src/hg/instinct/inc/tcgaTableDefs.h 1.2
1.2 2009/06/04 03:47:23 jsanborn
added copyright notices, removed cluster library
Index: src/hg/instinct/inc/tcgaTableDefs.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/inc/tcgaTableDefs.h,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/instinct/inc/tcgaTableDefs.h 9 May 2008 17:32:20 -0000 1.1
+++ src/hg/instinct/inc/tcgaTableDefs.h 4 Jun 2009 03:47:23 -0000 1.2
@@ -1,658 +1,662 @@
+/********************************************************************************/
+/* Copyright 2007-2009 -- The Regents of the University of California */
+/********************************************************************************/
+
/* tcgaTableDefs.h was originally generated by the autoSql program, which also
* generated tcgaTableDefs.c and tcgaTableDefs.sql. This header links the database and
* the RAM representation of objects. */
#ifndef TCGATABLEDEFS_H
#define TCGATABLEDEFS_H
#ifndef JKSQL_H
#include "jksql.h"
#endif
#define SUBJINFO_NUM_COLS 11
struct subjInfo
/* Table subjInfo */
{
struct subjInfo *next; /* Next in singly linked list. */
char *subjId; /* BCR Patient Barcode */
char *gender; /* Gender */
char *race; /* Race */
char *dateOfBirth; /* Date of Birth */
char *dateOfDeath; /* Date of Death */
char *informedConsentAcquired; /* Informed Consent Acquired */
char *dateOfLastFollowUp; /* Date of Last Followup */
char *examinationDate; /* Examination Date */
float *alcoholConsumption; /* Alcohol Consumption */
char *vitalStatus; /* Vital Status */
float *smokingHistory; /* Smoking History */
};
void subjInfoStaticLoadWithNull(char **row, struct subjInfo *ret);
/* Load a row from subjInfo table into ret. The contents of ret will
* be replaced at the next call to this function. */
struct subjInfo *subjInfoLoadWithNull(char **row);
/* Load a subjInfo from row fetched with select * from subjInfo
* from database. Dispose of this with subjInfoFree(). */
struct subjInfo *subjInfoLoadAll(char *fileName);
/* Load all subjInfo from whitespace-separated file.
* Dispose of this with subjInfoFreeList(). */
struct subjInfo *subjInfoLoadAllByChar(char *fileName, char chopper);
/* Load all subjInfo from chopper separated file.
* Dispose of this with subjInfoFreeList(). */
#define subjInfoLoadAllByTab(a) subjInfoLoadAllByChar(a, '\t');
/* Load all subjInfo from tab separated file.
* Dispose of this with subjInfoFreeList(). */
struct subjInfo *subjInfoLoadByQuery(struct sqlConnection *conn, char *query);
/* Load all subjInfo 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 subjInfoFreeList(). */
void subjInfoSaveToDb(struct sqlConnection *conn, struct subjInfo *el, char *tableName, int updateSize);
/* Save subjInfo as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Note that strings must be escaped to allow insertion into the database.
* For example "autosql's features include" --> "autosql\'s features include"
* If worried about this use subjInfoSaveToDbEscaped() */
void subjInfoSaveToDbEscaped(struct sqlConnection *conn, struct subjInfo *el, char *tableName, int updateSize);
/* Save subjInfo as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than subjInfoSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
struct subjInfo *subjInfoCommaIn(char **pS, struct subjInfo *ret);
/* Create a subjInfo out of a comma separated string.
* This will fill in ret if non-null, otherwise will
* return a new subjInfo */
void subjInfoFree(struct subjInfo **pEl);
/* Free a single dynamically allocated subjInfo such as created
* with subjInfoLoad(). */
void subjInfoFreeList(struct subjInfo **pList);
/* Free a list of dynamically allocated subjInfo's */
void subjInfoOutput(struct subjInfo *el, FILE *f, char sep, char lastSep);
/* Print out subjInfo. Separate fields with sep. Follow last field with lastSep. */
#define subjInfoTabOut(el,f) subjInfoOutput(el,f,'\t','\n');
/* Print out subjInfo as a line in a tab-separated file. */
#define subjInfoCommaOut(el,f) subjInfoOutput(el,f,',',',');
/* Print out subjInfo as a comma separated list including final comma. */
#define TCGAXREF_NUM_COLS 6
struct tcgaXref
/* Table tcgaXref */
{
struct tcgaXref *next; /* Next in singly linked list. */
char *subjId; /* BCR Patient Barcode */
char *sampleId; /* BCR Sample Barcode */
char *slideId; /* BCR Slide Barcode */
char *AliquotId; /* BCR Aliquot Barcode */
char *analyteId; /* BCR Analyte Barcode */
char *portionId; /* BCR Portion Barcode */
};
void tcgaXrefStaticLoadWithNull(char **row, struct tcgaXref *ret);
/* Load a row from tcgaXref table into ret. The contents of ret will
* be replaced at the next call to this function. */
struct tcgaXref *tcgaXrefLoadWithNull(char **row);
/* Load a tcgaXref from row fetched with select * from tcgaXref
* from database. Dispose of this with tcgaXrefFree(). */
struct tcgaXref *tcgaXrefLoadAll(char *fileName);
/* Load all tcgaXref from whitespace-separated file.
