/* eapDb.h was originally generated by the autoSql program, which also * generated eapDb.c and eapDb.sql. This header links the database and * the RAM representation of objects. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef EAPDB_H #define EAPDB_H #include "jksql.h" #define EAPJOB_NUM_COLS 8 extern char *eapJobCommaSepFieldNames; struct eapJob /* An analysis pipeline job to be run asynchronously and not too many all at once. */ { struct eapJob *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 cpusRequested; /* Number of CPUs to request from job control system */ char *parasolId; /* Parasol job id for process. */ }; void eapJobStaticLoad(char **row, struct eapJob *ret); /* Load a row from eapJob table into ret. The contents of ret will * be replaced at the next call to this function. */ struct eapJob *eapJobLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapJob 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 eapJobFreeList(). */ void eapJobSaveToDb(struct sqlConnection *conn, struct eapJob *el, char *tableName, int updateSize); /* Save eapJob 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 eapJob *eapJobLoad(char **row); /* Load a eapJob from row fetched with select * from eapJob * from database. Dispose of this with eapJobFree(). */ struct eapJob *eapJobLoadAll(char *fileName); /* Load all eapJob from whitespace-separated file. * Dispose of this with eapJobFreeList(). */ struct eapJob *eapJobLoadAllByChar(char *fileName, char chopper); /* Load all eapJob from chopper separated file. * Dispose of this with eapJobFreeList(). */ #define eapJobLoadAllByTab(a) eapJobLoadAllByChar(a, '\t'); /* Load all eapJob from tab separated file. * Dispose of this with eapJobFreeList(). */ struct eapJob *eapJobCommaIn(char **pS, struct eapJob *ret); /* Create a eapJob out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapJob */ void eapJobFree(struct eapJob **pEl); /* Free a single dynamically allocated eapJob such as created * with eapJobLoad(). */ void eapJobFreeList(struct eapJob **pList); /* Free a list of dynamically allocated eapJob's */ void eapJobOutput(struct eapJob *el, FILE *f, char sep, char lastSep); /* Print out eapJob. Separate fields with sep. Follow last field with lastSep. */ #define eapJobTabOut(el,f) eapJobOutput(el,f,'\t','\n'); /* Print out eapJob as a line in a tab-separated file. */ #define eapJobCommaOut(el,f) eapJobOutput(el,f,',',','); /* Print out eapJob as a comma separated list including final comma. */ #define EAPSOFTWARE_NUM_COLS 5 extern char *eapSoftwareCommaSepFieldNames; struct eapSoftware /* Software that is tracked by the analysis pipeline. */ { struct eapSoftware *next; /* Next in singly linked list. */ unsigned id; /* Software id */ char *name; /* Command line name */ char *url; /* Suggested reference URL */ char *email; /* Suggested contact email */ char metaUuid[37]; /* UUID into Stanford metadata system if synced */ }; void eapSoftwareStaticLoad(char **row, struct eapSoftware *ret); /* Load a row from eapSoftware table into ret. The contents of ret will * be replaced at the next call to this function. */ struct eapSoftware *eapSoftwareLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapSoftware 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 eapSoftwareFreeList(). */ void eapSoftwareSaveToDb(struct sqlConnection *conn, struct eapSoftware *el, char *tableName, int updateSize); /* Save eapSoftware 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 eapSoftware *eapSoftwareLoad(char **row); /* Load a eapSoftware from row fetched with select * from eapSoftware * from database. Dispose of this with eapSoftwareFree(). */ struct eapSoftware *eapSoftwareLoadAll(char *fileName); /* Load all eapSoftware from whitespace-separated file. * Dispose of this with eapSoftwareFreeList(). */ struct eapSoftware *eapSoftwareLoadAllByChar(char *fileName, char chopper); /* Load all eapSoftware from chopper separated file. * Dispose of this with eapSoftwareFreeList(). */ #define eapSoftwareLoadAllByTab(a) eapSoftwareLoadAllByChar(a, '\t'); /* Load all eapSoftware from tab separated file. * Dispose of this with eapSoftwareFreeList(). */ struct eapSoftware *eapSoftwareCommaIn(char **pS, struct eapSoftware *ret); /* Create a eapSoftware