/* cdw.h was originally generated by the autoSql program, which also * generated cdw.c and cdw.sql. This header links the database and * the RAM representation of objects. */ #ifndef CDW_H #define CDW_H #include "jksql.h" #define CDWSETTINGS_NUM_COLS 3 extern char *cdwSettingsCommaSepFieldNames; struct cdwSettings /* Settings used to configure warehouse */ { struct cdwSettings *next; /* Next in singly linked list. */ unsigned id; /* Settings ID */ char *name; /* Settings name, can't be reused */ char *val; /* Settings value, some undefined but not huge thing */ }; void cdwSettingsStaticLoad(char **row, struct cdwSettings *ret); /* Load a row from cdwSettings table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwSettings *cdwSettingsLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwSettings 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 cdwSettingsFreeList(). */ void cdwSettingsSaveToDb(struct sqlConnection *conn, struct cdwSettings *el, char *tableName, int updateSize); /* Save cdwSettings 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. This function automatically escapes quoted strings for mysql. */ struct cdwSettings *cdwSettingsLoad(char **row); /* Load a cdwSettings from row fetched with select * from cdwSettings * from database. Dispose of this with cdwSettingsFree(). */ struct cdwSettings *cdwSettingsLoadAll(char *fileName); /* Load all cdwSettings from whitespace-separated file. * Dispose of this with cdwSettingsFreeList(). */ struct cdwSettings *cdwSettingsLoadAllByChar(char *fileName, char chopper); /* Load all cdwSettings from chopper separated file. * Dispose of this with cdwSettingsFreeList(). */ #define cdwSettingsLoadAllByTab(a) cdwSettingsLoadAllByChar(a, '\t'); /* Load all cdwSettings from tab separated file. * Dispose of this with cdwSettingsFreeList(). */ struct cdwSettings *cdwSettingsCommaIn(char **pS, struct cdwSettings *ret); /* Create a cdwSettings out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwSettings */ void cdwSettingsFree(struct cdwSettings **pEl); /* Free a single dynamically allocated cdwSettings such as created * with cdwSettingsLoad(). */ void cdwSettingsFreeList(struct cdwSettings **pList); /* Free a list of dynamically allocated cdwSettings's */ void cdwSettingsOutput(struct cdwSettings *el, FILE *f, char sep, char lastSep); /* Print out cdwSettings. Separate fields with sep. Follow last field with lastSep. */ #define cdwSettingsTabOut(el,f) cdwSettingsOutput(el,f,'\t','\n'); /* Print out cdwSettings as a line in a tab-separated file. */ #define cdwSettingsCommaOut(el,f) cdwSettingsOutput(el,f,',',','); /* Print out cdwSettings as a comma separated list including final comma. */ #define CDWUSER_NUM_COLS 5 extern char *cdwUserCommaSepFieldNames; struct cdwUser /* Someone who submits files to or otherwise interacts with big data warehouse */ { struct cdwUser *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented user ID */ char *email; /* Email address - required */ char uuid[38]; /* Help to synchronize us with Stanford. */ signed char isAdmin; /* If true the use can modify other people's files too. */ unsigned primaryGroup; /* If this is non-zero then we'll make files with this group association. */ }; void cdwUserStaticLoad(char **row, struct cdwUser *ret); /* Load a row from cdwUser table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwUser *cdwUserLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwUser 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 cdwUserFreeList(). */ void cdwUserSaveToDb(struct sqlConnection *conn, struct cdwUser *el, char *tableName, int updateSize); /* Save cdwUser 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. This function automatically escapes quoted strings for mysql. */ struct cdwUser *cdwUserLoad(char **row); /* Load a cdwUser from row fetched with select * from cdwUser * from database. Dispose of this with cdwUserFree(). */ struct cdwUser *cdwUserLoadAll(char *fileName); /* Load all cdwUser from whitespace-separated file. * Dispose of this with cdwUserFreeList(). */ struct cdwUser *cdwUserLoadAllByChar(char *fileName, char chopper); /* Load all cdwUser from chopper separated file. * Dispose of this with cdwUserFreeList(). */ #define cdwUserLoadAllByTab(a) cdwUserLoadAllByChar(a, '\t'); /* Load all cdwUser from tab separated file. * Dispose of this with cdwUserFreeList(). */ struct cdwUser *cdwUserCommaIn(char **pS, struct cdwUser *ret); /* Create a cdwUser out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwUser */ void cdwUserFree(struct cdwUser **pEl); /* Free a single dynamically allocated cdwUser such as created * with cdwUserLoad(). */ void cdwUserFreeList(struct cdwUser **pList); /* Free a list of dynamically allocated cdwUser's */ void cdwUserOutput(struct cdwUser *el, FILE *f, char sep, char lastSep); /* Print out cdwUser. Separate fields with sep. Follow last field with lastSep. */ #define cdwUserTabOut(el,f) cdwUserOutput(el,f,'\t','\n'); /* Print out cdwUser as a line in a tab-separated file. */ #define cdwUserCommaOut(el,f) cdwUserOutput(el,f,',',','); /* Print out cdwUser as a comma separated list including final comma. */ #define CDWGROUP_NUM_COLS 3 extern char *cdwGroupCommaSepFieldNames; struct cdwGroup /* A group in the access control sense */ { struct cdwGroup *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented user ID */ char *name; /* Symbolic name for group, should follow rules of a lowercase C symbol. */ char *description; /* Description of group */ }; void cdwGroupStaticLoad(char **row, struct cdwGroup *ret); /* Load a row from cdwGroup table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwGroup *cdwGroupLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwGroup 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 cdwGroupFreeList(). */ void cdwGroupSaveToDb(struct sqlConnection *conn, struct cdwGroup *el, char *tableName, int updateSize); /* Save cdwGroup 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. This function automatically escapes quoted strings for mysql. */ struct cdwGroup *cdwGroupLoad(char **row); /* Load a cdwGroup from row fetched with select * from cdwGroup * from database. Dispose of this with cdwGroupFree(). */ struct cdwGroup *cdwGroupLoadAll(char *fileName); /* Load all cdwGroup from whitespace-separated file. * Dispose of this with cdwGroupFreeList(). */ struct cdwGroup *cdwGroupLoadAllByChar(char *fileName, char chopper); /* Load all cdwGroup from chopper separated file. * Dispose of this with cdwGroupFreeList(). */ #define cdwGroupLoadAllByTab(a) cdwGroupLoadAllByChar(a, '\t'); /* Load all cdwGroup from tab separated file. * Dispose of this with cdwGroupFreeList(). */ struct cdwGroup *cdwGroupCommaIn(char **pS, struct cdwGroup *ret); /* Create a cdwGroup out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwGroup */ void cdwGroupFree(struct cdwGroup **pEl); /* Free a single dynamically allocated cdwGroup such as created * with cdwGroupLoad(). */ void cdwGroupFreeList(struct cdwGroup **pList); /* Free a list of dynamically allocated cdwGroup's */ void cdwGroupOutput(struct cdwGroup *el, FILE *f, char sep, char lastSep); /* Print out cdwGroup. Separate fields with sep. Follow last field with lastSep. */ #define cdwGroupTabOut(el,f) cdwGroupOutput(el,f,'\t','\n'); /* Print out cdwGroup as a line in a tab-separated file. */ #define cdwGroupCommaOut(el,f) cdwGroupOutput(el,f,',',','); /* Print out cdwGroup as a comma separated list including final comma. */ #define CDWGROUPFILE_NUM_COLS 2 extern char *cdwGroupFileCommaSepFieldNames; struct cdwGroupFile /* Association table between cdwFile and cdwGroup */ { struct cdwGroupFile *next; /* Next in singly linked list. */ unsigned fileId; /* What is the file */ unsigned groupId; /* What is the group */ }; void cdwGroupFileStaticLoad(char **row, struct cdwGroupFile *ret); /* Load a row from cdwGroupFile table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwGroupFile *cdwGroupFileLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwGroupFile 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 cdwGroupFileFreeList(). */ void cdwGroupFileSaveToDb(struct sqlConnection *conn, struct cdwGroupFile *el, char *tableName, int updateSize); /* Save cdwGroupFile 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. This function automatically escapes quoted strings for mysql. */ struct cdwGroupFile *cdwGroupFileLoad(char **row); /* Load a cdwGroupFile from row fetched with select * from cdwGroupFile * from database. Dispose of this with cdwGroupFileFree(). */ struct cdwGroupFile *cdwGroupFileLoadAll(char *fileName); /* Load all cdwGroupFile from whitespace-separated file. * Dispose of this with cdwGroupFileFreeList(). */ struct cdwGroupFile *cdwGroupFileLoadAllByChar(char *fileName, char chopper); /* Load all cdwGroupFile from chopper separated file. * Dispose of this with cdwGroupFileFreeList(). */ #define cdwGroupFileLoadAllByTab(a) cdwGroupFileLoadAllByChar(a, '\t'); /* Load all cdwGroupFile from tab separated file. * Dispose of this with cdwGroupFileFreeList(). */ struct cdwGroupFile *cdwGroupFileCommaIn(char **pS, struct cdwGroupFile *ret); /* Create a cdwGroupFile out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwGroupFile */ void cdwGroupFileFree(struct cdwGroupFile **pEl); /* Free a single dynamically allocated cdwGroupFile such as created * with cdwGroupFileLoad(). */ void cdwGroupFileFreeList(struct cdwGroupFile **pList); /* Free a list of dynamically allocated cdwGroupFile's */ void cdwGroupFileOutput(struct cdwGroupFile *el, FILE *f, char sep, char lastSep); /* Print out cdwGroupFile. Separate fields with sep. Follow last field with lastSep. */ #define cdwGroupFileTabOut(el,f) cdwGroupFileOutput(el,f,'\t','\n'); /* Print out cdwGroupFile as a line in a tab-separated file. */ #define cdwGroupFileCommaOut(el,f) cdwGroupFileOutput(el,f,',',','); /* Print out cdwGroupFile as a comma separated list including final comma. */ #define CDWGROUPUSER_NUM_COLS 2 extern char *cdwGroupUserCommaSepFieldNames; struct cdwGroupUser /* Association table between cdwGroup and cdwUser */ { struct cdwGroupUser *next; /* Next in singly linked list. */ unsigned userId; /* What is the user */ unsigned groupId; /* What is the group */ }; void cdwGroupUserStaticLoad(char **row, struct cdwGroupUser *ret); /* Load a row from cdwGroupUser table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwGroupUser *cdwGroupUserLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwGroupUser 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 cdwGroupUserFreeList(). */ void cdwGroupUserSaveToDb(struct sqlConnection *conn, struct cdwGroupUser *el, char *tableName, int updateSize); /* Save cdwGroupUser 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. This function automatically escapes quoted strings for mysql. */ struct cdwGroupUser *cdwGroupUserLoad(char **row); /* Load a cdwGroupUser from row fetched with select * from cdwGroupUser * from database. Dispose of this with cdwGroupUserFree(). */ struct cdwGroupUser *cdwGroupUserLoadAll(char *fileName); /* Load all cdwGroupUser from whitespace-separated file. * Dispose of this with cdwGroupUserFreeList(). */ struct cdwGroupUser *cdwGroupUserLoadAllByChar(char *fileName, char chopper); /* Load all cdwGroupUser from chopper separated file. * Dispose of this with cdwGroupUserFreeList(). */ #define cdwGroupUserLoadAllByTab(a) cdwGroupUserLoadAllByChar(a, '\t'); /* Load all cdwGroupUser from tab separated file. * Dispose of this with cdwGroupUserFreeList(). */ struct cdwGroupUser *cdwGroupUserCommaIn(char **pS, struct cdwGroupUser *ret); /* Create a cdwGroupUser out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwGroupUser */ void cdwGroupUserFree(struct cdwGroupUser **pEl); /* Free a single dynamically allocated cdwGroupUser such as created * with cdwGroupUserLoad(). */ void cdwGroupUserFreeList(struct cdwGroupUser **pList); /* Free a list of dynamically allocated cdwGroupUser's */ void cdwGroupUserOutput(struct cdwGroupUser *el, FILE *f, char sep, char lastSep); /* Print out cdwGroupUser. Separate fields with sep. Follow last field with lastSep. */ #define cdwGroupUserTabOut(el,f) cdwGroupUserOutput(el,f,'\t','\n'); /* Print out cdwGroupUser as a line in a tab-separated file. */ #define cdwGroupUserCommaOut(el,f) cdwGroupUserOutput(el,f,',',','); /* Print out cdwGroupUser as a comma separated list including final comma. */ #define CDWLAB_NUM_COLS 5 extern char *cdwLabCommaSepFieldNames; struct cdwLab /* A contributing lab */ { struct cdwLab *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented user ID */ char *name; /* Shorthand name for lab, all lower case */ char *pi; /* Principle investigator responsible for lab */ char *institution; /* University or other institution hosting lab */ char *url; /* URL of lab page */ }; void cdwLabStaticLoad(char **row, struct cdwLab *ret); /* Load a row from