* Dispose of this with tcgaXrefFreeList(). */
struct tcgaXref *tcgaXrefLoadAllByChar(char *fileName, char chopper);
/* Load all tcgaXref from chopper separated file.
* Dispose of this with tcgaXrefFreeList(). */
#define tcgaXrefLoadAllByTab(a) tcgaXrefLoadAllByChar(a, '\t');
/* Load all tcgaXref from tab separated file.
* Dispose of this with tcgaXrefFreeList(). */
struct tcgaXref *tcgaXrefLoadByQuery(struct sqlConnection *conn, char *query);
/* Load all tcgaXref 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 tcgaXrefFreeList(). */
void tcgaXrefSaveToDb(struct sqlConnection *conn, struct tcgaXref *el, char *tableName, int updateSize);
/* Save tcgaXref as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Note that strings must be escaped to allow insertion into the database.
* For example "autosql's features include" --> "autosql\'s features include"
* If worried about this use tcgaXrefSaveToDbEscaped() */
void tcgaXrefSaveToDbEscaped(struct sqlConnection *conn, struct tcgaXref *el, char *tableName, int updateSize);
/* Save tcgaXref as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than tcgaXrefSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
struct tcgaXref *tcgaXrefCommaIn(char **pS, struct tcgaXref *ret);
/* Create a tcgaXref out of a comma separated string.
* This will fill in ret if non-null, otherwise will
* return a new tcgaXref */
void tcgaXrefFree(struct tcgaXref **pEl);
/* Free a single dynamically allocated tcgaXref such as created
* with tcgaXrefLoad(). */
void tcgaXrefFreeList(struct tcgaXref **pList);
/* Free a list of dynamically allocated tcgaXref's */
void tcgaXrefOutput(struct tcgaXref *el, FILE *f, char sep, char lastSep);
/* Print out tcgaXref. Separate fields with sep. Follow last field with lastSep. */
#define tcgaXrefTabOut(el,f) tcgaXrefOutput(el,f,'\t','\n');
/* Print out tcgaXref as a line in a tab-separated file. */
#define tcgaXrefCommaOut(el,f) tcgaXrefOutput(el,f,',',',');
/* Print out tcgaXref as a comma separated list including final comma. */
#define STATUS_NUM_COLS 12
struct status
/* Table status */
{
struct status *next; /* Next in singly linked list. */
char *subjId; /* BCR Patient Barcode */
char *tnmRecurrenceTumorStatus; /* TNM Recurrence Tumor Status */
char *tnmRecurrenceMetastaticStatus; /* TNM Recurrence Metastatic Status */
char *tnmClinicalTumorStatus; /* TNM Clinical Tumor Status */
char *tnmRecurrenceLymphnodeStatus; /* TNM Recurrence Lymphnode Status */
char *tnmPathologyMetastaticStatus; /* TNM Pathology Metastatic Status */
char *tnmClinicalMetastaticStatus; /* TNM Clinical Metastatic Status */
char *tnmPathologyTumorStatus; /* TNM Pathology Tumor Status */
char *tnmClinicalLymphnodeStatus; /* TNM Clinical Lymphnode Status */
char *tnmPathologyLymphnodeStatus; /* TNM Pathology Lymphnode Status */
char *progressionStatus; /* Progression Status */
char *vitalStatus; /* Vital Status */
};
void statusStaticLoadWithNull(char **row, struct status *ret);
/* Load a row from status table into ret. The contents of ret will
* be replaced at the next call to this function. */
struct status *statusLoadWithNull(char **row);
/* Load a status from row fetched with select * from status
* from database. Dispose of this with statusFree(). */
struct status *statusLoadAll(char *fileName);
/* Load all status from whitespace-separated file.