out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapSoftware */ void eapSoftwareFree(struct eapSoftware **pEl); /* Free a single dynamically allocated eapSoftware such as created * with eapSoftwareLoad(). */ void eapSoftwareFreeList(struct eapSoftware **pList); /* Free a list of dynamically allocated eapSoftware's */ void eapSoftwareOutput(struct eapSoftware *el, FILE *f, char sep, char lastSep); /* Print out eapSoftware. Separate fields with sep. Follow last field with lastSep. */ #define eapSoftwareTabOut(el,f) eapSoftwareOutput(el,f,'\t','\n'); /* Print out eapSoftware as a line in a tab-separated file. */ #define eapSoftwareCommaOut(el,f) eapSoftwareOutput(el,f,',',','); /* Print out eapSoftware as a comma separated list including final comma. */ #define EAPSWVERSION_NUM_COLS 7 extern char *eapSwVersionCommaSepFieldNames; struct eapSwVersion /* A version of a particular piece of software */ { struct eapSwVersion *next; /* Next in singly linked list. */ unsigned id; /* Version id */ char *software; /* Name field of software this is associated with */ char *version; /* Version as carved out of program run with --version or the like */ char md5[33]; /* md5 sum of executable file */ signed char redoPriority; /* -1 for routine recompile, 0 for unknown, 1 for recommended, 2 for required. */ char *notes; /* Any notes on the version */ char metaUuid[37]; /* UUID into Stanford metadata system if synced */ }; void eapSwVersionStaticLoad(char **row, struct eapSwVersion *ret); /* Load a row from eapSwVersion table into ret. The contents of ret will * be replaced at the next call to this function. */ struct eapSwVersion *eapSwVersionLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapSwVersion 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 eapSwVersionFreeList(). */ void eapSwVersionSaveToDb(struct sqlConnection *conn, struct eapSwVersion *el, char *tableName, int updateSize); /* Save eapSwVersion 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 eapSwVersion *eapSwVersionLoad(char **row); /* Load a eapSwVersion from row fetched with select * from eapSwVersion * from database. Dispose of this with eapSwVersionFree(). */ struct eapSwVersion *eapSwVersionLoadAll(char *fileName); /* Load all eapSwVersion from whitespace-separated file. * Dispose of this with eapSwVersionFreeList(). */ struct eapSwVersion *eapSwVersionLoadAllByChar(char *fileName, char chopper); /* Load all eapSwVersion from chopper separated file. * Dispose of this with eapSwVersionFreeList(). */ #define eapSwVersionLoadAllByTab(a) eapSwVersionLoadAllByChar(a, '\t'); /* Load all eapSwVersion from tab separated file. * Dispose of this with eapSwVersionFreeList(). */ struct eapSwVersion *eapSwVersionCommaIn(char **pS, struct eapSwVersion *ret); /* Create a eapSwVersion out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapSwVersion */ void eapSwVersionFree(struct eapSwVersion **pEl); /* Free a single dynamically allocated eapSwVersion such as created * with eapSwVersionLoad(). */ void eapSwVersionFreeList(struct eapSwVersion **pList); /* Free a list of dynamically allocated eapSwVersion's */ void eapSwVersionOutput(struct eapSwVersion *el, FILE *f, char sep, char lastSep); /* Print out eapSwVersion. Separate fields with sep. Follow last field with lastSep. */ #define eapSwVersionTabOut(el,f) eapSwVersionOutput(el,f,'\t','\n'); /* Print out eapSwVersion as a line in a tab-separated file. */ #define eapSwVersionCommaOut(el,f) eapSwVersionOutput(el,f,',',','); /* Print out eapSwVersion as a comma separated list including final comma. */ #define EAPSTEP_NUM_COLS 14 extern char *eapStepCommaSepFieldNames; struct eapStep /* A step in an analysis pipeline - something that takes one set of files to another */ { struct eapStep *next; /* Next in singly linked list. */ unsigned id; /* Step id */ char *name; /* Name of this analysis step */ int cpusRequested; /* Number of CPUs to request from job control system */ char *description; /* Description of step, about a sentence. */ unsigned inCount; /* Total number of inputs */ char **inputTypes; /* List of types to go with input files */ char **inputFormats; /* List of formats of input files */ char **inputDescriptions; /* List of descriptions of input files */ unsigned