cdwLab table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwLab *cdwLabLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwLab 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 cdwLabFreeList(). */ void cdwLabSaveToDb(struct sqlConnection *conn, struct cdwLab *el, char *tableName, int updateSize); /* Save cdwLab 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. This function automatically escapes quoted strings for mysql. */ struct cdwLab *cdwLabLoad(char **row); /* Load a cdwLab from row fetched with select * from cdwLab * from database. Dispose of this with cdwLabFree(). */ struct cdwLab *cdwLabLoadAll(char *fileName); /* Load all cdwLab from whitespace-separated file. * Dispose of this with cdwLabFreeList(). */ struct cdwLab *cdwLabLoadAllByChar(char *fileName, char chopper); /* Load all cdwLab from chopper separated file. * Dispose of this with cdwLabFreeList(). */ #define cdwLabLoadAllByTab(a) cdwLabLoadAllByChar(a, '\t'); /* Load all cdwLab from tab separated file. * Dispose of this with cdwLabFreeList(). */ struct cdwLab *cdwLabCommaIn(char **pS, struct cdwLab *ret); /* Create a cdwLab out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwLab */ void cdwLabFree(struct cdwLab **pEl); /* Free a single dynamically allocated cdwLab such as created * with cdwLabLoad(). */ void cdwLabFreeList(struct cdwLab **pList); /* Free a list of dynamically allocated cdwLab's */ void cdwLabOutput(struct cdwLab *el, FILE *f, char sep, char lastSep); /* Print out cdwLab. Separate fields with sep. Follow last field with lastSep. */ #define cdwLabTabOut(el,f) cdwLabOutput(el,f,'\t','\n'); /* Print out cdwLab as a line in a tab-separated file. */ #define cdwLabCommaOut(el,f) cdwLabOutput(el,f,',',','); /* Print out cdwLab as a comma separated list including final comma. */ #define CDWSCRIPTREGISTRY_NUM_COLS 6 extern char *cdwScriptRegistryCommaSepFieldNames; struct cdwScriptRegistry /* A script that is authorized to submit on behalf of a user */ { struct cdwScriptRegistry *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented script ID */ unsigned userId; /* Associated user */ char *name; /* Script name - unique in system and autogenerated */ char *description; /* Script description */ char *secretHash; /* Hashed script password */ int submitCount; /* Number of submissions attempted */ }; void cdwScriptRegistryStaticLoad(char **row, struct cdwScriptRegistry *ret); /* Load a row from cdwScriptRegistry table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwScriptRegistry *cdwScriptRegistryLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwScriptRegistry 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 cdwScriptRegistryFreeList(). */ void cdwScriptRegistrySaveToDb(struct sqlConnection *conn, struct cdwScriptRegistry *el, char *tableName, int updateSize); /* Save cdwScriptRegistry 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. This function automatically escapes quoted strings for mysql. */ struct cdwScriptRegistry *cdwScriptRegistryLoad(char **row); /* Load a cdwScriptRegistry from row fetched with select * from cdwScriptRegistry * from database. Dispose of this with cdwScriptRegistryFree(). */ struct cdwScriptRegistry *cdwScriptRegistryLoadAll(char *fileName); /* Load all cdwScriptRegistry from whitespace-separated file. * Dispose of this with cdwScriptRegistryFreeList(). */ struct cdwScriptRegistry *cdwScriptRegistryLoadAllByChar(char *fileName, char chopper); /* Load all cdwScriptRegistry from chopper separated file. * Dispose of this with cdwScriptRegistryFreeList(). */ #define cdwScriptRegistryLoadAllByTab(a) cdwScriptRegistryLoadAllByChar(a, '\t'); /* Load all cdwScriptRegistry from tab separated file. * Dispose of this with cdwScriptRegistryFreeList(). */ struct cdwScriptRegistry *cdwScriptRegistryCommaIn(char **pS, struct cdwScriptRegistry *ret); /* Create a cdwScriptRegistry out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwScriptRegistry */ void cdwScriptRegistryFree(struct cdwScriptRegistry **pEl); /* Free a single dynamically allocated cdwScriptRegistry such as created * with cdwScriptRegistryLoad(). */ void cdwScriptRegistryFreeList(struct cdwScriptRegistry **pList); /* Free a list of dynamically allocated cdwScriptRegistry's */ void cdwScriptRegistryOutput(struct cdwScriptRegistry *el, FILE *f, char sep, char lastSep); /* Print out cdwScriptRegistry. Separate fields with sep. Follow last field with lastSep. */ #define cdwScriptRegistryTabOut(el,f) cdwScriptRegistryOutput(el,f,'\t','\n'); /* Print out cdwScriptRegistry as a line in a tab-separated file. */ #define cdwScriptRegistryCommaOut(el,f) cdwScriptRegistryOutput(el,f,',',','); /* Print out cdwScriptRegistry as a comma separated list including final comma. */ #define CDWHOST_NUM_COLS 10 extern char *cdwHostCommaSepFieldNames; struct cdwHost /* A web host we have collected files from - something like www.ncbi.nlm.gov or google.com */ { struct cdwHost *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented host id */ char *name; /* Name (before DNS lookup) */ long long lastOkTime; /* Last time host was ok in seconds since 1970 */ long long lastNotOkTime; /* Last time host was not ok in seconds since 1970 */ long long firstAdded; /* Time host was first seen */ char *errorMessage; /* If non-empty contains last error message from host. If empty host is ok */ long long openSuccesses; /* Number of times files have been opened ok from this host */ long long openFails; /* Number of times files have failed to open from this host */ long long historyBits; /* Open history with most recent in least significant bit. 0 for connection failed, 1 for success */ int paraFetchStreams; /* Number of open streams for paraFetch command. 10 for most places, 30 for Barcelona */ }; void cdwHostStaticLoad(char **row, struct cdwHost *ret); /* Load a row from cdwHost table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwHost *cdwHostLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwHost 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 cdwHostFreeList(). */ void cdwHostSaveToDb(struct sqlConnection *conn, struct cdwHost *el, char *tableName, int updateSize); /* Save cdwHost 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. This function automatically escapes quoted strings for mysql. */ struct cdwHost *cdwHostLoad(char **row); /* Load a cdwHost from row fetched with select * from cdwHost * from database. Dispose of this with cdwHostFree(). */ struct cdwHost *cdwHostLoadAll(char *fileName); /* Load all cdwHost from whitespace-separated file. * Dispose of this with cdwHostFreeList(). */ struct cdwHost *cdwHostLoadAllByChar(char *fileName, char chopper); /* Load all cdwHost from chopper separated file. * Dispose of this with cdwHostFreeList(). */ #define cdwHostLoadAllByTab(a) cdwHostLoadAllByChar(a, '\t'); /* Load all cdwHost from tab separated file. * Dispose of this with cdwHostFreeList(). */ struct cdwHost *cdwHostCommaIn(char **pS, struct cdwHost *ret); /* Create a cdwHost out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwHost */ void cdwHostFree(struct cdwHost **pEl); /* Free a single dynamically allocated cdwHost such as created * with cdwHostLoad(). */ void cdwHostFreeList(struct cdwHost **pList); /* Free a list of dynamically allocated cdwHost's */ void cdwHostOutput(struct cdwHost *el, FILE *f, char sep, char lastSep); /* Print out cdwHost. Separate fields with sep. Follow last field with lastSep. */ #define cdwHostTabOut(el,f) cdwHostOutput(el,f,'\t','\n'); /* Print out cdwHost as a line in a tab-separated file. */ #define cdwHostCommaOut(el,f) cdwHostOutput(el,f,',',','); /* Print out cdwHost as a comma separated list including final comma. */ #define CDWSUBMITDIR_NUM_COLS 10 extern char *cdwSubmitDirCommaSepFieldNames; struct cdwSubmitDir /* An external data directory we have collected a submit from */ { struct cdwSubmitDir *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented id */ char *url; /* Web-mounted directory. Includes protocol, host, and final '/' */ unsigned hostId; /* Id of host it's on */ long long lastOkTime; /* Last time submit dir was ok in seconds since 1970 */ long long lastNotOkTime; /* Last time submit dir was not ok in seconds since 1970 */ long long firstAdded; /* Time submit dir was first seen */ char *errorMessage; /* If non-empty contains last error message from dir. If empty dir is ok */ long long openSuccesses; /* Number of times files have been opened ok from this dir */ long long openFails; /* Number of times files have failed to open from this dir */ long long historyBits; /* Open history with most recent in least significant bit. 0 for upload failed, 1 for success */ }; void cdwSubmitDirStaticLoad(char **row, struct cdwSubmitDir *ret); /* Load a row from cdwSubmitDir table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwSubmitDir *cdwSubmitDirLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwSubmitDir 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 cdwSubmitDirFreeList(). */ void cdwSubmitDirSaveToDb(struct sqlConnection *conn, struct cdwSubmitDir *el, char *tableName, int updateSize); /* Save cdwSubmitDir 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. This function automatically escapes quoted strings for mysql. */ struct cdwSubmitDir *cdwSubmitDirLoad(char **row); /* Load a cdwSubmitDir from row fetched with select * from cdwSubmitDir * from database. Dispose of this with cdwSubmitDirFree(). */ struct cdwSubmitDir *cdwSubmitDirLoadAll(char *fileName); /* Load all cdwSubmitDir from whitespace-separated file. * Dispose of this with cdwSubmitDirFreeList(). */ struct cdwSubmitDir *cdwSubmitDirLoadAllByChar(char *fileName, char chopper); /* Load all cdwSubmitDir from chopper separated file. * Dispose of this with cdwSubmitDirFreeList(). */ #define cdwSubmitDirLoadAllByTab(a) cdwSubmitDirLoadAllByChar(a, '\t'); /* Load all cdwSubmitDir from tab separated file. * Dispose of this with cdwSubmitDirFreeList(). */ struct cdwSubmitDir *cdwSubmitDirCommaIn(char **pS, struct cdwSubmitDir *ret); /* Create a cdwSubmitDir out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwSubmitDir */ void cdwSubmitDirFree(struct cdwSubmitDir **pEl); /* Free a single dynamically allocated cdwSubmitDir such as created * with cdwSubmitDirLoad(). */ void cdwSubmitDirFreeList(struct cdwSubmitDir **pList); /* Free a list of dynamically allocated cdwSubmitDir's */ void cdwSubmitDirOutput(struct cdwSubmitDir *el, FILE *f, char sep, char lastSep); /* Print out cdwSubmitDir. Separate fields with sep. Follow last field with lastSep. */ #define cdwSubmitDirTabOut(el,f) cdwSubmitDirOutput(el,f,'\t','\n'); /* Print out cdwSubmitDir as a line in a tab-separated file. */ #define cdwSubmitDirCommaOut(el,f) cdwSubmitDirOutput(el,f,',',','); /* Print out cdwSubmitDir as a comma separated list including final comma. */ #define CDWMETATAGS_NUM_COLS 3 extern char *cdwMetaTagsCommaSepFieldNames; struct cdwMetaTags /* Where we keep expanded metadata tags for each file, though many share. */ { struct cdwMetaTags *next; /* Next in singly linked list. */ unsigned id; /* Autoincrementing table id */ char md5[33]; /* md5 sum of tags string */ char *tags; /* CGI encoded name=val pairs from manifest */ }; void cdwMetaTagsStaticLoad(char **row, struct cdwMetaTags *ret); /* Load a row from cdwMetaTags table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwMetaTags *cdwMetaTagsLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwMetaTags 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 cdwMetaTagsFreeList(). */ void cdwMetaTagsSaveToDb(struct sqlConnection *conn, struct cdwMetaTags *el, char *tableName, int updateSize); /* Save cdwMetaTags 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. This function automatically escapes quoted strings for mysql. */ struct cdwMetaTags *cdwMetaTagsLoad(char **row); /* Load a cdwMetaTags from row fetched with select * from cdwMetaTags * from database. Dispose of this with cdwMetaTagsFree(). */ struct cdwMetaTags *cdwMetaTagsLoadAll(char *fileName); /* Load all cdwMetaTags from whitespace-separated file. * Dispose of this with cdwMetaTagsFreeList(). */ struct cdwMetaTags *cdwMetaTagsLoadAllByChar(char *fileName, char chopper); /* Load all cdwMetaTags from chopper separated file. * Dispose of this with cdwMetaTagsFreeList(). */ #define cdwMetaTagsLoadAllByTab(a) cdwMetaTagsLoadAllByChar(a, '\t'); /* Load all cdwMetaTags from tab separated file. * Dispose of this with cdwMetaTagsFreeList(). */ struct cdwMetaTags *cdwMetaTagsCommaIn(char **pS, struct cdwMetaTags *ret); /* Create a cdwMetaTags out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwMetaTags */ void cdwMetaTagsFree(struct cdwMetaTags **pEl); /* Free a single dynamically allocated cdwMetaTags such as created * with cdwMetaTagsLoad(). */ void cdwMetaTagsFreeList(struct cdwMetaTags **pList); /* Free a list of dynamically allocated cdwMetaTags's */ void cdwMetaTagsOutput(struct cdwMetaTags *el, FILE *f, char sep, char lastSep); /* Print out cdwMetaTags. Separate fields with sep. Follow last field with lastSep. */ #define cdwMetaTagsTabOut(el,f) cdwMetaTagsOutput(el,f,'\t','\n'); /* Print out cdwMetaTags as a line in a tab-separated file. */ #define cdwMetaTagsCommaOut(el,f) cdwMetaTagsOutput(el,f,',',','); /* Print out cdwMetaTags as a comma separated list including final comma. */ #define CDWFILE_NUM_COLS 19 extern char *cdwFileCommaSepFieldNames; struct cdwFile /* A file we are tracking that we intend to and maybe have uploaded */ { struct cdwFile *next; /* Next in singly linked list. */ unsigned id; /* Autoincrementing file id */ unsigned submitId; /* Links to id in submit table */ unsigned submitDirId; /* Links to id in submitDir table */ unsigned userId; /* Id in user table of file owner */ char *submitFileName; /* File name in submit relative to submit dir */ char *cdwFileName; /* File name in big data warehouse relative to cdw root dir */ long long startUploadTime; /* Time when upload started - 0 if not started */ long long endUploadTime; /* Time when upload finished - 0 if not finished */ long long updateTime; /* Update time (on system it was uploaded from) */ long long size; /* File size in manifest */ char md5[33]; /* md5 sum of file contents */ char *tags; /* CGI encoded name=val pairs from manifest */ unsigned metaTagsId; /* ID of associated metadata tags */ char *errorMessage; /* If non-empty contains last error message from upload. If empty upload is ok */ char *deprecated; /* If non-empty why you shouldn't use this file any more. */ unsigned replacedBy; /* If non-zero id of file that replaces this one. */ signed char userAccess; /* 0 - no, 1 - read, 2 - read/write */ signed char groupAccess; /* 0 - no, 1 - read, 2 - read/write */ signed char allAccess; /* 0 - no, 1 - read, 2 - read/write */ }; void cdwFileStaticLoad(char **row, struct cdwFile *ret); /* Load a row from cdwFile table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwFile *cdwFileLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwFile 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 cdwFileFreeList(). */ void cdwFileSaveToDb(struct sqlConnection *conn, struct cdwFile *el, char *tableName, int updateSize); /* Save cdwFile 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. This function automatically escapes quoted strings for mysql. */ struct cdwFile *cdwFileLoad(char **row); /* Load a cdwFile from row fetched with select * from cdwFile * from database. Dispose of this with cdwFileFree(). */ struct cdwFile *cdwFileLoadAll(char *fileName); /* Load all cdwFile from whitespace-separated file. * Dispose of this with cdwFileFreeList(). */ struct cdwFile *cdwFileLoadAllByChar(char *fileName, char chopper); /* Load all cdwFile from chopper separated file. * Dispose of this with cdwFileFreeList(). */ #define cdwFileLoadAllByTab(a) cdwFileLoadAllByChar(a, '\t'); /* Load all cdwFile from tab separated file. * Dispose of this with cdwFileFreeList(). */ struct cdwFile *cdwFileCommaIn(char **pS, struct cdwFile *ret); /* Create a cdwFile out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwFile */ void cdwFileFree(struct cdwFile **pEl); /* Free a single dynamically allocated cdwFile such as created * with cdwFileLoad(). */ void cdwFileFreeList(struct cdwFile **pList); /* Free a list of dynamically allocated cdwFile's */ void cdwFileOutput(struct cdwFile *el, FILE *f, char sep, char lastSep); /* Print out cdwFile. Separate fields with sep. Follow last field with lastSep. */ #define cdwFileTabOut(el,f) cdwFileOutput(el,f,'\t','\n'); /* Print out cdwFile as a line in a tab-separated file. */ #define cdwFileCommaOut(el,f) cdwFileOutput(el,f,',',','); /* Print out cdwFile as a comma separated list including final comma. */ #define CDWSUBMIT_NUM_COLS 18 extern char *cdwSubmitCommaSepFieldNames; struct cdwSubmit /* A data submit, typically containing many files. Always associated with a submit dir. */ { struct cdwSubmit *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented submit id */ char *url; /* Url to validated.txt format file. We copy this file over and give it a fileId if we can. */ long long startUploadTime; /* Time at start of submit */ long long endUploadTime; /* Time at end of upload - 0 if not finished */ unsigned userId; /* Connects to user table id field */ unsigned manifestFileId; /* Points to metadata.txt file for submit. */ unsigned metaFileId; /* Points to meta.txt file for submit */ unsigned submitDirId; /* Points to the submitDir */ unsigned fileCount; /* Number of files that will be in submit if it were complete. */ unsigned oldFiles; /* Number of files in submission that were already in warehouse. */ unsigned newFiles; /* Number of files in submission that are newly uploaded. */ long long byteCount; /* Total bytes in submission including old and new */ long long oldBytes; /* Bytes in old files. */ long long newBytes; /* Bytes in new files (so far). */ char *errorMessage; /* If non-empty contains last error message. If empty submit is ok */ unsigned fileIdInTransit; /* cdwFile.id of file currently being transferred or zero */ unsigned metaChangeCount; /* Number of files where metadata changed by submission */ char *wrangler; /* The UNIX ID of the person who ran cdwSubmit. */ }; void cdwSubmitStaticLoad(char **row, struct cdwSubmit *ret); /* Load a row from cdwSubmit table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwSubmit *cdwSubmitLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwSubmit 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 cdwSubmitFreeList(). */ void cdwSubmitSaveToDb(struct sqlConnection *conn, struct cdwSubmit *el, char *tableName, int updateSize); /* Save cdwSubmit 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. This function automatically escapes quoted strings for mysql. */ struct cdwSubmit *cdwSubmitLoad(char **row); /* Load a cdwSubmit from row fetched with select * from cdwSubmit * from database. Dispose of this with cdwSubmitFree(). */ struct cdwSubmit *cdwSubmitLoadAll(char *fileName); /* Load all cdwSubmit from whitespace-separated file. * Dispose of this with cdwSubmitFreeList(). */ struct cdwSubmit *cdwSubmitLoadAllByChar(char *fileName, char chopper); /* Load all cdwSubmit from chopper separated file. * Dispose of this with cdwSubmitFreeList(). */ #define cdwSubmitLoadAllByTab(a) cdwSubmitLoadAllByChar(a, '\t'); /* Load all cdwSubmit from tab separated file. * Dispose of this with cdwSubmitFreeList(). */ struct cdwSubmit *cdwSubmitCommaIn(char **pS, struct cdwSubmit *ret); /* Create a cdwSubmit out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwSubmit */ void cdwSubmitFree(struct cdwSubmit **pEl); /* Free a single dynamically allocated cdwSubmit such as created * with cdwSubmitLoad(). */ void cdwSubmitFreeList(struct cdwSubmit **pList); /* Free a list of dynamically allocated cdwSubmit's */ void cdwSubmitOutput(struct cdwSubmit *el, FILE *f, char sep, char lastSep); /* Print out cdwSubmit. Separate fields with sep. Follow last field with lastSep. */ #define cdwSubmitTabOut(el,f) cdwSubmitOutput(el,f,'\t','\n'); /* Print out cdwSubmit as a line in a tab-separated file. */ #define cdwSubmitCommaOut(el,f) cdwSubmitOutput(el,f,',',','); /* Print out cdwSubmit as a comma separated list including final comma. */ #define CDWSUBSCRIBER_NUM_COLS 7 extern char *cdwSubscriberCommaSepFieldNames; struct cdwSubscriber /* Subscribers can have programs that are called at various points during data submission */ { struct cdwSubscriber *next; /* Next in singly linked list. */ unsigned id; /* ID of subscriber */ char *name; /* Name of subscriber */ double runOrder; /* Determines order subscribers run in. In case of tie lowest id wins. */ char *filePattern; /* A string with * and ? wildcards to match files we care about */ char *dirPattern; /* A string with * and ? wildcards to match hub dir URLs we care about */ char *tagPattern; /* A cgi-encoded string of tag=wildcard pairs. */ char *onFileEndUpload; /* A unix command string to run with a %u where file id goes */ }; void cdwSubscriberStaticLoad(char **row, struct cdwSubscriber *ret); /* Load a row from cdwSubscriber table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwSubscriber *cdwSubscriberLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwSubscriber 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 cdwSubscriberFreeList(). */ void cdwSubscriberSaveToDb(struct sqlConnection *conn, struct cdwSubscriber *el, char *tableName, int updateSize); /* Save cdwSubscriber 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. This function automatically escapes quoted strings for mysql. */ struct cdwSubscriber *cdwSubscriberLoad(char **row); /* Load a cdwSubscriber from row fetched with select * from cdwSubscriber * from database. Dispose of this with cdwSubscriberFree(). */ struct cdwSubscriber *cdwSubscriberLoadAll(char *fileName); /* Load all cdwSubscriber from whitespace-separated file. * Dispose of this with cdwSubscriberFreeList(). */ struct cdwSubscriber *cdwSubscriberLoadAllByChar(char *fileName, char chopper); /* Load all cdwSubscriber from chopper separated file. * Dispose of this with cdwSubscriberFreeList(). */ #define cdwSubscriberLoadAllByTab(a) cdwSubscriberLoadAllByChar(a, '\t'); /* Load all cdwSubscriber from tab separated file. * Dispose of this with cdwSubscriberFreeList(). */ struct cdwSubscriber *cdwSubscriberCommaIn(char **pS, struct cdwSubscriber *ret); /* Create a cdwSubscriber out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwSubscriber */ void cdwSubscriberFree(struct cdwSubscriber **pEl); /* Free a single dynamically allocated cdwSubscriber such as created * with cdwSubscriberLoad(). */ void cdwSubscriberFreeList(struct cdwSubscriber **pList); /* Free a list of dynamically allocated cdwSubscriber's */ void cdwSubscriberOutput(struct cdwSubscriber *el, FILE *f, char sep, char lastSep); /* Print out cdwSubscriber. Separate fields with sep. Follow last field with lastSep. */ #define cdwSubscriberTabOut(el,f) cdwSubscriberOutput(el,f,'\t','\n'); /* Print out cdwSubscriber as a line in a tab-separated file. */ #define cdwSubscriberCommaOut(el,f) cdwSubscriberOutput(el,f,',',','); /* Print out cdwSubscriber as a comma separated list including final comma. */ #define CDWASSEMBLY_NUM_COLS 8 extern char *cdwAssemblyCommaSepFieldNames; struct cdwAssembly /* An assembly - includes reference to a two bit file, and a little name and summary info. */ { struct cdwAssembly *next; /* Next in singly linked list. */ unsigned id; /* Assembly ID */ unsigned taxon; /* NCBI taxon number */ char *name; /* Some human readable name to distinguish this from other collections of DNA */ char *ucscDb; /* Which UCSC database (mm9? hg19?) associated with it. */ unsigned twoBitId; /* File ID of associated twoBit file */ long long baseCount; /* Count of bases including N's */ long long realBaseCount; /* Count of non-N bases in assembly */ unsigned seqCount; /* Number of chromosomes or other distinct sequences in assembly */ }; void cdwAssemblyStaticLoad(char **row, struct cdwAssembly *ret); /* Load a row from cdwAssembly table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwAssembly *cdwAssemblyLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwAssembly 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 cdwAssemblyFreeList(). */ void cdwAssemblySaveToDb(struct sqlConnection *conn, struct cdwAssembly *el, char *tableName, int updateSize); /* Save cdwAssembly 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. This function automatically escapes quoted strings for mysql. */ struct cdwAssembly *cdwAssemblyLoad(char **row); /* Load a cdwAssembly from row fetched with select * from cdwAssembly * from database. Dispose of this with cdwAssemblyFree(). */ struct cdwAssembly *cdwAssemblyLoadAll(char *fileName); /* Load all cdwAssembly from whitespace-separated file. * Dispose of this with cdwAssemblyFreeList(). */ struct cdwAssembly *cdwAssemblyLoadAllByChar(char *fileName, char chopper); /* Load all cdwAssembly from chopper separated file. * Dispose of this with cdwAssemblyFreeList(). */ #define cdwAssemblyLoadAllByTab(a) cdwAssemblyLoadAllByChar(a, '\t'); /* Load all cdwAssembly from tab separated file. * Dispose of this with cdwAssemblyFreeList(). */ struct cdwAssembly *cdwAssemblyCommaIn(char **pS, struct cdwAssembly *ret); /* Create a cdwAssembly out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwAssembly */ void cdwAssemblyFree(struct cdwAssembly **pEl); /* Free a single dynamically allocated cdwAssembly such as created * with cdwAssemblyLoad(). */ void cdwAssemblyFreeList(struct cdwAssembly **pList); /* Free a list of dynamically allocated cdwAssembly's */ void cdwAssemblyOutput(struct cdwAssembly *el, FILE *f, char sep, char lastSep); /* Print out cdwAssembly. Separate fields with sep. Follow last