* Dispose of this with statusFreeList(). */
struct status *statusLoadAllByChar(char *fileName, char chopper);
/* Load all status from chopper separated file.
* Dispose of this with statusFreeList(). */
#define statusLoadAllByTab(a) statusLoadAllByChar(a, '\t');
/* Load all status from tab separated file.
* Dispose of this with statusFreeList(). */
struct status *statusLoadByQuery(struct sqlConnection *conn, char *query);
/* Load all status 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 statusFreeList(). */
void statusSaveToDb(struct sqlConnection *conn, struct status *el, char *tableName, int updateSize);
/* Save status as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Note that strings must be escaped to allow insertion into the database.
* For example "autosql's features include" --> "autosql\'s features include"
* If worried about this use statusSaveToDbEscaped() */
void statusSaveToDbEscaped(struct sqlConnection *conn, struct status *el, char *tableName, int updateSize);
/* Save status as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than statusSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
struct status *statusCommaIn(char **pS, struct status *ret);
/* Create a status out of a comma separated string.
* This will fill in ret if non-null, otherwise will
* return a new status */
void statusFree(struct status **pEl);
/* Free a single dynamically allocated status such as created
* with statusLoad(). */
void statusFreeList(struct status **pList);
/* Free a list of dynamically allocated status's */
void statusOutput(struct status *el, FILE *f, char sep, char lastSep);
/* Print out status. Separate fields with sep. Follow last field with lastSep. */
#define statusTabOut(el,f) statusOutput(el,f,'\t','\n');
/* Print out status as a line in a tab-separated file. */
#define statusCommaOut(el,f) statusOutput(el,f,',',',');
/* Print out status as a comma separated list including final comma. */
#define TREATMENT_NUM_COLS 16
struct treatment
/* Table treatment */
{
struct treatment *next; /* Next in singly linked list. */
char *subjId; /* BCR Patient Barcode */
char *startDate; /* Start Date */
char *endDate; /* End Date */
char *dateOfRadiation; /* Date of Radiation */
char *dateOfProcedure; /* Date of Procedure */
char *initialCourse; /* Initial Course */
char *primaryProcedure; /* Primary Procedure */
char *drugCategory; /* Drug Category */
char *drugName; /* Drug Name */
float *drugDosage; /* Drug Dosage */
char *dosageUnits; /* Dosage Units */
char *metastaticProcedure; /* Metastatic Procedure */
char *radiationType; /* Radiation Type */
float *radiationDosage; /* Radiation Dosage */
char *lymphnodeProcedure; /* Lymphnode Procedure */
char *anatomicTreatmentSite; /* Anatomic Treatment Site */
};
void treatmentStaticLoadWithNull(char **row, struct treatment *ret);
/* Load a row from treatment table into ret. The contents of ret will
* be replaced at the next call to this function. */
struct treatment *treatmentLoadWithNull(char **row);
/* Load a treatment from row fetched with select * from treatment
* from database. Dispose of this with treatmentFree(). */
struct treatment *treatmentLoadAll(char *fileName);
/* Load all treatment from whitespace-separated file.
* Dispose of this with treatmentFreeList(). */
struct treatment *treatmentLoadAllByChar(char *fileName, char chopper);
/* Load all treatment from chopper separated file.
* Dispose of this with treatmentFreeList(). */
#define treatmentLoadAllByTab(a) treatmentLoadAllByChar(a, '\t');
/* Load all treatment from tab separated file.
* Dispose of this with treatmentFreeList(). */
struct treatment *treatmentLoadByQuery(struct sqlConnection *conn, char *query);
/* Load all treatment 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 treatmentFreeList(). */
void treatmentSaveToDb(struct sqlConnection *conn, struct treatment *el, char *tableName, int updateSize);
/* Save treatment as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Note that strings must be escaped to allow insertion into the database.
* For example "autosql's features include" --> "autosql\'s features include"
* If worried about this use treatmentSaveToDbEscaped() */
void treatmentSaveToDbEscaped(struct sqlConnection *conn, struct treatment *el, char *tableName, int updateSize);
/* Save treatment as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than treatmentSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
struct treatment *treatmentCommaIn(char **pS, struct treatment *ret);
/* Create a treatment out of a comma separated string.