outCount; /* Total number of outputs */ char **outputNamesInTempDir; /* list of all output file names in output dir */ char **outputFormats; /* list of formats of output files */ char **outputTypes; /* list of outputType of output files */ char **outputDescriptions; /* list of descriptions of outputs */ char metaUuid[37]; /* UUID into Stanford metadata system if synced */ }; struct eapStep *eapStepLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapStep 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 eapStepFreeList(). */ void eapStepSaveToDb(struct sqlConnection *conn, struct eapStep *el, char *tableName, int updateSize); /* Save eapStep 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 eapStep *eapStepLoad(char **row); /* Load a eapStep from row fetched with select * from eapStep * from database. Dispose of this with eapStepFree(). */ struct eapStep *eapStepLoadAll(char *fileName); /* Load all eapStep from whitespace-separated file. * Dispose of this with eapStepFreeList(). */ struct eapStep *eapStepLoadAllByChar(char *fileName, char chopper); /* Load all eapStep from chopper separated file. * Dispose of this with eapStepFreeList(). */ #define eapStepLoadAllByTab(a) eapStepLoadAllByChar(a, '\t'); /* Load all eapStep from tab separated file. * Dispose of this with eapStepFreeList(). */ struct eapStep *eapStepCommaIn(char **pS, struct eapStep *ret); /* Create a eapStep out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapStep */ void eapStepFree(struct eapStep **pEl); /* Free a single dynamically allocated eapStep such as created * with eapStepLoad(). */ void eapStepFreeList(struct eapStep **pList); /* Free a list of dynamically allocated eapStep's */ void eapStepOutput(struct eapStep *el, FILE *f, char sep, char lastSep); /* Print out eapStep. Separate fields with sep. Follow last field with lastSep. */ #define eapStepTabOut(el,f) eapStepOutput(el,f,'\t','\n'); /* Print out eapStep as a line in a tab-separated file. */ #define eapStepCommaOut(el,f) eapStepOutput(el,f,',',','); /* Print out eapStep as a comma separated list including final comma. */ #define EAPSTEPSOFTWARE_NUM_COLS 3 extern char *eapStepSoftwareCommaSepFieldNames; struct eapStepSoftware /* Relates steps to the software they use */ { struct eapStepSoftware *next; /* Next in singly linked list. */ unsigned id; /* Link id - helps give order to software within step among other things */ char *step; /* name of associated step */ char *software; /* name of associated software */ }; void eapStepSoftwareStaticLoad(char **row, struct eapStepSoftware *ret); /* Load a row from eapStepSoftware table into ret. The contents of ret will * be replaced at the next call to this function. */ struct eapStepSoftware *eapStepSoftwareLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapStepSoftware 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 eapStepSoftwareFreeList(). */ void eapStepSoftwareSaveToDb(struct sqlConnection *conn, struct eapStepSoftware *el, char *tableName, int updateSize); /* Save eapStepSoftware 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 eapStepSoftware *eapStepSoftwareLoad(char **row); /* Load a eapStepSoftware from row fetched with select * from eapStepSoftware * from database. Dispose of this with eapStepSoftwareFree(). */ struct eapStepSoftware *eapStepSoftwareLoadAll(char *fileName); /* Load all eapStepSoftware from whitespace-separated file. * Dispose of this with eapStepSoftwareFreeList(). */ struct eapStepSoftware *eapStepSoftwareLoadAllByChar(char *fileName, char chopper); /* Load all eapStepSoftware from chopper separated file. * Dispose of this with eapStepSoftwareFreeList(). */ #define eapStepSoftwareLoadAllByTab(a) eapStepSoftwareLoadAllByChar(a, '\t'); /* Load all eapStepSoftware from tab separated file. * Dispose of this with eapStepSoftwareFreeList(). */ struct eapStepSoftware *eapStepSoftwareCommaIn(char **pS, struct eapStepSoftware *ret); /* Create a eapStepSoftware out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapStepSoftware */ void eapStepSoftwareFree(struct eapStepSoftware **pEl); /* Free a single dynamically allocated eapStepSoftware such as created * with eapStepSoftwareLoad(). */ void eapStepSoftwareFreeList(struct eapStepSoftware **pList); /* Free a