field with lastSep. */ #define cdwAssemblyTabOut(el,f) cdwAssemblyOutput(el,f,'\t','\n'); /* Print out cdwAssembly as a line in a tab-separated file. */ #define cdwAssemblyCommaOut(el,f) cdwAssemblyOutput(el,f,',',','); /* Print out cdwAssembly as a comma separated list including final comma. */ #define CDWBIOSAMPLE_NUM_COLS 4 extern char *cdwBiosampleCommaSepFieldNames; struct cdwBiosample /* A biosample - not much info here, just enough to drive analysis pipeline */ { struct cdwBiosample *next; /* Next in singly linked list. */ unsigned id; /* Biosample id */ char *term; /* Human readable.. */ unsigned taxon; /* NCBI taxon number - 9606 for human. */ char *sex; /* One letter code: M male, F female, B both, U unknown */ }; void cdwBiosampleStaticLoad(char **row, struct cdwBiosample *ret); /* Load a row from cdwBiosample table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwBiosample *cdwBiosampleLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwBiosample 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 cdwBiosampleFreeList(). */ void cdwBiosampleSaveToDb(struct sqlConnection *conn, struct cdwBiosample *el, char *tableName, int updateSize); /* Save cdwBiosample 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. This function automatically escapes quoted strings for mysql. */ struct cdwBiosample *cdwBiosampleLoad(char **row); /* Load a cdwBiosample from row fetched with select * from cdwBiosample * from database. Dispose of this with cdwBiosampleFree(). */ struct cdwBiosample *cdwBiosampleLoadAll(char *fileName); /* Load all cdwBiosample from whitespace-separated file. * Dispose of this with cdwBiosampleFreeList(). */ struct cdwBiosample *cdwBiosampleLoadAllByChar(char *fileName, char chopper); /* Load all cdwBiosample from chopper separated file. * Dispose of this with cdwBiosampleFreeList(). */ #define cdwBiosampleLoadAllByTab(a) cdwBiosampleLoadAllByChar(a, '\t'); /* Load all cdwBiosample from tab separated file. * Dispose of this with cdwBiosampleFreeList(). */ struct cdwBiosample *cdwBiosampleCommaIn(char **pS, struct cdwBiosample *ret); /* Create a cdwBiosample out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwBiosample */ void cdwBiosampleFree(struct cdwBiosample **pEl); /* Free a single dynamically allocated cdwBiosample such as created * with cdwBiosampleLoad(). */ void cdwBiosampleFreeList(struct cdwBiosample **pList); /* Free a list of dynamically allocated cdwBiosample's */ void cdwBiosampleOutput(struct cdwBiosample *el, FILE *f, char sep, char lastSep); /* Print out cdwBiosample. Separate fields with sep. Follow last field with lastSep. */ #define cdwBiosampleTabOut(el,f) cdwBiosampleOutput(el,f,'\t','\n'); /* Print out cdwBiosample as a line in a tab-separated file. */ #define cdwBiosampleCommaOut(el,f) cdwBiosampleOutput(el,f,',',','); /* Print out cdwBiosample as a comma separated list including final comma. */ #define CDWEXPERIMENT_NUM_COLS 8 extern char *cdwExperimentCommaSepFieldNames; struct cdwExperiment /* An experiment - ideally will include a couple of biological replicates. Downloaded from Stanford. */ { struct cdwExperiment *next; /* Next in singly linked list. */ char accession[17]; /* ID shared with metadata system. */ char *dataType; /* Something liek RNA-seq, DNase-seq, ChIP-seq. Computed at UCSC. */ char *lab; /* Lab PI name and institution. Is lab.title at Stanford. */ char *biosample; /* Cell line name, tissue source, etc. Is biosample_term_name at Stanford. */ char *rfa; /* Something like 'ENCODE2' or 'ENCODE3'. Is award.rfa at Stanford. */ char *assayType; /* Similar to dataType. Is assay_term_name at Stanford. */ char *ipTarget; /* The target for the immunoprecipitation in ChIP & RIP. */ char *control; /* Primary control for experiment. Usually another experiment accession. */ }; void cdwExperimentStaticLoad(char **row, struct cdwExperiment *ret); /* Load a row from cdwExperiment table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwExperiment *cdwExperimentLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwExperiment 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 cdwExperimentFreeList(). */ void cdwExperimentSaveToDb(struct sqlConnection *conn, struct cdwExperiment *el, char *tableName, int updateSize); /* Save cdwExperiment 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. This function automatically escapes quoted strings for mysql. */ struct cdwExperiment *cdwExperimentLoad(char **row); /* Load a cdwExperiment from row fetched with select * from cdwExperiment * from database. Dispose of this with cdwExperimentFree(). */ struct cdwExperiment *cdwExperimentLoadAll(char *fileName); /* Load all cdwExperiment from whitespace-separated file. * Dispose of this with cdwExperimentFreeList(). */ struct cdwExperiment *cdwExperimentLoadAllByChar(char *fileName, char chopper); /* Load all cdwExperiment from chopper separated file. * Dispose of this with cdwExperimentFreeList(). */ #define cdwExperimentLoadAllByTab(a) cdwExperimentLoadAllByChar(a, '\t'); /* Load all cdwExperiment from tab separated file. * Dispose of this with cdwExperimentFreeList(). */ struct cdwExperiment *cdwExperimentCommaIn(char **pS, struct cdwExperiment *ret); /* Create a cdwExperiment out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwExperiment */ void cdwExperimentFree(struct cdwExperiment **pEl); /* Free a single dynamically allocated cdwExperiment such as created * with cdwExperimentLoad(). */ void cdwExperimentFreeList(struct cdwExperiment **pList); /* Free a list of dynamically allocated cdwExperiment's */ void cdwExperimentOutput(struct cdwExperiment *el, FILE *f, char sep, char lastSep); /* Print out cdwExperiment. Separate fields with sep. Follow last field with lastSep. */ #define cdwExperimentTabOut(el,f) cdwExperimentOutput(el,f,'\t','\n'); /* Print out cdwExperiment as a line in a tab-separated file. */ #define cdwExperimentCommaOut(el,f) cdwExperimentOutput(el,f,',',','); /* Print out cdwExperiment as a comma separated list including final comma. */ #define CDWVALIDFILE_NUM_COLS 24 extern char *cdwValidFileCommaSepFieldNames; struct cdwValidFile /* A file that has been uploaded, the format checked, and for which at least minimal metadata exists */ { struct cdwValidFile *next; /* Next in singly linked list. */ unsigned id; /* ID of validated file */ char licensePlate[17]; /* A abc123 looking license-platish thing. */ unsigned fileId; /* Pointer to file in main file table */ char *format; /* What format it's in from manifest */ char *outputType; /* What output_type it is from manifest */ char *experiment; /* What experiment it's in from manifest */ char *replicate; /* What replicate it is from manifest. Values 1,2,3... pooled, or '' */ char *enrichedIn; /* The enriched_in tag from manifest */ char *ucscDb; /* Something like hg19 or mm9 */ long long itemCount; /* # of items in file: reads for fastqs, lines for beds, bases w/data for wig. */ long long basesInItems; /* # of bases in items */ long long sampleCount; /* # of items in sample if we are just subsampling as we do for reads. */ long long basesInSample; /* # of bases in our sample */ char *sampleBed; /* Path to a temporary bed file holding sample items */ double mapRatio; /* Proportion of items that map to genome */ double sampleCoverage; /* Proportion of assembly covered by at least one item in sample */ double depth; /* Estimated genome-equivalents covered by possibly overlapping data */ signed char singleQaStatus; /* 0 = untested, 1 = pass, -1 = fail, 2 = forced pass, -2 = forced fail */ signed char replicateQaStatus; /* 0 = untested, 1 = pass, -1 = fail, 2 = forced pass, -2 = forced fail */ char *part; /* Manifest's file_part. Values 1,2,3... Used for fastqs split for analysis */ char *pairedEnd; /* The paired_end tag from the manifest. Values 1,2 or '' */ signed char qaVersion; /* Version of QA pipeline making status decisions */ double uniqueMapRatio; /* Fraction of reads that map uniquely to genome for bams and fastqs */ char *lane; /* What sequencing lane if any associated with this file. */ }; void cdwValidFileStaticLoad(char **row, struct cdwValidFile *ret); /* Load a row from cdwValidFile table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwValidFile *cdwValidFileLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwValidFile 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 cdwValidFileFreeList(). */ void cdwValidFileSaveToDb(struct sqlConnection *conn, struct cdwValidFile *el, char *tableName, int updateSize); /* Save cdwValidFile 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. This function automatically escapes quoted strings for mysql. */ struct cdwValidFile *cdwValidFileLoad(char **row); /* Load a cdwValidFile from row fetched with select * from cdwValidFile * from database. Dispose of this with cdwValidFileFree(). */ struct cdwValidFile *cdwValidFileLoadAll(char *fileName); /* Load all cdwValidFile from whitespace-separated file. * Dispose of this with cdwValidFileFreeList(). */ struct cdwValidFile *cdwValidFileLoadAllByChar(char *fileName, char chopper); /* Load all cdwValidFile from chopper separated file. * Dispose of this with cdwValidFileFreeList(). */ #define cdwValidFileLoadAllByTab(a) cdwValidFileLoadAllByChar(a, '\t'); /* Load all cdwValidFile from tab separated file. * Dispose of this with cdwValidFileFreeList(). */ struct cdwValidFile *cdwValidFileCommaIn(char **pS, struct cdwValidFile *ret); /* Create a cdwValidFile out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwValidFile */ void cdwValidFileFree(struct cdwValidFile **pEl); /* Free a single dynamically allocated cdwValidFile such as created * with cdwValidFileLoad(). */ void cdwValidFileFreeList(struct cdwValidFile **pList); /* Free a list of dynamically allocated cdwValidFile's */ void cdwValidFileOutput(struct cdwValidFile *el, FILE *f, char sep, char lastSep); /* Print out cdwValidFile. Separate fields with sep. Follow last field with lastSep. */ #define cdwValidFileTabOut(el,f) cdwValidFileOutput(el,f,'\t','\n'); /* Print out cdwValidFile as a line in a tab-separated file. */ #define cdwValidFileCommaOut(el,f) cdwValidFileOutput(el,f,',',','); /* Print out cdwValidFile as a comma separated list including final comma. */ #define CDWFASTQFILE_NUM_COLS 29 extern char *cdwFastqFileCommaSepFieldNames; struct cdwFastqFile /* info on a file in fastq short read format beyond what's in cdwValidFile */ { struct cdwFastqFile *next; /* Next in singly linked list. */ unsigned id; /* ID in this table */ unsigned fileId; /* ID in cdwFile table */ long long sampleCount; /* # of reads in sample. */ long long basesInSample; /* # of bases in sample. */ char *sampleFileName; /* Name of file containing sampleCount randomly selected items from file. */ long long readCount; /* # of reads in file */ long long baseCount; /* # of bases in all reads added up */ double readSizeMean; /* Average read size */ double readSizeStd; /* Standard deviation of read size */ int readSizeMin; /* Minimum read size */ int readSizeMax; /* Maximum read size */ double qualMean; /* Mean quality scored as 10*-log10(errorProbability) or close to it. >25 is good */ double qualStd; /* Standard deviation of quality */ double qualMin; /* Minimum observed quality */ double qualMax; /* Maximum observed quality */ char *qualType; /* For fastq files either 'sanger' or 'illumina' */ int qualZero; /* For fastq files offset to get to zero value in ascii encoding */ double atRatio; /* Ratio of A+T to total sequence (not including Ns) */ double aRatio; /* Ratio of A to total sequence (including Ns) */ double cRatio; /* Ratio of C to total sequence (including Ns) */ double gRatio; /* Ratio of G to total sequence (including Ns) */ double tRatio; /* Ratio of T to total sequence (including Ns) */ double nRatio; /* Ratio of N or . to total sequence */ double *qualPos; /* Mean value for each position in a read up to some max. */ double *aAtPos; /* % of As at each pos */ double *cAtPos; /* % of Cs at each pos */ double *gAtPos; /* % of Gs at each pos */ double *tAtPos; /* % of Ts at each pos */ double *nAtPos; /* % of '.' or 'N' at each pos */ }; struct cdwFastqFile *cdwFastqFileLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwFastqFile 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 cdwFastqFileFreeList(). */ void cdwFastqFileSaveToDb(struct sqlConnection *conn, struct cdwFastqFile *el, char *tableName, int updateSize); /* Save cdwFastqFile 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. This function automatically escapes quoted strings for mysql. */ struct cdwFastqFile *cdwFastqFileLoad(char **row); /* Load a cdwFastqFile from row fetched with select * from cdwFastqFile * from database. Dispose of this with cdwFastqFileFree(). */ struct cdwFastqFile *cdwFastqFileLoadAll(char *fileName); /* Load all cdwFastqFile from whitespace-separated file. * Dispose of this with cdwFastqFileFreeList(). */ struct cdwFastqFile *cdwFastqFileLoadAllByChar(char *fileName, char chopper); /* Load all cdwFastqFile from chopper separated file. * Dispose of this with cdwFastqFileFreeList(). */ #define cdwFastqFileLoadAllByTab(a) cdwFastqFileLoadAllByChar(a, '\t'); /* Load all cdwFastqFile from tab separated file. * Dispose of this with cdwFastqFileFreeList(). */ struct cdwFastqFile *cdwFastqFileCommaIn(char **pS, struct cdwFastqFile *ret); /* Create a cdwFastqFile out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwFastqFile */ void cdwFastqFileFree(struct cdwFastqFile **pEl); /* Free a single dynamically allocated cdwFastqFile such as created * with cdwFastqFileLoad(). */ void cdwFastqFileFreeList(struct cdwFastqFile **pList); /* Free a list of dynamically allocated cdwFastqFile's */ void cdwFastqFileOutput(struct cdwFastqFile *el, FILE *f, char sep, char lastSep); /* Print out cdwFastqFile. Separate fields with sep. Follow last field with lastSep. */ #define cdwFastqFileTabOut(el,f) cdwFastqFileOutput(el,f,'\t','\n'); /* Print out cdwFastqFile as a line in a tab-separated file. */ #define cdwFastqFileCommaOut(el,f) cdwFastqFileOutput(el,f,',',','); /* Print out cdwFastqFile as a comma separated list including final comma. */ #define CDWBAMFILE_NUM_COLS 17 extern char *cdwBamFileCommaSepFieldNames; struct cdwBamFile /* Info on what is in a bam file beyond whet's in cdwValidFile */ { struct cdwBamFile *next; /* Next in singly linked list. */ unsigned id; /* ID in this table */ unsigned fileId; /* ID in cdwFile table. */ signed char isPaired; /* Set to 1 if paired reads, 0 if single */ signed char isSortedByTarget; /* Set to 1 if sorted by target,pos */ long long readCount; /* # of reads in file */ long long readBaseCount; /* # of bases in all reads added up */ long long mappedCount; /* # of reads that map */ long long uniqueMappedCount; /* # of reads that map to a unique position */ double readSizeMean; /* Average read size */ double readSizeStd; /* Standard deviation of read size */ int readSizeMin; /* Minimum read size */ int readSizeMax; /* Maximum read size */ int u4mReadCount; /* Uniquely-mapped 4 million read actual read # (usually 4M) */ int u4mUniquePos; /* Unique positions in target of the 4M reads that map to single pos */ double u4mUniqueRatio; /* u4mUniqPos/u4mReadCount - measures library diversity */ long long targetBaseCount; /* Count of bases in mapping target */ unsigned targetSeqCount; /* Number of chromosomes or other distinct sequences in mapping target */ }; void cdwBamFileStaticLoad(char **row, struct cdwBamFile *ret); /* Load a row from cdwBamFile table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwBamFile *cdwBamFileLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwBamFile 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 cdwBamFileFreeList(). */ void cdwBamFileSaveToDb(struct sqlConnection *conn, struct cdwBamFile *el, char *tableName, int updateSize); /* Save cdwBamFile 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. This function automatically escapes quoted strings for mysql. */ struct cdwBamFile *cdwBamFileLoad(char **row); /* Load a cdwBamFile from row fetched with select * from cdwBamFile * from database. Dispose of this with cdwBamFileFree(). */ struct cdwBamFile *cdwBamFileLoadAll(char *fileName); /* Load all cdwBamFile from whitespace-separated file. * Dispose of this with cdwBamFileFreeList(). */ struct cdwBamFile *cdwBamFileLoadAllByChar(char *fileName, char chopper); /* Load all cdwBamFile from chopper separated file. * Dispose of this with cdwBamFileFreeList(). */ #define cdwBamFileLoadAllByTab(a) cdwBamFileLoadAllByChar(a, '\t'); /* Load all cdwBamFile from tab separated file. * Dispose of this with cdwBamFileFreeList(). */ struct cdwBamFile *cdwBamFileCommaIn(char **pS, struct cdwBamFile *ret); /* Create a cdwBamFile out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwBamFile */ void cdwBamFileFree(struct cdwBamFile **pEl); /* Free a single dynamically allocated cdwBamFile such as created * with cdwBamFileLoad(). */ void cdwBamFileFreeList(struct cdwBamFile **pList); /* Free a list of dynamically allocated cdwBamFile's */ void cdwBamFileOutput(struct cdwBamFile *el, FILE *f, char sep, char lastSep); /* Print out cdwBamFile. Separate fields with sep. Follow last field with lastSep. */ #define cdwBamFileTabOut(el,f) cdwBamFileOutput(el,f,'\t','\n'); /* Print out cdwBamFile as a line in a tab-separated file. */ #define cdwBamFileCommaOut(el,f) cdwBamFileOutput(el,f,',',','); /* Print out cdwBamFile as a comma separated list including final comma. */ #define CDWVCFFILE_NUM_COLS 25 extern char *cdwVcfFileCommaSepFieldNames; struct cdwVcfFile /* Info on what is in a vcf file beyond whet's in cdwValidFile */ { struct cdwVcfFile *next; /* Next in singly linked list. */ unsigned id; /* ID in this table */ unsigned fileId; /* ID in cdwFile table. */ int vcfMajorVersion; /* VCF file major version */ int vcfMinorVersion; /* VCF file minor version */ int genotypeCount; /* How many genotypes of data */ long long itemCount; /* Number of records in VCF file */ int chromsHit; /* Number of chromosomes (or contigs) with data */ long long passItemCount; /* Number of records that PASS listed filter */ double passRatio; /* passItemCount/itemCount */ long long snpItemCount; /* Number of records that are just single base substitution, no indels */ double snpRatio; /* snpItemCount/itemCount */ long long sumOfSizes; /* The sum of sizes of all records */ long long basesCovered; /* Bases with data. Equals sumOfSizes if no overlap of records. */ int xBasesCovered; /* Number of bases of chrX covered */ int yBasesCovered; /* Number of bases of chrY covered */ int mBasesCovered; /* Number of bases of chrM covered */ long long haploidCount; /* Number of genotype calls that are haploid */ double haploidRatio; /* Ratio of hapload to total calls */ long long phasedCount; /* Number of genotype calls that are phased */ double phasedRatio; /* Ration of phased calls to total calls */ signed char gotDepth; /* If true then have DP value in file and in depth stats below */ double depthMin; /* Min DP reported depth */ double depthMean; /* Mean DP value */ double depthMax; /* Max DP value */ double depthStd; /* Standard DP deviation */ }; void cdwVcfFileStaticLoad(char **row, struct cdwVcfFile *ret); /* Load a row from cdwVcfFile table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwVcfFile *cdwVcfFileLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwVcfFile 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 cdwVcfFileFreeList(). */ void cdwVcfFileSaveToDb(struct sqlConnection *conn, struct cdwVcfFile *el, char *tableName, int updateSize); /* Save cdwVcfFile 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. This function automatically escapes quoted strings for mysql. */ struct cdwVcfFile *cdwVcfFileLoad(char **row); /* Load a cdwVcfFile from row fetched with select * from cdwVcfFile * from database. Dispose of this with cdwVcfFileFree(). */ struct cdwVcfFile *cdwVcfFileLoadAll(char *fileName); /* Load all cdwVcfFile from whitespace-separated file. * Dispose of this with cdwVcfFileFreeList(). */ struct cdwVcfFile *cdwVcfFileLoadAllByChar(char *fileName, char chopper); /* Load all cdwVcfFile from chopper separated file. * Dispose of this with cdwVcfFileFreeList(). */ #define cdwVcfFileLoadAllByTab(a) cdwVcfFileLoadAllByChar(a, '\t'); /* Load all cdwVcfFile from tab separated file. * Dispose of this with cdwVcfFileFreeList(). */ struct cdwVcfFile *cdwVcfFileCommaIn(char **pS, struct cdwVcfFile *ret); /* Create a cdwVcfFile out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwVcfFile */ void cdwVcfFileFree(struct cdwVcfFile **pEl); /* Free a single dynamically allocated cdwVcfFile such as created * with cdwVcfFileLoad(). */ void cdwVcfFileFreeList(struct cdwVcfFile **pList); /* Free a list of dynamically allocated cdwVcfFile's */ void cdwVcfFileOutput(struct cdwVcfFile *el, FILE *f, char sep, char lastSep); /* Print out cdwVcfFile. Separate fields with sep. Follow last field with lastSep. */ #define cdwVcfFileTabOut(el,f) cdwVcfFileOutput(el,f,'\t','\n'); /* Print out cdwVcfFile as a line in a tab-separated file. */ #define cdwVcfFileCommaOut(el,f) cdwVcfFileOutput(el,f,',',','); /* Print out cdwVcfFile as a comma separated list including final comma. */ #define CDWQAFAIL_NUM_COLS 4 extern char *cdwQaFailCommaSepFieldNames; struct cdwQaFail /* Record of a QA failure. */ { struct cdwQaFail *next; /* Next in singly linked list. */ unsigned id; /* ID of failure */ unsigned fileId; /* File that failed */ unsigned qaVersion; /* QA pipeline version */ char *reason; /* reason for failure */ }; void cdwQaFailStaticLoad(char **row, struct cdwQaFail *ret); /* Load a row from cdwQaFail table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaFail *cdwQaFailLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaFail 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 cdwQaFailFreeList(). */ void cdwQaFailSaveToDb(struct sqlConnection *conn, struct cdwQaFail *el, char *tableName, int updateSize); /* Save cdwQaFail 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaFail *cdwQaFailLoad(char **row); /* Load a cdwQaFail from row fetched with select * from cdwQaFail * from database. Dispose of this with cdwQaFailFree(). */ struct cdwQaFail *cdwQaFailLoadAll(char *fileName); /* Load all cdwQaFail from whitespace-separated file. * Dispose of this with cdwQaFailFreeList(). */ struct cdwQaFail *cdwQaFailLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaFail from chopper separated file. * Dispose of this with cdwQaFailFreeList(). */ #define cdwQaFailLoadAllByTab(a) cdwQaFailLoadAllByChar(a, '\t'); /* Load all cdwQaFail from tab separated file. * Dispose of this with cdwQaFailFreeList(). */ struct cdwQaFail *cdwQaFailCommaIn(char **pS, struct cdwQaFail *ret); /* Create a cdwQaFail out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaFail */ void cdwQaFailFree(struct cdwQaFail **pEl); /* Free a single dynamically allocated cdwQaFail such as created * with cdwQaFailLoad(). */ void cdwQaFailFreeList(struct cdwQaFail **pList); /* Free a list of dynamically allocated cdwQaFail's */ void cdwQaFailOutput(struct cdwQaFail *el, FILE *f, char sep, char lastSep); /* Print out cdwQaFail. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaFailTabOut(el,f) cdwQaFailOutput(el,f,'\t','\n'); /* Print out cdwQaFail as a line in a tab-separated file. */ #define cdwQaFailCommaOut(el,f) cdwQaFailOutput(el,f,',',','); /* Print out cdwQaFail as a comma separated list including final comma. */ #define CDWQAENRICHTARGET_NUM_COLS 5 extern char *cdwQaEnrichTargetCommaSepFieldNames; struct cdwQaEnrichTarget /* A target for our enrichment analysis. */ { struct cdwQaEnrichTarget *next; /* Next in singly linked list. */ unsigned id; /* ID of this enrichment target */ unsigned assemblyId; /* Which assembly this goes to */ char *name; /* Something like 'exon' or 'promoter' */ unsigned fileId; /* A simple BED 3 format file that defines target. Bases covered are unique */ long long targetSize; /* Total number of bases covered by target */ }; void cdwQaEnrichTargetStaticLoad(char **row, struct cdwQaEnrichTarget *ret); /* Load a row from cdwQaEnrichTarget table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaEnrichTarget *cdwQaEnrichTargetLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaEnrichTarget 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 cdwQaEnrichTargetFreeList(). */ void cdwQaEnrichTargetSaveToDb(struct sqlConnection *conn, struct cdwQaEnrichTarget *el, char *tableName, int updateSize); /* Save cdwQaEnrichTarget 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaEnrichTarget *cdwQaEnrichTargetLoad(char **row); /* Load a cdwQaEnrichTarget from row fetched with select * from cdwQaEnrichTarget * from database. Dispose of this with cdwQaEnrichTargetFree(). */ struct cdwQaEnrichTarget *cdwQaEnrichTargetLoadAll(char *fileName); /* Load all cdwQaEnrichTarget from whitespace-separated file. * Dispose of this with cdwQaEnrichTargetFreeList(). */ struct cdwQaEnrichTarget *cdwQaEnrichTargetLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaEnrichTarget from chopper separated file. * Dispose of this with cdwQaEnrichTargetFreeList(). */ #define cdwQaEnrichTargetLoadAllByTab(a) cdwQaEnrichTargetLoadAllByChar(a, '\t'); /* Load all cdwQaEnrichTarget from tab separated file. * Dispose of this with cdwQaEnrichTargetFreeList(). */ struct cdwQaEnrichTarget *cdwQaEnrichTargetCommaIn(char **pS, struct cdwQaEnrichTarget *ret); /* Create a cdwQaEnrichTarget out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaEnrichTarget */ void cdwQaEnrichTargetFree(struct cdwQaEnrichTarget **pEl); /* Free a single dynamically allocated cdwQaEnrichTarget such as created * with cdwQaEnrichTargetLoad(). */ void cdwQaEnrichTargetFreeList(struct cdwQaEnrichTarget **pList); /* Free a list of dynamically allocated cdwQaEnrichTarget's */ void cdwQaEnrichTargetOutput(struct cdwQaEnrichTarget *el, FILE *f, char sep, char lastSep); /* Print out cdwQaEnrichTarget. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaEnrichTargetTabOut(el,f) cdwQaEnrichTargetOutput(el,f,'\t','\n'); /* Print out cdwQaEnrichTarget as a line in a tab-separated file. */ #define cdwQaEnrichTargetCommaOut(el,f) cdwQaEnrichTargetOutput(el,f,',',','); /* Print out cdwQaEnrichTarget as a comma separated list including final comma. */ #define CDWQAENRICH_NUM_COLS 8 extern char *cdwQaEnrichCommaSepFieldNames; struct cdwQaEnrich /* An enrichment analysis applied to file. */ { struct cdwQaEnrich *next; /* Next in singly linked list. */ unsigned id; /* ID of this enrichment analysis */ unsigned fileId; /* File we are looking at skeptically */ unsigned qaEnrichTargetId; /* Information about a target for this analysis */ long long targetBaseHits; /* Number of hits to bases in target */ long long targetUniqHits; /* Number of unique bases hit in target */ double coverage; /* Coverage of target - just targetUniqHits/targetSize */ double enrichment; /* Amount we hit target/amount we hit genome */ double uniqEnrich; /* coverage/sampleCoverage */ }; void cdwQaEnrichStaticLoad(char **row, struct cdwQaEnrich *ret); /* Load a row from cdwQaEnrich table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaEnrich *cdwQaEnrichLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaEnrich 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 cdwQaEnrichFreeList(). */ void cdwQaEnrichSaveToDb(struct sqlConnection *conn, struct cdwQaEnrich *el, char *tableName, int updateSize); /* Save cdwQaEnrich 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaEnrich *cdwQaEnrichLoad(char **row); /* Load a cdwQaEnrich from row fetched with select * from cdwQaEnrich * from database. Dispose of this with cdwQaEnrichFree(). */ struct cdwQaEnrich *cdwQaEnrichLoadAll(char *fileName); /* Load all cdwQaEnrich from whitespace-separated file. * Dispose of this with cdwQaEnrichFreeList(). */ struct cdwQaEnrich *cdwQaEnrichLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaEnrich from chopper separated file. * Dispose of this with cdwQaEnrichFreeList(). */ #define cdwQaEnrichLoadAllByTab(a) cdwQaEnrichLoadAllByChar(a, '\t'); /* Load all cdwQaEnrich from tab separated file. * Dispose of this with cdwQaEnrichFreeList(). */ struct cdwQaEnrich *cdwQaEnrichCommaIn(char **pS, struct cdwQaEnrich *ret); /* Create a cdwQaEnrich out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaEnrich */ void cdwQaEnrichFree(struct cdwQaEnrich **pEl); /* Free a single dynamically allocated cdwQaEnrich such as created * with cdwQaEnrichLoad(). */ void cdwQaEnrichFreeList(struct cdwQaEnrich **pList); /* Free a list of dynamically allocated cdwQaEnrich's */ void cdwQaEnrichOutput(struct cdwQaEnrich *el, FILE *f, char sep, char lastSep); /* Print out cdwQaEnrich. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaEnrichTabOut(el,f) cdwQaEnrichOutput(el,f,'\t','\n'); /* Print out cdwQaEnrich as a line in a tab-separated file. */ #define cdwQaEnrichCommaOut(el,f) cdwQaEnrichOutput(el,f,',',','); /* Print out cdwQaEnrich as a comma separated list including final comma. */ #define CDWQACONTAMTARGET_NUM_COLS 2 extern char *cdwQaContamTargetCommaSepFieldNames; struct cdwQaContamTarget /* A target for our contamination analysis. */ { struct cdwQaContamTarget *next; /* Next in singly linked list. */ unsigned id; /* ID of this contamination target */ unsigned assemblyId; /* Assembly we're aligning against to check for contamination. */ }; void cdwQaContamTargetStaticLoad(char **row, struct cdwQaContamTarget *ret); /* Load a row from cdwQaContamTarget table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaContamTarget *cdwQaContamTargetLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaContamTarget 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 cdwQaContamTargetFreeList(). */ void cdwQaContamTargetSaveToDb(struct sqlConnection *conn, struct cdwQaContamTarget *el, char *tableName, int updateSize); /* Save cdwQaContamTarget 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaContamTarget *cdwQaContamTargetLoad(char **row); /* Load a cdwQaContamTarget from row fetched with select * from cdwQaContamTarget * from database. Dispose of this with cdwQaContamTargetFree(). */ struct cdwQaContamTarget *cdwQaContamTargetLoadAll(char *fileName); /* Load all cdwQaContamTarget from whitespace-separated file. * Dispose of this with cdwQaContamTargetFreeList(). */ struct cdwQaContamTarget *cdwQaContamTargetLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaContamTarget from chopper separated file. * Dispose of this with cdwQaContamTargetFreeList(). */ #define cdwQaContamTargetLoadAllByTab(a) cdwQaContamTargetLoadAllByChar(a, '\t'); /* Load all cdwQaContamTarget from tab separated file. * Dispose of this with cdwQaContamTargetFreeList(). */ struct cdwQaContamTarget *cdwQaContamTargetCommaIn(char **pS, struct cdwQaContamTarget *ret); /* Create a cdwQaContamTarget out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaContamTarget */ void cdwQaContamTargetFree(struct cdwQaContamTarget **pEl); /* Free a single dynamically allocated cdwQaContamTarget such as created * with cdwQaContamTargetLoad(). */ void cdwQaContamTargetFreeList(struct cdwQaContamTarget **pList); /* Free a list of dynamically allocated cdwQaContamTarget's */ void cdwQaContamTargetOutput(struct cdwQaContamTarget *el, FILE *f, char sep, char lastSep); /* Print out cdwQaContamTarget. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaContamTargetTabOut(el,f) cdwQaContamTargetOutput(el,f,'\t','\n'); /* Print out cdwQaContamTarget as a line in a tab-separated file. */ #define cdwQaContamTargetCommaOut(el,f) cdwQaContamTargetOutput(el,f,',',','); /* Print out cdwQaContamTarget as a comma separated list including final comma. */ #define CDWQACONTAM_NUM_COLS 4 extern char *cdwQaContamCommaSepFieldNames; struct cdwQaContam /* Results of contamination analysis of one file against one target */ { struct cdwQaContam *next; /* Next in singly linked list. */ unsigned id; /* ID of this contamination analysis */ unsigned fileId; /* File we are looking at skeptically */ unsigned qaContamTargetId; /* Information about a target for this analysis */ double mapRatio; /* Proportion of items that map to target */ }; void cdwQaContamStaticLoad(char **row, struct cdwQaContam *ret); /* Load a row from cdwQaContam table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaContam *cdwQaContamLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaContam 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 cdwQaContamFreeList(). */ void cdwQaContamSaveToDb(struct sqlConnection *conn, struct cdwQaContam *el, char *tableName, int updateSize); /* Save cdwQaContam 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaContam *cdwQaContamLoad(char **row); /* Load a cdwQaContam from row fetched with select * from cdwQaContam * from database. Dispose of this with cdwQaContamFree(). */ struct cdwQaContam *cdwQaContamLoadAll(char *fileName); /* Load all cdwQaContam from whitespace-separated file. * Dispose of this with cdwQaContamFreeList(). */ struct cdwQaContam *cdwQaContamLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaContam from chopper separated file. * Dispose of this with cdwQaContamFreeList(). */ #define cdwQaContamLoadAllByTab(a) cdwQaContamLoadAllByChar(a, '\t'); /* Load all cdwQaContam from tab separated file. * Dispose of this with cdwQaContamFreeList(). */ struct cdwQaContam *cdwQaContamCommaIn(char **pS, struct cdwQaContam *ret); /* Create a cdwQaContam out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaContam */ void cdwQaContamFree(struct cdwQaContam **pEl); /* Free a single dynamically allocated cdwQaContam such as created * with cdwQaContamLoad(). */ void cdwQaContamFreeList(struct cdwQaContam **pList); /* Free a list of dynamically allocated cdwQaContam's */ void cdwQaContamOutput(struct cdwQaContam *el, FILE *f, char sep, char lastSep); /* Print out cdwQaContam. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaContamTabOut(el,f) cdwQaContamOutput(el,f,'\t','\n'); /* Print out cdwQaContam as a line in a tab-separated file. */ #define cdwQaContamCommaOut(el,f) cdwQaContamOutput(el,f,',',','); /* Print out cdwQaContam as a comma separated list including final comma. */ #define CDWQAREPEAT_NUM_COLS 4 extern char *cdwQaRepeatCommaSepFieldNames; struct cdwQaRepeat /* What percentage of data set aligns to various repeat classes. */ { struct cdwQaRepeat *next; /* Next in singly linked list. */ unsigned id; /* ID of this repeat analysis. */ unsigned fileId; /* File we are analysing. */ char *repeatClass; /* RepeatMasker high end classification, or 'total' for all repeats. */ double mapRatio; /* Proportion that map to this repeat. */ }; void cdwQaRepeatStaticLoad(char **row, struct cdwQaRepeat *ret); /* Load a row from cdwQaRepeat table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaRepeat *cdwQaRepeatLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaRepeat 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 cdwQaRepeatFreeList(). */ void cdwQaRepeatSaveToDb(struct sqlConnection *conn, struct cdwQaRepeat *el, char *tableName, int updateSize); /* Save cdwQaRepeat 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaRepeat *cdwQaRepeatLoad(char **row); /* Load a cdwQaRepeat from row fetched with select * from cdwQaRepeat * from database. Dispose of this with cdwQaRepeatFree(). */ struct cdwQaRepeat *cdwQaRepeatLoadAll(char *fileName); /* Load all cdwQaRepeat from whitespace-separated file. * Dispose of this with cdwQaRepeatFreeList(). */ struct cdwQaRepeat *cdwQaRepeatLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaRepeat from chopper separated file. * Dispose of this with cdwQaRepeatFreeList(). */ #define cdwQaRepeatLoadAllByTab(a) cdwQaRepeatLoadAllByChar(a, '\t'); /* Load all cdwQaRepeat from tab separated file. * Dispose of this with cdwQaRepeatFreeList(). */ struct cdwQaRepeat *cdwQaRepeatCommaIn(char **pS, struct cdwQaRepeat *ret); /* Create a cdwQaRepeat out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaRepeat */ void cdwQaRepeatFree(struct cdwQaRepeat **pEl); /* Free a single dynamically allocated cdwQaRepeat such as created * with cdwQaRepeatLoad(). */ void cdwQaRepeatFreeList(struct cdwQaRepeat **pList); /* Free a list of dynamically allocated cdwQaRepeat's */ void cdwQaRepeatOutput(struct cdwQaRepeat *el, FILE *f, char sep, char lastSep); /* Print out cdwQaRepeat. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaRepeatTabOut(el,f) cdwQaRepeatOutput(el,f,'\t','\n'); /* Print out cdwQaRepeat as a line in a tab-separated file. */ #define cdwQaRepeatCommaOut(el,f) cdwQaRepeatOutput(el,f,',',','); /* Print out cdwQaRepeat as a comma separated list including final comma. */ #define CDWQAPAIRSAMPLEOVERLAP_NUM_COLS 7 extern char *cdwQaPairSampleOverlapCommaSepFieldNames; struct cdwQaPairSampleOverlap /* A comparison of the amount of overlap between two samples that cover ~0.1% to 10% of target. */ { struct cdwQaPairSampleOverlap *next; /* Next in singly linked list. */ unsigned id; /* Id of this qa pair */ unsigned elderFileId; /* Id of elder (smaller fileId) in correlated pair */ unsigned youngerFileId; /* Id of younger (larger fileId) in correlated pair */ long long elderSampleBases; /* Number of bases in elder sample */ long long youngerSampleBases; /* Number of bases in younger sample */ long long sampleOverlapBases; /* Number of bases that overlap between younger and elder sample */ double sampleSampleEnrichment; /* Amount samples overlap more than expected. */ }; void cdwQaPairSampleOverlapStaticLoad(char **row, struct cdwQaPairSampleOverlap *ret); /* Load a row from cdwQaPairSampleOverlap table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaPairSampleOverlap *cdwQaPairSampleOverlapLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaPairSampleOverlap 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 cdwQaPairSampleOverlapFreeList(). */ void cdwQaPairSampleOverlapSaveToDb(struct sqlConnection *conn, struct cdwQaPairSampleOverlap *el, char *tableName, int updateSize); /* Save cdwQaPairSampleOverlap 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaPairSampleOverlap *cdwQaPairSampleOverlapLoad(char **row); /* Load a cdwQaPairSampleOverlap from row fetched with select * from cdwQaPairSampleOverlap * from database. Dispose of this with cdwQaPairSampleOverlapFree(). */ struct cdwQaPairSampleOverlap *cdwQaPairSampleOverlapLoadAll(char *fileName); /* Load all cdwQaPairSampleOverlap from whitespace-separated file. * Dispose of this with cdwQaPairSampleOverlapFreeList(). */ struct cdwQaPairSampleOverlap *cdwQaPairSampleOverlapLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaPairSampleOverlap from chopper separated file. * Dispose of this with cdwQaPairSampleOverlapFreeList(). */ #define cdwQaPairSampleOverlapLoadAllByTab(a) cdwQaPairSampleOverlapLoadAllByChar(a, '\t'); /* Load all cdwQaPairSampleOverlap from tab separated file. * Dispose of this with cdwQaPairSampleOverlapFreeList(). */ struct cdwQaPairSampleOverlap *cdwQaPairSampleOverlapCommaIn(char **pS, struct cdwQaPairSampleOverlap *ret); /* Create a cdwQaPairSampleOverlap out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaPairSampleOverlap */ void cdwQaPairSampleOverlapFree(struct cdwQaPairSampleOverlap **pEl); /* Free a single dynamically allocated cdwQaPairSampleOverlap such as created * with cdwQaPairSampleOverlapLoad(). */ void cdwQaPairSampleOverlapFreeList(struct cdwQaPairSampleOverlap **pList); /* Free a list of dynamically allocated cdwQaPairSampleOverlap's */ void cdwQaPairSampleOverlapOutput(struct cdwQaPairSampleOverlap *el, FILE *f, char sep, char lastSep); /* Print out cdwQaPairSampleOverlap. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaPairSampleOverlapTabOut(el,f) cdwQaPairSampleOverlapOutput(el,f,'\t','\n'); /* Print out cdwQaPairSampleOverlap as a line in a tab-separated file. */ #define cdwQaPairSampleOverlapCommaOut(el,f) cdwQaPairSampleOverlapOutput(el,f,',',','); /* Print out cdwQaPairSampleOverlap as a comma separated list including final comma. */ #define CDWQAPAIRCORRELATION_NUM_COLS 6 extern char *cdwQaPairCorrelationCommaSepFieldNames; struct cdwQaPairCorrelation /* A correlation between two files of the same type. */ { struct cdwQaPairCorrelation *next; /* Next in singly linked list. */ unsigned id; /* Id of this correlation pair */ unsigned elderFileId; /* Id of elder (smaller fileId) in correlated pair */ unsigned youngerFileId; /* Id of younger (larger fileId) in correlated pair */ double pearsonInEnriched; /* Pearson's R inside enriched areas where there is overlap */ double pearsonOverall; /* Pearson's R over all places where both have data */ double pearsonClipped; /* Pearson's R clipped at two standard deviations up from the mean */ }; void cdwQaPairCorrelationStaticLoad(char **row, struct cdwQaPairCorrelation *ret); /* Load a row from cdwQaPairCorrelation table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaPairCorrelation *cdwQaPairCorrelationLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaPairCorrelation 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 cdwQaPairCorrelationFreeList(). */ void cdwQaPairCorrelationSaveToDb(struct sqlConnection *conn, struct cdwQaPairCorrelation *el, char *tableName, int updateSize); /* Save cdwQaPairCorrelation 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaPairCorrelation *cdwQaPairCorrelationLoad(char **row); /* Load a cdwQaPairCorrelation from row fetched with select * from cdwQaPairCorrelation * from database. Dispose of this with cdwQaPairCorrelationFree(). */ struct cdwQaPairCorrelation *cdwQaPairCorrelationLoadAll(char *fileName); /* Load all cdwQaPairCorrelation from whitespace-separated file. * Dispose of this with cdwQaPairCorrelationFreeList(). */ struct cdwQaPairCorrelation *cdwQaPairCorrelationLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaPairCorrelation from chopper separated file. * Dispose of this with cdwQaPairCorrelationFreeList(). */ #define cdwQaPairCorrelationLoadAllByTab(a) cdwQaPairCorrelationLoadAllByChar(a, '\t'); /* Load all cdwQaPairCorrelation from tab separated file. * Dispose of this with cdwQaPairCorrelationFreeList(). */ struct cdwQaPairCorrelation *cdwQaPairCorrelationCommaIn(char **pS, struct cdwQaPairCorrelation *ret); /* Create a cdwQaPairCorrelation out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaPairCorrelation */ void cdwQaPairCorrelationFree(struct cdwQaPairCorrelation **pEl); /* Free a single dynamically allocated cdwQaPairCorrelation such as created * with cdwQaPairCorrelationLoad(). */ void cdwQaPairCorrelationFreeList(struct cdwQaPairCorrelation **pList); /* Free a list of dynamically allocated cdwQaPairCorrelation's */ void cdwQaPairCorrelationOutput(struct cdwQaPairCorrelation *el, FILE *f, char sep, char lastSep); /* Print out cdwQaPairCorrelation. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaPairCorrelationTabOut(el,f) cdwQaPairCorrelationOutput(el,f,'\t','\n'); /* Print out cdwQaPairCorrelation as a line in a tab-separated file. */ #define cdwQaPairCorrelationCommaOut(el,f) cdwQaPairCorrelationOutput(el,f,',',','); /* Print out cdwQaPairCorrelation as a comma separated list including final comma. */ #define CDWQAPAIREDENDFASTQ_NUM_COLS 9 extern char *cdwQaPairedEndFastqCommaSepFieldNames; struct cdwQaPairedEndFastq /* Information about two paired-end fastqs */ { struct cdwQaPairedEndFastq *next; /* Next in singly linked list. */ unsigned id; /* Id of this set of paired end files */ unsigned fileId1; /* Id of first in pair */ unsigned fileId2; /* Id of second in pair */ double concordance; /* % of uniquely aligning reads where pairs nearby and point right way */ double distanceMean; /* Average distance between reads */ double distanceStd; /* Standard deviation of distance */ double distanceMin; /* Minimum distance */ double distanceMax; /* Maximum distatnce */ signed char recordComplete; /* Flag to avoid a race condition. Ignore record if this is 0 */ }; void cdwQaPairedEndFastqStaticLoad(char **row, struct cdwQaPairedEndFastq *ret); /* Load a row from cdwQaPairedEndFastq table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaPairedEndFastq *cdwQaPairedEndFastqLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaPairedEndFastq 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 cdwQaPairedEndFastqFreeList(). */ void cdwQaPairedEndFastqSaveToDb(struct sqlConnection *conn, struct cdwQaPairedEndFastq *el, char *tableName, int updateSize); /* Save cdwQaPairedEndFastq 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaPairedEndFastq *cdwQaPairedEndFastqLoad(char **row); /* Load a cdwQaPairedEndFastq from row fetched with select * from cdwQaPairedEndFastq * from database. Dispose of this with cdwQaPairedEndFastqFree(). */ struct cdwQaPairedEndFastq *cdwQaPairedEndFastqLoadAll(char *fileName); /* Load all cdwQaPairedEndFastq from whitespace-separated file. * Dispose of this with cdwQaPairedEndFastqFreeList(). */ struct cdwQaPairedEndFastq *cdwQaPairedEndFastqLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaPairedEndFastq from chopper separated file. * Dispose of this with cdwQaPairedEndFastqFreeList(). */ #define cdwQaPairedEndFastqLoadAllByTab(a) cdwQaPairedEndFastqLoadAllByChar(a, '\t'); /* Load all cdwQaPairedEndFastq from tab separated file. * Dispose of this with cdwQaPairedEndFastqFreeList(). */ struct cdwQaPairedEndFastq *cdwQaPairedEndFastqCommaIn(char **pS, struct cdwQaPairedEndFastq *ret); /* Create a cdwQaPairedEndFastq out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaPairedEndFastq */ void cdwQaPairedEndFastqFree(struct cdwQaPairedEndFastq **pEl); /* Free a single dynamically allocated cdwQaPairedEndFastq such as created * with cdwQaPairedEndFastqLoad(). */ void cdwQaPairedEndFastqFreeList(struct cdwQaPairedEndFastq **pList); /* Free a list of dynamically allocated cdwQaPairedEndFastq's */ void cdwQaPairedEndFastqOutput(struct cdwQaPairedEndFastq *el, FILE *f, char sep, char lastSep); /* Print out cdwQaPairedEndFastq. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaPairedEndFastqTabOut(el,f) cdwQaPairedEndFastqOutput(el,f,'\t','\n'); /* Print out cdwQaPairedEndFastq as a line in a tab-separated file. */ #define cdwQaPairedEndFastqCommaOut(el,f) cdwQaPairedEndFastqOutput(el,f,',',','); /* Print out cdwQaPairedEndFastq as a comma separated list including final comma. */ #define CDWQAWIGSPOT_NUM_COLS 9 extern char *cdwQaWigSpotCommaSepFieldNames; struct cdwQaWigSpot /* Information about proportion of signal in a wig that lands under spots in a peak or bed file */ { struct cdwQaWigSpot *next; /* Next in singly linked list. */ unsigned id; /* Id of this wig/spot intersection */ unsigned wigId; /* Id of bigWig file */ unsigned spotId; /* Id of a bigBed file probably broadPeak or narrowPeak */ double spotRatio; /* Ratio of signal in spots to total signal, between 0 and 1 */ double enrichment; /* Enrichment in spots compared to genome overall */ long long basesInGenome; /* Number of bases in genome */ long long basesInSpots; /* Number of bases in spots */ double sumSignal; /* Total signal */ double spotSumSignal; /* Total signal in spots */ }; void cdwQaWigSpotStaticLoad(char **row, struct cdwQaWigSpot *ret); /* Load a row from cdwQaWigSpot table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaWigSpot *cdwQaWigSpotLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaWigSpot 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 cdwQaWigSpotFreeList(). */ void cdwQaWigSpotSaveToDb(struct sqlConnection *conn, struct cdwQaWigSpot *el, char *tableName, int updateSize); /* Save cdwQaWigSpot 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaWigSpot *cdwQaWigSpotLoad(char **row); /* Load a cdwQaWigSpot from row fetched with select * from cdwQaWigSpot * from database. Dispose of this with cdwQaWigSpotFree(). */ struct cdwQaWigSpot *cdwQaWigSpotLoadAll(char *fileName); /* Load all cdwQaWigSpot from whitespace-separated file. * Dispose of this with cdwQaWigSpotFreeList(). */ struct cdwQaWigSpot *cdwQaWigSpotLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaWigSpot from chopper separated file. * Dispose of this with cdwQaWigSpotFreeList(). */ #define cdwQaWigSpotLoadAllByTab(a) cdwQaWigSpotLoadAllByChar(a, '\t'); /* Load all cdwQaWigSpot from tab separated file. * Dispose of this with cdwQaWigSpotFreeList(). */ struct cdwQaWigSpot *cdwQaWigSpotCommaIn(char **pS, struct cdwQaWigSpot *ret); /* Create a cdwQaWigSpot out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaWigSpot */ void cdwQaWigSpotFree(struct cdwQaWigSpot **pEl); /* Free a single dynamically allocated cdwQaWigSpot such as created * with cdwQaWigSpotLoad(). */ void cdwQaWigSpotFreeList(struct cdwQaWigSpot **pList); /* Free a list of dynamically allocated cdwQaWigSpot's */ void cdwQaWigSpotOutput(struct cdwQaWigSpot *el, FILE *f, char sep, char lastSep); /* Print out cdwQaWigSpot. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaWigSpotTabOut(el,f) cdwQaWigSpotOutput(el,f,'\t','\n'); /* Print out cdwQaWigSpot as a line in a tab-separated file. */ #define cdwQaWigSpotCommaOut(el,f) cdwQaWigSpotOutput(el,f,',',','); /* Print out cdwQaWigSpot as a comma separated list including final comma. */ #define CDWQADNASESINGLESTATS5M_NUM_COLS 18 extern char *cdwQaDnaseSingleStats5mCommaSepFieldNames; struct cdwQaDnaseSingleStats5m /* Statistics calculated based on a 5M sample of DNAse aligned reads from a bam file. */ { struct cdwQaDnaseSingleStats5m *next; /* Next in singly linked list. */ unsigned id; /* Id of this row in table. */ unsigned fileId; /* Id of bam file this is calculated from */ unsigned sampleReads; /* Number of mapped reads */ double spotRatio; /* Ratio of signal in spots to total signal, between 0 and 1 */ double enrichment; /* Enrichment in spots compared to genome overall */ long long basesInGenome; /* Number of bases in genome */ long long basesInSpots; /* Number of bases in spots */ double sumSignal; /* Total signal */ double spotSumSignal; /* Total signal in spots */ char *estFragLength; /* Up to three comma separated strand cross-correlation peaks */ char *corrEstFragLen; /* Up to three cross strand correlations at the given peaks */ int phantomPeak; /* Read length/phantom peak strand shift */ double corrPhantomPeak; /* Correlation value at phantom peak */ int argMinCorr; /* strand shift at which cross-correlation is lowest */ double minCorr; /* minimum value of cross-correlation */ double nsc; /* Normalized strand cross-correlation coefficient (NSC) = corrEstFragLen/minCorr */ double rsc; /* Relative strand cross-correlation coefficient (RSC) */ int rscQualityTag; /* based on thresholded RSC (codes: -2:veryLow,-1:Low,0:Medium,1:High,2:veryHigh) */ }; void cdwQaDnaseSingleStats5mStaticLoad(char **row, struct cdwQaDnaseSingleStats5m *ret); /* Load a row from cdwQaDnaseSingleStats5m table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwQaDnaseSingleStats5m *cdwQaDnaseSingleStats5mLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwQaDnaseSingleStats5m 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 cdwQaDnaseSingleStats5mFreeList(). */ void cdwQaDnaseSingleStats5mSaveToDb(struct sqlConnection *conn, struct cdwQaDnaseSingleStats5m *el, char *tableName, int updateSize); /* Save cdwQaDnaseSingleStats5m 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. This function automatically escapes quoted strings for mysql. */ struct cdwQaDnaseSingleStats5m *cdwQaDnaseSingleStats5mLoad(char **row); /* Load a cdwQaDnaseSingleStats5m from row fetched with select * from cdwQaDnaseSingleStats5m * from database. Dispose of this with cdwQaDnaseSingleStats5mFree(). */ struct cdwQaDnaseSingleStats5m *cdwQaDnaseSingleStats5mLoadAll(char *fileName); /* Load all cdwQaDnaseSingleStats5m from whitespace-separated file. * Dispose of this with cdwQaDnaseSingleStats5mFreeList(). */ struct cdwQaDnaseSingleStats5m *cdwQaDnaseSingleStats5mLoadAllByChar(char *fileName, char chopper); /* Load all cdwQaDnaseSingleStats5m from chopper separated file. * Dispose of this with cdwQaDnaseSingleStats5mFreeList(). */ #define cdwQaDnaseSingleStats5mLoadAllByTab(a) cdwQaDnaseSingleStats5mLoadAllByChar(a, '\t'); /* Load all cdwQaDnaseSingleStats5m from tab separated file. * Dispose of this with cdwQaDnaseSingleStats5mFreeList(). */ struct cdwQaDnaseSingleStats5m *cdwQaDnaseSingleStats5mCommaIn(char **pS, struct cdwQaDnaseSingleStats5m *ret); /* Create a cdwQaDnaseSingleStats5m out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwQaDnaseSingleStats5m */ void cdwQaDnaseSingleStats5mFree(struct cdwQaDnaseSingleStats5m **pEl); /* Free a single dynamically allocated cdwQaDnaseSingleStats5m such as created * with cdwQaDnaseSingleStats5mLoad(). */ void cdwQaDnaseSingleStats5mFreeList(struct cdwQaDnaseSingleStats5m **pList); /* Free a list of dynamically allocated cdwQaDnaseSingleStats5m's */ void cdwQaDnaseSingleStats5mOutput(struct cdwQaDnaseSingleStats5m *el, FILE *f, char sep, char lastSep); /* Print out cdwQaDnaseSingleStats5m. Separate fields with sep. Follow last field with lastSep. */ #define cdwQaDnaseSingleStats5mTabOut(el,f) cdwQaDnaseSingleStats5mOutput(el,f,'\t','\n'); /* Print out cdwQaDnaseSingleStats5m as a line in a tab-separated file. */ #define cdwQaDnaseSingleStats5mCommaOut(el,f) cdwQaDnaseSingleStats5mOutput(el,f,',',','); /* Print out cdwQaDnaseSingleStats5m as a comma separated list including final comma. */ #define CDWJOB_NUM_COLS 8 extern char *cdwJobCommaSepFieldNames; struct cdwJob /* A job to be run asynchronously and not too many all at once. */ { struct cdwJob *next; /* Next in singly linked list. */ unsigned id; /* Job id */ char *commandLine; /* Command line of job */ long long startTime; /* Start time in seconds since 1970 */ long long endTime; /* End time in seconds since 1970 */ char *stderr; /* The output to stderr of the run - may be nonempty even with success */ int returnCode; /* The return code from system command - 0 for success */ int pid; /* Process ID for running processes */ int submitId; /* Associated submission ID if any */ }; void cdwJobStaticLoad(char **row, struct cdwJob *ret); /* Load a row from cdwJob table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwJob *cdwJobLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwJob 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 cdwJobFreeList(). */ void cdwJobSaveToDb(struct sqlConnection *conn, struct cdwJob *el, char *tableName, int updateSize); /* Save cdwJob 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. This function automatically escapes quoted strings for mysql. */ struct cdwJob *cdwJobLoad(char **row); /* Load a cdwJob from row fetched with select * from cdwJob * from database. Dispose of this with cdwJobFree(). */ struct cdwJob *cdwJobLoadAll(char *fileName); /* Load all cdwJob from whitespace-separated file. * Dispose of this with cdwJobFreeList(). */ struct cdwJob *cdwJobLoadAllByChar(char *fileName, char chopper); /* Load all cdwJob from chopper separated file. * Dispose of this with cdwJobFreeList(). */ #define cdwJobLoadAllByTab(a) cdwJobLoadAllByChar(a, '\t'); /* Load all cdwJob from tab separated file. * Dispose of this with cdwJobFreeList(). */ struct cdwJob *cdwJobCommaIn(char **pS, struct cdwJob *ret); /* Create a cdwJob out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwJob */ void cdwJobFree(struct cdwJob **pEl); /* Free a single dynamically allocated cdwJob such as created * with cdwJobLoad(). */ void cdwJobFreeList(struct cdwJob **pList); /* Free a list of dynamically allocated cdwJob's */ void cdwJobOutput(struct cdwJob *el, FILE *f, char sep, char lastSep); /* Print out cdwJob. Separate fields with sep. Follow last field with lastSep. */ #define cdwJobTabOut(el,f) cdwJobOutput(el,f,'\t','\n'); /* Print out cdwJob as a line in a tab-separated file. */ #define cdwJobCommaOut(el,f) cdwJobOutput(el,f,',',','); /* Print out cdwJob as a comma separated list including final comma. */ #define CDWTRACKVIZ_NUM_COLS 6 extern char *cdwTrackVizCommaSepFieldNames; struct cdwTrackViz /* Some files can be visualized as a track. Stuff to help define that track goes here. */ { struct cdwTrackViz *next; /* Next in singly linked list. */ unsigned id; /* Id of this row in the table */ unsigned fileId; /* File this is a viz of */ char *shortLabel; /* Up to 17 char label for track */ char *longLabel; /* Up to 100 char label for track */ char *type; /* One of the customTrack types such as bam,vcfTabix,bigWig,bigBed */ char *bigDataFile; /* Where big data file lives relative to cdwRootDir */ }; void cdwTrackVizStaticLoad(char **row, struct cdwTrackViz *ret); /* Load a row from cdwTrackViz table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwTrackViz *cdwTrackVizLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwTrackViz 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 cdwTrackVizFreeList(). */ void cdwTrackVizSaveToDb(struct sqlConnection *conn, struct cdwTrackViz *el, char *tableName, int updateSize); /* Save cdwTrackViz 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. This function automatically escapes quoted strings for mysql. */ struct cdwTrackViz *cdwTrackVizLoad(char **row); /* Load a cdwTrackViz from row fetched with select * from cdwTrackViz * from database. Dispose of this with cdwTrackVizFree(). */ struct cdwTrackViz *cdwTrackVizLoadAll(char *fileName); /* Load all cdwTrackViz from whitespace-separated file. * Dispose of this with cdwTrackVizFreeList(). */ struct cdwTrackViz *cdwTrackVizLoadAllByChar(char *fileName, char chopper); /* Load all cdwTrackViz from chopper separated file. * Dispose of this with cdwTrackVizFreeList(). */ #define cdwTrackVizLoadAllByTab(a) cdwTrackVizLoadAllByChar(a, '\t'); /* Load all cdwTrackViz from tab separated file. * Dispose of this with cdwTrackVizFreeList(). */ struct cdwTrackViz *cdwTrackVizCommaIn(char **pS, struct cdwTrackViz *ret); /* Create a cdwTrackViz out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwTrackViz */ void cdwTrackVizFree(struct cdwTrackViz **pEl); /* Free a single dynamically allocated cdwTrackViz such as created * with cdwTrackVizLoad(). */ void cdwTrackVizFreeList(struct cdwTrackViz **pList); /* Free a list of dynamically allocated cdwTrackViz's */ void cdwTrackVizOutput(struct cdwTrackViz *el, FILE *f, char sep, char lastSep); /* Print out cdwTrackViz. Separate fields with sep. Follow last field with lastSep. */ #define cdwTrackVizTabOut(el,f) cdwTrackVizOutput(el,f,'\t','\n'); /* Print out cdwTrackViz as a line in a tab-separated file. */ #define cdwTrackVizCommaOut(el,f) cdwTrackVizOutput(el,f,',',','); /* Print out cdwTrackViz as a comma separated list including final comma. */ #define CDWDATASET_NUM_COLS 8 extern char *cdwDatasetCommaSepFieldNames; struct cdwDataset /* A dataset is a collection of files, usually associated with a paper */ { struct cdwDataset *next; /* Next in singly linked list. */ unsigned id; /* Dataset ID */ char *name; /* Short name of this dataset, one word, no spaces */ char *label; /* short title of the dataset, a few words */ char *description; /* Description of dataset, can be a complete html paragraph. */ char *pmid; /* Pubmed ID of abstract */ char *pmcid; /* PubmedCentral ID of paper full text */ char *metaDivTags; /* Comma separated list of fields used to make tree out of metadata */ char *metaLabelTags; /* Comma separated list of fields good to use in labels for graphs etc. */ }; void cdwDatasetStaticLoad(char **row, struct cdwDataset *ret); /* Load a row from cdwDataset table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwDataset *cdwDatasetLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwDataset 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 cdwDatasetFreeList(). */ void cdwDatasetSaveToDb(struct sqlConnection *conn, struct cdwDataset *el, char *tableName, int updateSize); /* Save cdwDataset 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. This function automatically escapes quoted strings for mysql. */ struct cdwDataset *cdwDatasetLoad(char **row); /* Load a cdwDataset from row fetched with select * from cdwDataset * from database. Dispose of this with cdwDatasetFree(). */ struct cdwDataset *cdwDatasetLoadAll(char *fileName); /* Load all cdwDataset from whitespace-separated file. * Dispose of this with cdwDatasetFreeList(). */ struct cdwDataset *cdwDatasetLoadAllByChar(char *fileName, char chopper); /* Load all cdwDataset from chopper separated file. * Dispose of this with cdwDatasetFreeList(). */ #define cdwDatasetLoadAllByTab(a) cdwDatasetLoadAllByChar(a, '\t'); /* Load all cdwDataset from tab separated file. * Dispose of this with cdwDatasetFreeList(). */ struct cdwDataset *cdwDatasetCommaIn(char **pS, struct cdwDataset *ret); /* Create a cdwDataset out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwDataset */ void cdwDatasetFree(struct cdwDataset **pEl); /* Free a single dynamically allocated cdwDataset such as created * with cdwDatasetLoad(). */ void cdwDatasetFreeList(struct cdwDataset **pList); /* Free a list of dynamically allocated cdwDataset's */ void cdwDatasetOutput(struct cdwDataset *el, FILE *f, char sep, char lastSep); /* Print out cdwDataset. Separate fields with sep. Follow last field with lastSep. */ #define cdwDatasetTabOut(el,f) cdwDatasetOutput(el,f,'\t','\n'); /* Print out cdwDataset as a line in a tab-separated file. */ #define cdwDatasetCommaOut(el,f) cdwDatasetOutput(el,f,',',','); /* Print out cdwDataset as a comma separated list including final comma. */ #define CDWJOINTDATASET_NUM_COLS 6 extern char *cdwJointDatasetCommaSepFieldNames; struct cdwJointDataset /* A joint dataset is a collection of datasets, usually associated with a common trait. */ { struct cdwJointDataset *next; /* Next in singly linked list. */ unsigned id; /* Dataset ID */ char *name; /* Short name of this dataset, one word, no spaces */ char *label; /* short title of the dataset, a few words */ char *description; /* Description of dataset, can be a complete html paragraph. */ char *childrenNames; /* Comma separated list of children data set names. */ char *metaDivTags; /* Comma separated list of fields used to make tree out of metadata */ }; void cdwJointDatasetStaticLoad(char **row, struct cdwJointDataset *ret); /* Load a row from cdwJointDataset table into ret. The contents of ret will * be replaced at the next call to this function. */ struct cdwJointDataset *cdwJointDatasetLoadByQuery(struct sqlConnection *conn, char *query); /* Load all cdwJointDataset 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 cdwJointDatasetFreeList(). */ void cdwJointDatasetSaveToDb(struct sqlConnection *conn, struct cdwJointDataset *el, char *tableName, int updateSize); /* Save cdwJointDataset 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. This function automatically escapes quoted strings for mysql. */ struct cdwJointDataset *cdwJointDatasetLoad(char **row); /* Load a cdwJointDataset from row fetched with select * from cdwJointDataset * from database. Dispose of this with cdwJointDatasetFree(). */ struct cdwJointDataset *cdwJointDatasetLoadAll(char *fileName); /* Load all cdwJointDataset from whitespace-separated file. * Dispose of this with cdwJointDatasetFreeList(). */ struct cdwJointDataset *cdwJointDatasetLoadAllByChar(char *fileName, char chopper); /* Load all cdwJointDataset from chopper separated file. * Dispose of this with cdwJointDatasetFreeList(). */ #define cdwJointDatasetLoadAllByTab(a) cdwJointDatasetLoadAllByChar(a, '\t'); /* Load all cdwJointDataset from tab separated file. * Dispose of this with cdwJointDatasetFreeList(). */ struct cdwJointDataset *cdwJointDatasetCommaIn(char **pS, struct cdwJointDataset *ret); /* Create a cdwJointDataset out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new cdwJointDataset */ void cdwJointDatasetFree(struct cdwJointDataset **pEl); /* Free a single dynamically allocated cdwJointDataset such as created * with cdwJointDatasetLoad(). */ void cdwJointDatasetFreeList(struct cdwJointDataset **pList); /* Free a list of dynamically allocated cdwJointDataset's */ void cdwJointDatasetOutput(struct cdwJointDataset *el, FILE *f, char sep, char lastSep); /* Print out cdwJointDataset. Separate fields with sep. Follow last field with lastSep. */ #define cdwJointDatasetTabOut(el,f) cdwJointDatasetOutput(el,f,'\t','\n'); /* Print out cdwJointDataset as a line in a tab-separated file. */ #define cdwJointDatasetCommaOut(el,f) cdwJointDatasetOutput(el,f,',',','); /* Print out cdwJointDataset as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* CDW_H */