* This will fill in ret if non-null, otherwise will
* return a new treatment */
void treatmentFree(struct treatment **pEl);
/* Free a single dynamically allocated treatment such as created
* with treatmentLoad(). */
void treatmentFreeList(struct treatment **pList);
/* Free a list of dynamically allocated treatment's */
void treatmentOutput(struct treatment *el, FILE *f, char sep, char lastSep);
/* Print out treatment. Separate fields with sep. Follow last field with lastSep. */
#define treatmentTabOut(el,f) treatmentOutput(el,f,'\t','\n');
/* Print out treatment as a line in a tab-separated file. */
#define treatmentCommaOut(el,f) treatmentOutput(el,f,',',',');
/* Print out treatment as a comma separated list including final comma. */
#define SAMPLEINFO_NUM_COLS 14
struct sampleInfo
/* Table sampleInfo */
{
struct sampleInfo *next; /* Next in singly linked list. */
char *subjId; /* BCR Patient Barcode */
char *sampleId; /* BCR Sample Barcode */
char *sampleType; /* Sample Type */
char *tumorSampleAnatomicLocation; /* Tumor Sample Anatomic Location */
char *dateOfCollection; /* Date of Collection */
char *timeBetweenClampingAndFreezing; /* Time Between Clamping and Freezing */
char *timeBetweenExcisionAndFreezing; /* Time Between Excision and Freezing */
char *tumorTissueSite; /* Tumor Tissue Site */
char *freezingMethod; /* Freezing Method */
char *histologicalType; /* Histological Type */
char *verificationByBCR; /* Verification By BCR */
char *progressionDeterminedBy; /* Progression Determined By */
char *wellnNmber; /* Well Number */
char *bcrSiteId; /* BCR Site ID */
};
void sampleInfoStaticLoadWithNull(char **row, struct sampleInfo *ret);
/* Load a row from sampleInfo table into ret. The contents of ret will
* be replaced at the next call to this function. */
struct sampleInfo *sampleInfoLoadWithNull(char **row);
/* Load a sampleInfo from row fetched with select * from sampleInfo
* from database. Dispose of this with sampleInfoFree(). */
struct sampleInfo *sampleInfoLoadAll(char *fileName);
/* Load all sampleInfo from whitespace-separated file.
* Dispose of this with sampleInfoFreeList(). */
struct sampleInfo *sampleInfoLoadAllByChar(char *fileName, char chopper);
/* Load all sampleInfo from chopper separated file.
* Dispose of this with sampleInfoFreeList(). */
#define sampleInfoLoadAllByTab(a) sampleInfoLoadAllByChar(a, '\t');
/* Load all sampleInfo from tab separated file.
* Dispose of this with sampleInfoFreeList(). */
struct sampleInfo *sampleInfoLoadByQuery(struct sqlConnection *conn, char *query);
/* Load all sampleInfo 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 sampleInfoFreeList(). */
void sampleInfoSaveToDb(struct sqlConnection *conn, struct sampleInfo *el, char *tableName, int updateSize);
/* Save sampleInfo as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Note that strings must be escaped to allow insertion into the database.
* For example "autosql's features include" --> "autosql\'s features include"
* If worried about this use sampleInfoSaveToDbEscaped() */
void sampleInfoSaveToDbEscaped(struct sqlConnection *conn, struct sampleInfo *el, char *tableName, int updateSize);
/* Save sampleInfo as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than sampleInfoSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
struct sampleInfo *sampleInfoCommaIn(char **pS, struct sampleInfo *ret);
/* Create a sampleInfo out of a comma separated string.