list of dynamically allocated eapStepSoftware's */ void eapStepSoftwareOutput(struct eapStepSoftware *el, FILE *f, char sep, char lastSep); /* Print out eapStepSoftware. Separate fields with sep. Follow last field with lastSep. */ #define eapStepSoftwareTabOut(el,f) eapStepSoftwareOutput(el,f,'\t','\n'); /* Print out eapStepSoftware as a line in a tab-separated file. */ #define eapStepSoftwareCommaOut(el,f) eapStepSoftwareOutput(el,f,',',','); /* Print out eapStepSoftware as a comma separated list including final comma. */ #define EAPSTEPVERSION_NUM_COLS 3 extern char *eapStepVersionCommaSepFieldNames; struct eapStepVersion /* All the versions of a step - a new row if any subcomponent is versioned too. */ { struct eapStepVersion *next; /* Next in singly linked list. */ unsigned id; /* ID of step version -used to tie together rows in edwAnalysisStepVector */ char *step; /* name of associated step */ unsigned version; /* Version of given step - just increases by 1 with each change */ }; void eapStepVersionStaticLoad(char **row, struct eapStepVersion *ret); /* Load a row from eapStepVersion table into ret. The contents of ret will * be replaced at the next call to this function. */ struct eapStepVersion *eapStepVersionLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapStepVersion 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 eapStepVersionFreeList(). */ void eapStepVersionSaveToDb(struct sqlConnection *conn, struct eapStepVersion *el, char *tableName, int updateSize); /* Save eapStepVersion 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 eapStepVersion *eapStepVersionLoad(char **row); /* Load a eapStepVersion from row fetched with select * from eapStepVersion * from database. Dispose of this with eapStepVersionFree(). */ struct eapStepVersion *eapStepVersionLoadAll(char *fileName); /* Load all eapStepVersion from whitespace-separated file. * Dispose of this with eapStepVersionFreeList(). */ struct eapStepVersion *eapStepVersionLoadAllByChar(char *fileName, char chopper); /* Load all eapStepVersion from chopper separated file. * Dispose of this with eapStepVersionFreeList(). */ #define eapStepVersionLoadAllByTab(a) eapStepVersionLoadAllByChar(a, '\t'); /* Load all eapStepVersion from tab separated file. * Dispose of this with eapStepVersionFreeList(). */ struct eapStepVersion *eapStepVersionCommaIn(char **pS, struct eapStepVersion *ret); /* Create a eapStepVersion out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapStepVersion */ void eapStepVersionFree(struct eapStepVersion **pEl); /* Free a single dynamically allocated eapStepVersion such as created * with eapStepVersionLoad(). */ void eapStepVersionFreeList(struct eapStepVersion **pList); /* Free a list of dynamically allocated eapStepVersion's */ void eapStepVersionOutput(struct eapStepVersion *el, FILE *f, char sep, char lastSep); /* Print out eapStepVersion. Separate fields with sep. Follow last field with lastSep. */ #define eapStepVersionTabOut(el,f) eapStepVersionOutput(el,f,'\t','\n'); /* Print out eapStepVersion as a line in a tab-separated file. */ #define eapStepVersionCommaOut(el,f) eapStepVersionOutput(el,f,',',','); /* Print out eapStepVersion as a comma separated list including final comma. */ #define EAPSTEPSWVERSION_NUM_COLS 3 extern char *eapStepSwVersionCommaSepFieldNames; struct eapStepSwVersion /* A table that is queried for list of all software versions used in a step */ { struct eapStepSwVersion *next; /* Next in singly linked list. */ unsigned id; /* Link id - helps give order to steps in a given version */ unsigned stepVersionId; /* Key in edwAnalysisStepVersion table */ unsigned swVersionId; /* Key in edwAnalysisSwVersion table */ }; void eapStepSwVersionStaticLoad(char **row, struct eapStepSwVersion *ret); /* Load a row from eapStepSwVersion table into ret. The contents of ret will * be replaced at the next call to this function. */ struct eapStepSwVersion *eapStepSwVersionLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapStepSwVersion 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 eapStepSwVersionFreeList(). */ void eapStepSwVersionSaveToDb(struct sqlConnection *conn, struct eapStepSwVersion *el, char *tableName, int updateSize); /* Save eapStepSwVersion 