/* edwAnalysis.h was originally generated by the autoSql program, which also * generated edwAnalysis.c and edwAnalysis.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 EDWANALYSIS_H #define EDWANALYSIS_H #include "jksql.h" #define EDWANALYSISJOB_NUM_COLS 9 extern char *edwAnalysisJobCommaSepFieldNames; struct edwAnalysisJob /* An analysis pipeline job to be run asynchronously and not too many all at once. */ { struct edwAnalysisJob *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 cpusRequested; /* Number of CPUs to request from job control system */ char *parasolId; /* Parasol job id for process. */ }; void edwAnalysisJobStaticLoad(char **row, struct edwAnalysisJob *ret); /* Load a row from edwAnalysisJob table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwAnalysisJob *edwAnalysisJobLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwAnalysisJob 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 edwAnalysisJobFreeList(). */ void edwAnalysisJobSaveToDb(struct sqlConnection *conn, struct edwAnalysisJob *el, char *tableName, int updateSize); /* Save edwAnalysisJob 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 edwAnalysisJob *edwAnalysisJobLoad(char **row); /* Load a edwAnalysisJob from row fetched with select * from edwAnalysisJob * from database. Dispose of this with edwAnalysisJobFree(). */ struct edwAnalysisJob *edwAnalysisJobLoadAll(char *fileName); /* Load all edwAnalysisJob from whitespace-separated file. * Dispose of this with edwAnalysisJobFreeList(). */ struct edwAnalysisJob *edwAnalysisJobLoadAllByChar(char *fileName, char chopper); /* Load all edwAnalysisJob from chopper separated file. * Dispose of this with edwAnalysisJobFreeList(). */ #define edwAnalysisJobLoadAllByTab(a) edwAnalysisJobLoadAllByChar(a, '\t'); /* Load all edwAnalysisJob from tab separated file. * Dispose of this with edwAnalysisJobFreeList(). */ struct edwAnalysisJob *edwAnalysisJobCommaIn(char **pS, struct edwAnalysisJob *ret); /* Create a edwAnalysisJob out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwAnalysisJob */ void edwAnalysisJobFree(struct edwAnalysisJob **pEl); /* Free a single dynamically allocated edwAnalysisJob such as created * with edwAnalysisJobLoad(). */ void edwAnalysisJobFreeList(struct edwAnalysisJob **pList); /* Free a list of dynamically allocated edwAnalysisJob's */ void edwAnalysisJobOutput(struct edwAnalysisJob *el, FILE *f, char sep, char lastSep); /* Print out edwAnalysisJob. Separate fields with sep. Follow last field with lastSep. */ #define edwAnalysisJobTabOut(el,f) edwAnalysisJobOutput(el,f,'\t','\n'); /* Print out edwAnalysisJob as a line in a tab-separated file. */ #define edwAnalysisJobCommaOut(el,f) edwAnalysisJobOutput(el,f,',',','); /* Print out edwAnalysisJob as a comma separated list including final comma. */ #define EDWANALYSISSOFTWARE_NUM_COLS 4 extern char *edwAnalysisSoftwareCommaSepFieldNames; struct edwAnalysisSoftware /* Software that is tracked by the analysis pipeline. */ { struct edwAnalysisSoftware *next; /* Next in singly linked list. */ unsigned id; /* Software id */ char *name; /* Command line name */ char *version; /* Current version */ char md5[33]; /* md5 sum of executable file */ }; void edwAnalysisSoftwareStaticLoad(char **row, struct edwAnalysisSoftware *ret); /* Load a row from edwAnalysisSoftware table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwAnalysisSoftware *edwAnalysisSoftwareLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwAnalysisSoftware 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 edwAnalysisSoftwareFreeList(). */ void edwAnalysisSoftwareSaveToDb(struct sqlConnection *conn, struct edwAnalysisSoftware *el, char *tableName, int updateSize); /* Save edwAnalysisSoftware 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 edwAnalysisSoftware *edwAnalysisSoftwareLoad(char **row); /* Load a edwAnalysisSoftware