* This will fill in ret if non-null, otherwise will
* return a new sampleInfo */
void sampleInfoFree(struct sampleInfo **pEl);
/* Free a single dynamically allocated sampleInfo such as created
* with sampleInfoLoad(). */
void sampleInfoFreeList(struct sampleInfo **pList);
/* Free a list of dynamically allocated sampleInfo's */
void sampleInfoOutput(struct sampleInfo *el, FILE *f, char sep, char lastSep);
/* Print out sampleInfo. Separate fields with sep. Follow last field with lastSep. */
#define sampleInfoTabOut(el,f) sampleInfoOutput(el,f,'\t','\n');
/* Print out sampleInfo as a line in a tab-separated file. */
#define sampleInfoCommaOut(el,f) sampleInfoOutput(el,f,',',',');
/* Print out sampleInfo as a comma separated list including final comma. */
#define RESULT_NUM_COLS 45
struct result
/* Table result */
{
struct result *next; /* Next in singly linked list. */
char *subjId; /* BCR Patient Barcode */
char *sampleId; /* BCR Sample Barcode */
float *a260a280Ratio; /* A260 A280 Ratio */
float *shortestDimension; /* Shortest Dimension */
float *longestDimension; /* Longest Dimension */
char *percentLymphocyteInfiltration; /* Percent Lymphocyte Infiltration */
char *ratio28s18s; /* ratio28s18s */
char *oligoDendroglialComponent; /* Oligo Dendroglial Component */
char *numberRegionalLymphnodesPos; /* number regional lymphnodes pos */
char *tnmPathologyStageGrouping; /* TNM Pathology Stage Grouping */
float *numFractions; /* Num Fractions */
float *numberCycles; /* Number Cycles */
char *histologicNuclearGrade; /* Histologic Nuclear Grade */
char *percentGranulocyteInfiltration; /* Percent Granulocyte Infiltration */
char *marginsInvolved; /* Margins Involved */
char *percentStromalCells; /* Percent Stromal Cells */
char *numberProliferatingCells; /* Number Proliferating Cells */
char *percentTumorNuclei; /* Percent Tumor Nuclei */
char *histologicalNuclearGrade; /* Histological Nuclear Grade */
char *percentInflamInfiltration; /* Percent Inflam Infiltration */
char *percentTumorCells; /* Percent Tumor Cells */
float *concentration; /* Concentration */
char *palisadingNecrosis; /* Palisading Necrosis */
char *percentNeutrophilInfiltration; /* Percent Neutrophil Infiltration */
char *normalTumorGenotypeMatch; /* Normal Tumor Genotype Match */
char *tnmClinicalStageGrouping; /* TNM Clinical Stage Grouping */
char *intermediateDimension; /* Intermediate Dimension */
char *leptomeningealInvolement; /* Leptomeningeal Involement */
char *gfap_positive; /* GFAP Positive */
char *percentEosinophilInfiltration; /* Percent Eosinophil Infiltration */
float *karnofskyPerformanceScore; /* karnofskyperformancescore */
char *lymphaticInvasion; /* Lymphatic Invasion */
char *percentNormalCells; /* Percent Normal Cells */
char *mib1_positive; /* MIB1 Positive */
char *endothelialProliferation; /* Endothelial Proliferation */
char *tnmRecurrenceStageGrouping; /* TNM Recurrence Stage Grouping */
char *gemistocytesPresent; /* Gemistocytes Present */
char *cellularity; /* Cellularity */
char *percentMonocyteInfiltration; /* Percent Monocyte Infiltration */
char *numberRegionalLymphnodesExam; /* Number Regionally Mphnodes Exam */
char *percentNecrosis; /* Percent Necrosis */
char *rinValue; /* RIN Value */
char *nuclearPleomorphism; /* Nuclear Pleomorphism */
char *venousInvasion; /* Venous Invasion */
char *octEmbedded; /* Oct Embedded */
};
void resultStaticLoadWithNull(char **row, struct result *ret);
/* Load a row from result table into ret. The contents of ret will
* be replaced at the next call to this function. */
struct result *resultLoadWithNull(char **row);
/* Load a result from row fetched with select * from result
* from database. Dispose of this with resultFree(). */
struct result *resultLoadAll(char *fileName);
/* Load all result from whitespace-separated file.
* Dispose of this with resultFreeList(). */
struct result *resultLoadAllByChar(char *fileName, char chopper);
/* Load all result from chopper separated file.
* Dispose of this with resultFreeList(). */
#define resultLoadAllByTab(a) resultLoadAllByChar(a, '\t');
/* Load all result from tab separated file.
* Dispose of this with resultFreeList(). */
struct result *resultLoadByQuery(struct sqlConnection *conn, char *query);
/* Load all result 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 resultFreeList(). */
void resultSaveToDb(struct sqlConnection *conn, struct result *el, char *tableName, int updateSize);
/* Save result as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Note that strings must be escaped to allow insertion into the database.
* For example "autosql's features include" --> "autosql\'s features include"
* If worried about this use resultSaveToDbEscaped() */
void resultSaveToDbEscaped(struct sqlConnection *conn, struct result *el, char *tableName, int updateSize);
/* Save result as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than resultSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
struct result *resultCommaIn(char **pS, struct result *ret);
/* Create a result out of a comma separated string.