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 eapStepSwVersion *eapStepSwVersionLoad(char **row); /* Load a eapStepSwVersion from row fetched with select * from eapStepSwVersion * from database. Dispose of this with eapStepSwVersionFree(). */ struct eapStepSwVersion *eapStepSwVersionLoadAll(char *fileName); /* Load all eapStepSwVersion from whitespace-separated file. * Dispose of this with eapStepSwVersionFreeList(). */ struct eapStepSwVersion *eapStepSwVersionLoadAllByChar(char *fileName, char chopper); /* Load all eapStepSwVersion from chopper separated file. * Dispose of this with eapStepSwVersionFreeList(). */ #define eapStepSwVersionLoadAllByTab(a) eapStepSwVersionLoadAllByChar(a, '\t'); /* Load all eapStepSwVersion from tab separated file. * Dispose of this with eapStepSwVersionFreeList(). */ struct eapStepSwVersion *eapStepSwVersionCommaIn(char **pS, struct eapStepSwVersion *ret); /* Create a eapStepSwVersion out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapStepSwVersion */ void eapStepSwVersionFree(struct eapStepSwVersion **pEl); /* Free a single dynamically allocated eapStepSwVersion such as created * with eapStepSwVersionLoad(). */ void eapStepSwVersionFreeList(struct eapStepSwVersion **pList); /* Free a list of dynamically allocated eapStepSwVersion's */ void eapStepSwVersionOutput(struct eapStepSwVersion *el, FILE *f, char sep, char lastSep); /* Print out eapStepSwVersion. Separate fields with sep. Follow last field with lastSep. */ #define eapStepSwVersionTabOut(el,f) eapStepSwVersionOutput(el,f,'\t','\n'); /* Print out eapStepSwVersion as a line in a tab-separated file. */ #define eapStepSwVersionCommaOut(el,f) eapStepSwVersionOutput(el,f,',',','); /* Print out eapStepSwVersion as a comma separated list including final comma. */ #define EAPRUN_NUM_COLS 10 extern char *eapRunCommaSepFieldNames; struct eapRun /* Information on an compute job that produces files by running a step. */ { struct eapRun *next; /* Next in singly linked list. */ unsigned id; /* Analysis run ID */ unsigned jobId; /* ID in edwAnalysisJob table */ char experiment[17]; /* Something like ENCSR000CFA. */ char *analysisStep; /* Name of analysis step. Different data can be analysed with same step */ unsigned stepVersionId; /* Keep track of versions of everything */ char *tempDir; /* Where analysis is to be computed */ unsigned assemblyId; /* Id of assembly we are working with if analysis is all on one assembly */ char *jsonResult; /* JSON formatted object with result for Stanford metaDatabase */ signed char createStatus; /* 1 if output files made 0 if not made, -1 if make tried and failed */ char metaUuid[37]; /* UUID into Stanford metadata system if synced */ }; void eapRunStaticLoad(char **row, struct eapRun *ret); /* Load a row from eapRun table into ret. The contents of ret will * be replaced at the next call to this function. */ struct eapRun *eapRunLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapRun 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 eapRunFreeList(). */ void eapRunSaveToDb(struct sqlConnection *conn, struct eapRun *el, char *tableName, int updateSize); /* Save eapRun 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 eapRun *eapRunLoad(char **row); /* Load a eapRun from row fetched with select * from eapRun * from database. Dispose of this with eapRunFree(). */ struct eapRun *eapRunLoadAll(char *fileName); /* Load all eapRun from whitespace-separated file. * Dispose of this with eapRunFreeList(). */ struct eapRun *eapRunLoadAllByChar(char *fileName, char chopper); /* Load all eapRun from chopper separated file. * Dispose of this with eapRunFreeList(). */ #define eapRunLoadAllByTab(a) eapRunLoadAllByChar(a, '\t'); /* Load all eapRun from tab separated file. * Dispose of this with eapRunFreeList(). */ struct eapRun *eapRunCommaIn(char **pS, struct eapRun *ret); /* Create a eapRun out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapRun */ void eapRunFree(struct eapRun **pEl); /* Free a single dynamically allocated eapRun such as created * with eapRunLoad(). */ void eapRunFreeList(struct eapRun **pList); /* Free a list of dynamically allocated eapRun's */ void eapRunOutput(struct eapRun *el, FILE *f, char sep, char lastSep); /* Print out eapRun. Separate fields