap, there are 3 possibilites: tables, files, table && files struct mdbObj *mdbObjIntersection(struct mdbObj **a, struct mdbObj *b); // return objs removed from pA while making an intersection of two mdbObj lists. // List b is untouched but pA will contain the resulting intersection void mdbObjTransformToUpdate(struct mdbObj *mdbObjs, char *var, char *val,boolean deleteThis); // Turns one or more mdbObjs into the stucture needed to add/update or delete. struct mdbObj *mdbObjClone(const struct mdbObj *mdbObj); // Clones a single mdbObj, including hash and maintining order struct slName *mdbObjToSlName(struct mdbObj *mdbObjs); // Creates slNames list of mdbObjs->obj. mdbObjs remains untouched int mdbVarCmp(const void *va, const void *vb); /* Compare to sort on label. */ // ----------------- Validation and specialty APIs ----------------- boolean mdbObjIsComposite(struct mdbObj *mdbObj); // returns TRUE if this is a valid composite object boolean mdbObjIsCompositeMember(struct mdbObj *mdbObj); -// returns TRUE if this is a valid member of a composite. DOES not confirm that composite obj exists +// returns TRUE if this is valid member of a composite. DOES not confirm that composite obj exists int mdbObjsValidate(struct mdbObj *mdbObjs, boolean full); // Validates vars and vals against cv.ra. Returns count of errors found. // Full considers vars not defined in cv as invalids -struct slName *mdbObjFindCompositeNamedEncodeEdvs(struct sqlConnection *conn,char *tableName,struct mdbObj *mdbObj); +struct slName *mdbObjFindCompositeNamedEncodeEdvs(struct sqlConnection *conn, + char *tableName,struct mdbObj *mdbObj); // returns NULL or the Experiment Defining Variable names for this composite -#define mdbObjFindCompositeEncodeEdvs(conn,mdbObj) mdbObjFindCompositeNamedEncodeEdvs((conn),NULL,(mdbObj)) +#define mdbObjFindCompositeEncodeEdvs(conn,mdbObj) \ + mdbObjFindCompositeNamedEncodeEdvs((conn),NULL,(mdbObj)) -struct mdbVar *mdbObjFindEncodeEdvPairs(struct sqlConnection *conn,char *tableName,struct mdbObj *mdbObj,boolean includeNone); +struct mdbVar *mdbObjFindEncodeEdvPairs(struct sqlConnection *conn,char *tableName, + struct mdbObj *mdbObj,boolean includeNone); // returns NULL or the Experiment Defining Variables and values for this composite member object // If includeNone, then defined variables not found in obj will be included as {var}="None". -#define mdbObjFindEncodeEdvs(conn,mdbObj,includeNone) mdbObjFindEncodeEdvPairs((conn),NULL,(mdbObj),(includeNone)) - -struct mdbObj *mdbObjsEncodeExperimentify(struct sqlConnection *conn,char *db,char *tableName,char *expTable, - struct mdbObj **pMdbObjs,int warn,boolean createExpIfNecessary,boolean updateAccession); -// Organizes objects into experiments and validates experiment IDs. Will add/update the ids in the structures. +#define mdbObjFindEncodeEdvs(conn,mdbObj,includeNone) \ + mdbObjFindEncodeEdvPairs((conn),NULL,(mdbObj),(includeNone)) + +struct mdbObj *mdbObjsEncodeExperimentify(struct sqlConnection *conn,char *db,char *tableName, + char *expTable,struct mdbObj **pMdbObjs,int warn, + boolean createExpIfNecessary,boolean updateAccession); +// Organizes objects into experiments and validates experiment IDs. +// Will add/update the ids in the structures. // If warn=1, then prints to stdout all the experiments/obs with missing or wrong expIds; // warn=2, then print line for each obj with expId or warning. // createExpIfNecessary means add expId to encodeExp table. updateAccession too if necessary. -// Returns a new set of mdbObjs that is what can (and should) be used to update the mdb via mdbObjsSetToDb(). +// Returns a new set of mdbObjs that is what can (and should) +// be used to update the mdb via mdbObjsSetToDb(). boolean mdbObjIsEncode(struct mdbObj *mdbObj); // Returns TRUE if MDB object is an ENCODE object (project=wgEncode) boolean mdbObjInComposite(struct mdbObj *mdb, char *composite); // Returns TRUE if metaDb object is in specified composite. -// If composite is NULL, always return true // FIXME: KATE Why return true if composite not defined??? +// If composite is NULL, always return true +// FIXME: KATE Why return true if composite not defined??? // -- Requested by Kate? -- //struct encodeExp *encodeExps(char *composite,char *expTable); //struct mdbObjs *mdbObjsForDefinedExpId(int expId); // Returns the mdb objects belonging to a single encode experiment defined in the encodExp table // --------------- Free at last ---------------- void mdbObjsFree(struct mdbObj **mdbObjsPtr); // Frees one or more metadata objects and any contained mdbVars. Will free any hashes as well. #define mdbObjFree(mdbObjPtr) mdbObjsFree(mdbObjPtr) void mdbVarsFree(struct mdbVar **mdbVarsPtr); // Frees one or more metadata vars and any val as well #define