87e7961d71523fd532a5cac11b5dae5a81587520 ann Thu Dec 8 15:28:10 2016 -0800 removed Hiram's new license blurb from these files. Jim asked me to pull all of them out into their own LICENSE files. refs #13978 diff --git src/README src/README index 48941d9..3b47ea3 100644 --- src/README +++ src/README @@ -1,309 +1,294 @@ -LICENSE - -The Genome Browser binaries and source code are freely available for -academic, nonprofit, and personal use. A license is required for -commercial download and installation of most Genome Browser binaries -and source code, with the exception of specific items in some directories -that are freely available for all uses. Please note the current -license information with the list of specific directory permissions: - - http://genome.ucsc.edu/license/ - -============================================================================ - -SOURCE TREE ORGANIZATION - This file describes the most commonly used modules, and the code conventions used throughout the code base in and under this directory. SOURCE TREE ORGANIZATION The major source subdirectories of this source code are: o - lib - General purpose library routines, some with a biological bent, many just generally useful for computing. o - inc - Interfaces to the library modules. o - utils - Command line utility programs. Like the library a mix of bioinformatically motivated, and general purpose. o - hg - Stuff developed for the Human Genome Project and it's successors. Much of the code in this directory requires MySQL. o - hg/lib - Human Genome Project specific libraries. o - hg/inc - Interfaces to the same libraries o - hg/hgTracks - The part of the UCSC Genome Browser that displays annotation tracks graphically. o - hg/hgc - The part of the Genome Browser that responds to a click on an item in a track. o - hg/hgTrackUi - The part of the Genome Browser that allows users to configure a particular track. o - hg/hgTables - The UCSC Table Browser o - jkOwnLib - Libraries that support blat, isPcr, gfClient, gfServer. In general each program, either command line, or web CGI based, has its source in a different subdirectory. For simple programs, like what is in utils, these often just have a single C module that is linked with the libraries. For more complex programs, such as the hgTracks CGI, there may be multiple C source modules in the dir. COMMONLY USED LIBRARY MODULES o - common - String handling, singly-linked list handling. Other basic stuff every other module uses. o - hash - Simple but effective hash table routines. o - linefile - Line oriented file input, on some systems much faster than fgets(). o - dystring - Dynamically sized strings in C. o - cheapcgi - Parses out cgi variables for scripts called from web pages. o - htmshell - Helps generate HTML output for scripts that are called from web pages or just want to make web pages. o - htmlPage - Read html pages, programatically submit html forms. o - memgfx - Creates a 256 color image in memory which can be drawn on, then saved as a .GIF file which can be encorperated into a web page. o - dnautils and dnaseq - Simple utilities on DNA. o - fa - Read/write fasta format files. o - basicBed - Functions for working with BED format files. o - psl - Functions for working with PSL (blat) format files. o - twoBit - Functions for working with twoBit DNA files. o - bPlusTree - Create/user B+ Tree indexes, the backbone of many databases. o - udc - URL Data Cache - code to locally cache remote files. CODE CONVENTIONS INDENTATION AND SPACING: The code follows an indentation convention that is a bit unusual for C. Opening and closing braces are on a line by themselves and are indented at the same level as the block they enclose: if (someTest) { doSomething(); doSomethingElse(); } Each block of code is indented by 4 from the previous block. As per Unix standard practice, tab stops are set to 8, not 4 as is the common practice in Windows, so some care must be taken when using tabs for indenting. Tabs continue to be a problem for the programmer even in 2012. Currently our makefiles require tabs, while our python code forbids them. The C code can go either way so long as tabs are treated as advancing to the next multiple-of-eight column. Please consult local users of your favorite editor for help configuring it with these indentation and tab standards. Lines should be no more than 100 characters wide. Lines that are longer than this are broken and indented at least 8 spaces more than the original line to indicate the line continuation. Where possible simplifying techniques should be applied to the code in preference to using line continuations, since line continuations obscure the logic conveyed in the indentation of the program. Line continuations may be unavoidable when calling functions with long parameter lists. In most other situations lines can be shortened in better ways than line continuations. Complex expressions can be broken into parts that are assigned to intermediate variables. Long variable names can be revisited and sometimes shortened. Deep indenting can be avoided by simplifying logic and by moving blocks into their own functions. These are just some ways of avoiding long lines. NAMES Symbol names generally begin with a lower-case letter. The second and subsequent words in a name begin with a capital letter to help visually separate the words. Abbreviation of words is strongly discouraged. Words of five letters and less should generally not be abbreviated. If a word is abbreviated in general it is abbreviated to the first three letters: tabSeparatedFile -> tabSepFile