from row fetched with select * from edwAnalysisSoftware * from database. Dispose of this with edwAnalysisSoftwareFree(). */ struct edwAnalysisSoftware *edwAnalysisSoftwareLoadAll(char *fileName); /* Load all edwAnalysisSoftware from whitespace-separated file. * Dispose of this with edwAnalysisSoftwareFreeList(). */ struct edwAnalysisSoftware *edwAnalysisSoftwareLoadAllByChar(char *fileName, char chopper); /* Load all edwAnalysisSoftware from chopper separated file. * Dispose of this with edwAnalysisSoftwareFreeList(). */ #define edwAnalysisSoftwareLoadAllByTab(a) edwAnalysisSoftwareLoadAllByChar(a, '\t'); /* Load all edwAnalysisSoftware from tab separated file. * Dispose of this with edwAnalysisSoftwareFreeList(). */ struct edwAnalysisSoftware *edwAnalysisSoftwareCommaIn(char **pS, struct edwAnalysisSoftware *ret); /* Create a edwAnalysisSoftware out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwAnalysisSoftware */ void edwAnalysisSoftwareFree(struct edwAnalysisSoftware **pEl); /* Free a single dynamically allocated edwAnalysisSoftware such as created * with edwAnalysisSoftwareLoad(). */ void edwAnalysisSoftwareFreeList(struct edwAnalysisSoftware **pList); /* Free a list of dynamically allocated edwAnalysisSoftware's */ void edwAnalysisSoftwareOutput(struct edwAnalysisSoftware *el, FILE *f, char sep, char lastSep); /* Print out edwAnalysisSoftware. Separate fields with sep. Follow last field with lastSep. */ #define edwAnalysisSoftwareTabOut(el,f) edwAnalysisSoftwareOutput(el,f,'\t','\n'); /* Print out edwAnalysisSoftware as a line in a tab-separated file. */ #define edwAnalysisSoftwareCommaOut(el,f) edwAnalysisSoftwareOutput(el,f,',',','); /* Print out edwAnalysisSoftware as a comma separated list including final comma. */ #define EDWANALYSISSTEP_NUM_COLS 5 extern char *edwAnalysisStepCommaSepFieldNames; struct edwAnalysisStep /* A step in an analysis pipeline - something that takes one file to another */ { struct edwAnalysisStep *next; /* Next in singly linked list. */ unsigned id; /* Step id */ char *name; /* Name of this analysis step */ int softwareCount; /* Number of pieces of software used in step */ char **software; /* Names of software used. First is the glue script */ int cpusRequested; /* Number of CPUs to request from job control system */ }; struct edwAnalysisStep *edwAnalysisStepLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwAnalysisStep 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 edwAnalysisStepFreeList(). */ void edwAnalysisStepSaveToDb(struct sqlConnection *conn, struct edwAnalysisStep *el, char *tableName, int updateSize); /* Save edwAnalysisStep 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 edwAnalysisStep *edwAnalysisStepLoad(char **row); /* Load a edwAnalysisStep from row fetched with select * from edwAnalysisStep * from database. Dispose of this with edwAnalysisStepFree(). */ struct edwAnalysisStep *edwAnalysisStepLoadAll(char *fileName); /* Load all edwAnalysisStep from whitespace-separated file. * Dispose of this with edwAnalysisStepFreeList(). */ struct edwAnalysisStep *edwAnalysisStepLoadAllByChar(char *fileName, char chopper); /* Load all edwAnalysisStep from chopper separated file. * Dispose of this with edwAnalysisStepFreeList(). */ #define edwAnalysisStepLoadAllByTab(a) edwAnalysisStepLoadAllByChar(a, '\t'); /* Load all edwAnalysisStep from tab separated file. * Dispose of this with edwAnalysisStepFreeList(). */ struct edwAnalysisStep *edwAnalysisStepCommaIn(char **pS, struct edwAnalysisStep *ret); /* Create a edwAnalysisStep out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwAnalysisStep */ void edwAnalysisStepFree(struct edwAnalysisStep **pEl); /* Free a single dynamically allocated edwAnalysisStep such as created * with edwAnalysisStepLoad(). */ void edwAnalysisStepFreeList(struct edwAnalysisStep **pList); /* Free a list of dynamically