mdbVarFree(mdbVarPtr) mdbVarsFree(mdbVarPtr) void mdbByVarsFree(struct mdbByVar **mdbByVarsPtr); // Frees one or more metadata vars and any contained vals and objs. Will free any hashes as well. #define mdbByVarFree(mdbByVarPtr) mdbByVarsFree(mdbByVarPtr) // ----------------- CGI specific routines for use with tdb ----------------- const struct mdbObj *metadataForTable(char *db,struct trackDb *tdb,char *table); // Returns the metadata for a table. NEVER FREE THIS STRUCT! // This is the main routine for CGIs to access metadata const char *metadataFindValue(struct trackDb *tdb, char *var); // Finds the val associated with the var or retruns NULL #define MDB_VAL_STD_TRUNCATION 64 struct mdbObj *mdbObjSearch(struct sqlConnection *conn, char *var, char *val, char *op, int limit); -// Search the metaDb table for objs by var and val. Can restrict by op "is", "like", "in" and accept (non-zero) limited string size +// Search the metaDb table for objs by var and val. +// Can restrict by op "is", "like", "in" and accept (non-zero) limited string size // Search is via mysql, so it's case-insensitive. Return is sorted on obj. -struct mdbObj *mdbObjRepeatedSearch(struct sqlConnection *conn,struct slPair *varValPairs,boolean tables,boolean files); +struct mdbObj *mdbObjRepeatedSearch(struct sqlConnection *conn,struct slPair *varValPairs, + boolean tables,boolean files); // Search the metaDb table for objs by var,val pairs. Uses mdbCvSearchMethod() if available. // This method will use mdbObjsQueryByVars() -struct slName *mdbObjNameSearch(struct sqlConnection *conn, char *var, char *val, char *op, int limit, boolean tables, boolean files); -// Search the metaDb table for objs by var and val. Can restrict by op "is" or "like" and accept (non-zero) limited string size +struct slName *mdbObjNameSearch(struct sqlConnection *conn, char *var, char *val, char *op, + int limit, boolean tables, boolean files); +// Search the metaDb table for objs by var and val. +// Can restrict by op "is" or "like" and accept (non-zero) limited string size // Search is via mysql, so it's case-insensitive. Return is sorted on obj. -struct slName *mdbValSearch(struct sqlConnection *conn, char *var, int limit, boolean hasTableName, boolean hasFileName); -// Search the metaDb table for vals by var. Can impose (non-zero) limit on returned string size of val +struct slName *mdbValSearch(struct sqlConnection *conn, char *var, int limit, + boolean hasTableName, boolean hasFileName); +// Search the metaDb table for vals by var. +// Can impose (non-zero) limit on returned string size of val // Search is via mysql, so it's case-insensitive. Return is sorted on val. -// Searchable vars are only for table or file objects. Further restrict to vars associated with tableName, fileName or both. - -struct slPair *mdbValLabelSearch(struct sqlConnection *conn, char *var, int limit, boolean tags, boolean hasTableName, boolean hasFileName); -// Search the metaDb table for vals by var and returns val (as pair->name) and controlled vocabulary (cv) label -// (if it exists) (as pair->val). Can impose (non-zero) limit on returned string size of name. -// Searchable vars are only for table or file objects. Further restrict to vars associated with tableName, fileName or both. -// Return is case insensitive sorted on label (cv label or else val). If requested, return cv tag instead of mdb val. +// Searchable vars are only for table or file objects. +// Further restrict to vars associated with tableName, fileName or both. + +struct slPair *mdbValLabelSearch(struct sqlConnection *conn, char *var, int limit, boolean tags, + boolean hasTableName, boolean hasFileName); +// Search the metaDb table for vals by var and returns val (as pair->name) +// and controlled vocabulary (cv) label (if it exists) (as pair->val). +// Can impose (non-zero) limit on returned string size of name. +// Searchable vars are only for table or file objects. +// Further restrict to vars associated with tableName, fileName or both. +// Return is case insensitive sorted on label (cv label or else val). +// If requested, return cv tag instead of mdb val. #define mdbPairVal(pair) (pair)->name #define mdbPairLabel(pair) (pair)->val -struct slPair *mdbVarsSearchable(struct sqlConnection *conn, boolean hasTableName, boolean hasFileName); +struct slPair *mdbVarsSearchable(struct sqlConnection *conn, boolean hasTableName, + boolean hasFileName); // returns a white list of mdb vars that actually exist in the current DB. -// Searchable vars are only for table or file objects. Further restrict to vars associated with tableName, fileName or both. +// Searchable vars are only for table or file objects. +// Further restrict to vars associated with tableName, fileName or both. #endif /* MDB_H */