* This will fill in ret if non-null, otherwise will
* return a new result */
void resultFree(struct result **pEl);
/* Free a single dynamically allocated result such as created
* with resultLoad(). */
void resultFreeList(struct result **pList);
/* Free a list of dynamically allocated result's */
void resultOutput(struct result *el, FILE *f, char sep, char lastSep);
/* Print out result. Separate fields with sep. Follow last field with lastSep. */
#define resultTabOut(el,f) resultOutput(el,f,'\t','\n');
/* Print out result as a line in a tab-separated file. */
#define resultCommaOut(el,f) resultOutput(el,f,',',',');
/* Print out result as a comma separated list including final comma. */
#define MISC_NUM_COLS 21
struct misc
/* Table misc */
{
struct misc *next; /* Next in singly linked list. */
char *subjId; /* BCR Patient Barcode */
char *sampleId; /* BCR Sample Barcode */
char *revision; /* Revision */
float *amount; /* Amount */
float *initialWeight; /* Initial Weight */
float *currentWeight; /* Current Weight */
char *primaryOrMetastaticStatus; /* Primary or Metastatic Status */
char *protocolText; /* Protocol Text */
char *protocolName; /* Protocol Name */
char *protocolFileName; /* Protocol File Name */
char *analyteType; /* Analyte Type */
char *sectionLocation; /* Section Location */
char *pcrAmplificationSuccessful; /* PCR Amplification Successful */
float *weight; /* Weight */
char *experimentalProtocolType; /* Experimental Protocol Type */
char *shippingDate; /* Shipping Date */
char *gelImageFile; /* Gel Image File */
char *histologicType; /* Histologic Type */
char *dateCreated; /* Date Created */
char *environmentalExposure; /* Environmental Exposure */
char *cancerStatus; /* Cancer Status */
};
void miscStaticLoadWithNull(char **row, struct misc *ret);
/* Load a row from misc table into ret. The contents of ret will
* be replaced at the next call to this function. */
struct misc *miscLoadWithNull(char **row);
/* Load a misc from row fetched with select * from misc
* from database. Dispose of this with miscFree(). */
struct misc *miscLoadAll(char *fileName);
/* Load all misc from whitespace-separated file.
* Dispose of this with miscFreeList(). */
struct misc *miscLoadAllByChar(char *fileName, char chopper);
/* Load all misc from chopper separated file.
* Dispose of this with miscFreeList(). */
#define miscLoadAllByTab(a) miscLoadAllByChar(a, '\t');
/* Load all misc from tab separated file.
* Dispose of this with miscFreeList(). */
struct misc *miscLoadByQuery(struct sqlConnection *conn, char *query);
/* Load all misc 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 miscFreeList(). */
void miscSaveToDb(struct sqlConnection *conn, struct misc *el, char *tableName, int updateSize);
/* Save misc as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size
* of a string that would contain the entire query. Arrays of native types are
* converted to comma separated strings and loaded as such, User defined types are
* inserted as NULL. Note that strings must be escaped to allow insertion into the database.
* For example "autosql's features include" --> "autosql\'s features include"
* If worried about this use miscSaveToDbEscaped() */
void miscSaveToDbEscaped(struct sqlConnection *conn, struct misc *el, char *tableName, int updateSize);
/* Save misc as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than miscSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
struct misc *miscCommaIn(char **pS, struct misc *ret);
/* Create a misc out of a comma separated string.
* This will fill in ret if non-null, otherwise will
* return a new misc */
void miscFree(struct misc **pEl);
/* Free a single dynamically allocated misc such as created
* with miscLoad(). */
void miscFreeList(struct misc **pList);
/* Free a list of dynamically allocated misc's */
void miscOutput(struct misc *el, FILE *f, char sep, char lastSep);
/* Print out misc. Separate fields with sep. Follow last field with lastSep. */
#define miscTabOut(el,f) miscOutput(el,f,'\t','\n');
/* Print out misc as a line in a tab-separated file. */
#define miscCommaOut(el,f) miscOutput(el,f,',',',');
/* Print out misc as a comma separated list including final comma. */
/* -------------------------------- End autoSql Generated Code -------------------------------- */
#endif /* TCGATABLEDEFS_H */