allocated edwAnalysisStep's */ void edwAnalysisStepOutput(struct edwAnalysisStep *el, FILE *f, char sep, char lastSep); /* Print out edwAnalysisStep. Separate fields with sep. Follow last field with lastSep. */ #define edwAnalysisStepTabOut(el,f) edwAnalysisStepOutput(el,f,'\t','\n'); /* Print out edwAnalysisStep as a line in a tab-separated file. */ #define edwAnalysisStepCommaOut(el,f) edwAnalysisStepOutput(el,f,',',','); /* Print out edwAnalysisStep as a comma separated list including final comma. */ #define EDWANALYSISRUN_NUM_COLS 20 extern char *edwAnalysisRunCommaSepFieldNames; struct edwAnalysisRun /* Information on an analysis job that we're planning on running */ { struct edwAnalysisRun *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 */ char *configuration; /* Configuration for analysis step */ char *tempDir; /* Where analysis is to be computed */ unsigned firstInputId; /* ID in edwFile of first input */ unsigned inputFileCount; /* Total number of input files */ unsigned *inputFileIds; /* list of all input files as fileIds */ char **inputTypes; /* List of types to go with input files in json output */ unsigned assemblyId; /* Id of assembly we are working with */ unsigned outputFileCount; /* Total number of output files */ char **outputNamesInTempDir; /* list of all output file names in output dir */ char **outputFormats; /* list of formats of output files */ char **outputTypes; /* list of formats of output files */ char *jsonResult; /* JSON formatted object with result for Stanford metaDatabase */ char uuid[38]; /* Help to synchronize us with Stanford. */ signed char createStatus; /* 1 if output files made 0 if not made, -1 if make tried and failed */ unsigned createCount; /* Count of files made */ unsigned *createFileIds; /* list of ids of output files in warehouse */ }; struct edwAnalysisRun *edwAnalysisRunLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwAnalysisRun 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 edwAnalysisRunFreeList(). */ void edwAnalysisRunSaveToDb(struct sqlConnection *conn, struct edwAnalysisRun *el, char *tableName, int updateSize); /* Save edwAnalysisRun 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 edwAnalysisRun *edwAnalysisRunLoad(char **row); /* Load a edwAnalysisRun from row fetched with select * from edwAnalysisRun * from database. Dispose of this with edwAnalysisRunFree(). */ struct edwAnalysisRun *edwAnalysisRunLoadAll(char *fileName); /* Load all edwAnalysisRun from whitespace-separated file. * Dispose of this with edwAnalysisRunFreeList(). */ struct edwAnalysisRun *edwAnalysisRunLoadAllByChar(char *fileName, char chopper); /* Load all edwAnalysisRun from chopper separated file. * Dispose of this with edwAnalysisRunFreeList(). */ #define edwAnalysisRunLoadAllByTab(a) edwAnalysisRunLoadAllByChar(a, '\t'); /* Load all edwAnalysisRun from tab separated file. * Dispose of this with edwAnalysisRunFreeList(). */ struct edwAnalysisRun *edwAnalysisRunCommaIn(char **pS, struct edwAnalysisRun *ret); /* Create a edwAnalysisRun out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwAnalysisRun */ void edwAnalysisRunFree(struct edwAnalysisRun **pEl); /* Free a single dynamically allocated edwAnalysisRun such as created * with edwAnalysisRunLoad(). */ void edwAnalysisRunFreeList(struct edwAnalysisRun **pList); /* Free a list of dynamically allocated edwAnalysisRun's */ void edwAnalysisRunOutput(struct edwAnalysisRun *el, FILE *f, char sep, char lastSep); /* Print out edwAnalysisRun. Separate fields with sep. Follow last field with lastSep. */ #define edwAnalysisRunTabOut(el,f) edwAnalysisRunOutput(el,f,'\t','\n'); /* Print out edwAnalysisRun as a line in a tab-separated file. */ #define edwAnalysisRunCommaOut(el,f) edwAnalysisRunOutput(el,f,',',','); /* Print out edwAnalysisRun as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* EDWANALYSIS_H */