with sep. Follow last field with lastSep. */ #define eapRunTabOut(el,f) eapRunOutput(el,f,'\t','\n'); /* Print out eapRun as a line in a tab-separated file. */ #define eapRunCommaOut(el,f) eapRunOutput(el,f,',',','); /* Print out eapRun as a comma separated list including final comma. */ #define EAPINPUT_NUM_COLS 6 extern char *eapInputCommaSepFieldNames; struct eapInput /* Inputs to an eapAnalysis */ { struct eapInput *next; /* Next in singly linked list. */ unsigned id; /* Input table ID */ unsigned runId; /* Which eapAnalysis this is associated with */ char *name; /* Input name within step */ unsigned ix; /* Inputs always potentially vectors. Have single one with zero ix for scalar input */ unsigned fileId; /* Associated file - 0 for no file, look perhaps to val below instead. */ char *val; /* Non-file data */ }; void eapInputStaticLoad(char **row, struct eapInput *ret); /* Load a row from eapInput table into ret. The contents of ret will * be replaced at the next call to this function. */ struct eapInput *eapInputLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapInput 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 eapInputFreeList(). */ void eapInputSaveToDb(struct sqlConnection *conn, struct eapInput *el, char *tableName, int updateSize); /* Save eapInput 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 eapInput *eapInputLoad(char **row); /* Load a eapInput from row fetched with select * from eapInput * from database. Dispose of this with eapInputFree(). */ struct eapInput *eapInputLoadAll(char *fileName); /* Load all eapInput from whitespace-separated file. * Dispose of this with eapInputFreeList(). */ struct eapInput *eapInputLoadAllByChar(char *fileName, char chopper); /* Load all eapInput from chopper separated file. * Dispose of this with eapInputFreeList(). */ #define eapInputLoadAllByTab(a) eapInputLoadAllByChar(a, '\t'); /* Load all eapInput from tab separated file. * Dispose of this with eapInputFreeList(). */ struct eapInput *eapInputCommaIn(char **pS, struct eapInput *ret); /* Create a eapInput out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapInput */ void eapInputFree(struct eapInput **pEl); /* Free a single dynamically allocated eapInput such as created * with eapInputLoad(). */ void eapInputFreeList(struct eapInput **pList); /* Free a list of dynamically allocated eapInput's */ void eapInputOutput(struct eapInput *el, FILE *f, char sep, char lastSep); /* Print out eapInput. Separate fields with sep. Follow last field with lastSep. */ #define eapInputTabOut(el,f) eapInputOutput(el,f,'\t','\n'); /* Print out eapInput as a line in a tab-separated file. */ #define eapInputCommaOut(el,f) eapInputOutput(el,f,',',','); /* Print out eapInput as a comma separated list including final comma. */ #define EAPOUTPUT_NUM_COLS 6 extern char *eapOutputCommaSepFieldNames; struct eapOutput /* Outputs to an eapAnalysis */ { struct eapOutput *next; /* Next in singly linked list. */ unsigned id; /* Output table ID */ unsigned runId; /* Which eapAnalysis this is associated with */ char *name; /* Output name within step */ unsigned ix; /* Outputs always potentially vectors. Have single one with zero ix for scalar output */ unsigned fileId; /* Associated file - 0 for no file, look perhaps to val below instead. */ char *val; /* Non-file data */ }; void eapOutputStaticLoad(char **row, struct eapOutput *ret); /* Load a row from eapOutput table into ret. The contents of ret will * be replaced at the next call to this function. */ struct eapOutput *eapOutputLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapOutput 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 eapOutputFreeList(). */ void eapOutputSaveToDb(struct sqlConnection *conn, struct eapOutput *el, char *tableName, int updateSize); /* Save eapOutput 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 eapOutput *eapOutputLoad(char **row); /* Load a eapOutput from row fetched with select * from eapOutput * from database. Dispose of this with eapOutputFree(). */ struct eapOutput *eapOutputLoadAll(char *fileName); /* Load all eapOutput from whitespace-separated file. * Dispose of this with eapOutputFreeList(). */ struct eapOutput *eapOutputLoadAllByChar(char *fileName, char chopper); /* Load all eapOutput from chopper separated file. * Dispose of this with eapOutputFreeList(). */ #define eapOutputLoadAllByTab(a) eapOutputLoadAllByChar(a, '\t'); /* Load all eapOutput from tab separated file. * Dispose of this with eapOutputFreeList(). */ struct eapOutput *eapOutputCommaIn(char **pS, struct eapOutput *ret); /* Create a eapOutput out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapOutput */ void eapOutputFree(struct eapOutput **pEl); /* Free a single dynamically allocated eapOutput such as created * with eapOutputLoad(). */ void eapOutputFreeList(struct eapOutput **pList); /* Free a list of dynamically allocated eapOutput's */ void eapOutputOutput(struct eapOutput *el, FILE *f, char sep, char lastSep); /* Print out eapOutput. Separate fields with sep. Follow last field with lastSep. */ #define eapOutputTabOut(el,f) eapOutputOutput(el,f,'\t','\n'); /* Print out eapOutput as a line in a tab-separated file. */ #define eapOutputCommaOut(el,f) eapOutputOutput(el,f,',',','); /* Print out eapOutput as a comma separated list including final comma. */ #define EAPPHANTOMPEAKSTATS_NUM_COLS 11 extern char *eapPhantomPeakStatsCommaSepFieldNames; struct eapPhantomPeakStats /* Statistics on a BAM file that contains reads that will align in a peaky fashion - deprecated */ { struct eapPhantomPeakStats *next; /* Next in singly linked list. */ unsigned fileId; /* ID of BAM file this is taken from */ unsigned numReads; /* Number of mapped reads in that file */ 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) = COL4 / COL8 */ double rsc; /* Relative strand cross-correlation coefficient (RSC) = (COL4 - COL8) / (COL6 - COL8)A */ int qualityTag; /* based on thresholded RSC (codes: -2:veryLow,-1:Low,0:Medium,1:High,2:veryHigh) */ }; void eapPhantomPeakStatsStaticLoad(char **row, struct eapPhantomPeakStats *ret); /* Load a row from eapPhantomPeakStats table into ret. The contents of ret will * be replaced at the next call to this function. */ struct eapPhantomPeakStats *eapPhantomPeakStatsLoadByQuery(struct sqlConnection *conn, char *query); /* Load all eapPhantomPeakStats 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 eapPhantomPeakStatsFreeList(). */ void eapPhantomPeakStatsSaveToDb(struct sqlConnection *conn, struct eapPhantomPeakStats *el, char *tableName, int updateSize); /* Save eapPhantomPeakStats 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 eapPhantomPeakStats *eapPhantomPeakStatsLoad(char **row); /* Load a eapPhantomPeakStats from row fetched with select * from eapPhantomPeakStats * from database. Dispose of this with eapPhantomPeakStatsFree(). */ struct eapPhantomPeakStats *eapPhantomPeakStatsLoadAll(char *fileName); /* Load all eapPhantomPeakStats from whitespace-separated file. * Dispose of this with eapPhantomPeakStatsFreeList(). */ struct eapPhantomPeakStats *eapPhantomPeakStatsLoadAllByChar(char *fileName, char chopper); /* Load all eapPhantomPeakStats from chopper separated file. * Dispose of this with eapPhantomPeakStatsFreeList(). */ #define eapPhantomPeakStatsLoadAllByTab(a) eapPhantomPeakStatsLoadAllByChar(a, '\t'); /* Load all eapPhantomPeakStats from tab separated file. * Dispose of this with eapPhantomPeakStatsFreeList(). */ struct eapPhantomPeakStats *eapPhantomPeakStatsCommaIn(char **pS, struct eapPhantomPeakStats *ret); /* Create a eapPhantomPeakStats out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new eapPhantomPeakStats */ void eapPhantomPeakStatsFree(struct eapPhantomPeakStats **pEl); /* Free a single dynamically allocated eapPhantomPeakStats such as created * with eapPhantomPeakStatsLoad(). */ void eapPhantomPeakStatsFreeList(struct eapPhantomPeakStats **pList); /* Free a list of dynamically allocated eapPhantomPeakStats's */ void eapPhantomPeakStatsOutput(struct eapPhantomPeakStats *el, FILE *f, char sep, char lastSep); /* Print out eapPhantomPeakStats. Separate fields with sep. Follow last field with lastSep. */ #define eapPhantomPeakStatsTabOut(el,f) eapPhantomPeakStatsOutput(el,f,'\t','\n'); /* Print out eapPhantomPeakStats as a line in a tab-separated file. */ #define eapPhantomPeakStatsCommaOut(el,f) eapPhantomPeakStatsOutput(el,f,',',','); /* Print out eapPhantomPeakStats as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* EAPDB_H */