In some cases, for local variables abbreviating to a single letter for each word is ok: tabSeparatedFile -> tsf In complex cases you may treat the abbreviation itself as a word, and only the first letter is capitalized. genscanTabSeparatedFile -> genscanTsf Numbers are considered words. You would represent "chromosome 22 annotations" as "chromosome22Annotations" or "chr22Ann." Note the capitalized 'A" after the 22. Since both numbers and single letter words (or abbreviations) disrupt the visual flow of the word separation by capitalization, it is better to avoid these except at the end of the name. These naming rules apply to variables, constants, functions, fields, and structures. They generally are used for file names, database tables, database columns, and C macros as well, though there is a bit less consistency there in the existing code base. Variables that are global should begin with the small letter "g." This is a relatively recent convention, and is not so widely used, but when maintaining code or writing new code it would be good to adopt it. ERROR HANDLING AND MEMORY ALLOCATION Another convention is that errors are reported at a fairly low level, and the programs simply print an error message and abort using errAbort. If you need to catch errors underneath you see the file errAbort.h and install an "abort handler". Memory is generally allocated through "needMem" (which aborts on failure to allocate) and the macros "AllocVar" and "AllocArray". This memory is initially set to zero, and the programs very much depend on this fact. COMMENTING Every module should have a comment at the start of a file that explains concisely what the module does. Explanations of algorithms also belong at the top of the file in most cases. Comments can be of the /* */ or the // form. Structures should be commented following the pattern of this example: struct dyString /* Dynamically resizable string that you can do formatted * output to. */ { struct dyString *next; /* Next in list. */ char *string; /* Current buffer. */ int bufSize; /* Size of buffer. */ int stringSize; /* Size of string. */ }; That is, there is a comment describing the overall purpose of the object between the struct name, and the opening brace, and there is a short comment by each field. In many cases these may not say much more than well-chosen field names, but that's ok. Almost any structure with more than three or four elements includes a "next" pointer as its first member, so that it can be part of a singly-linked list. There's a whole set of routines (see common.c and common.h) which work on singly-linked lists where the next field comes first. Their names all start with "sl." Functions which work on a structure by convention begin with the name of the structure, simulating an object-oriented coding style. In general these functions are all grouped in a file, in this case in dyString.c. Static functions in this file need not have the prefix, though they may. Functions have a comment between their prototype and the opening brace as in this example: char dyStringAppendC(struct dyString *ds, char c) // Append char to end of string. { char *s; if (ds->stringSize >= ds->bufSize) dyStringExpandBuf(ds, ds->bufSize+256); s = ds->string + ds->stringSize++; *s++ = c; *s = 0; return c; } For short functions like this, the opening comment may be the only comment. Longer functions should be broken into logical 'paragraphs' with a comment at the start of each paragraph and blank lines between paragraphs as in this example: struct twoBit *twoBitFromDnaSeq(struct dnaSeq *seq, boolean doMask) /* Convert dnaSeq representation in memory to twoBit representation. * If doMask is true interpret lower-case letters as masked. */ { /* Allocate structure and fill in name and size fields. */ struct twoBit *twoBit; AllocVar(twoBit); int ubyteSize = packedSize(seq->size); UBYTE *pt = AllocArray(twoBit->data, ubyteSize); twoBit->name = cloneString(seq->name); twoBit->size = seq->size; /* Convert to 4-bases per byte representation. */ char *dna = seq->dna; int i, end; end = seq->size - 4; for (i=0; i<end; i += 4) { *pt++ = packDna4(dna+i); } /* Take care of conversion of last few bases, padding arbitrarily with 'T'. */ DNA last4[4]; last4[0] = last4[1] = last4[2] = last4[3] = 'T'; memcpy(last4, dna+i, seq->size-i); *pt = packDna4(last4); /* Deal with blocks of N, saving end points of blocks. */ twoBit->nBlockCount = countBlocksOfN(dna, seq->size); if (twoBit->nBlockCount > 0) { AllocArray(twoBit->nStarts, twoBit->nBlockCount); AllocArray(twoBit->nSizes, twoBit->nBlockCount); storeBlocksOfN(dna, seq->size, twoBit->nStarts, twoBit->nSizes); } /* Deal with masking, saving end points of blocks. */ if (doMask) { twoBit->maskBlockCount = countBlocksOfLower(dna, seq->size); if (twoBit->maskBlockCount > 0) { AllocArray(twoBit->maskStarts, twoBit->maskBlockCount); AllocArray(twoBit->maskSizes, twoBit->maskBlockCount); storeBlocksOfLower(dna, seq->size, twoBit->maskStarts, twoBit->maskSizes); } } return twoBit; } Though code paragraphs help make long functions readable, in general smaller functions are preferred. It is rare that a function longer than 100 lines couldn't be improved by moving some blocks of code into new functions or simplifying what the function is trying to do. STRUCTURE OF A TYPICAL C MODULE To avoid having to declare function prototypes, C modules are generally ordered with the lowest level functions written before higher level functions. In particular, if a module includes a main() routine, then it is the last function in the module. If a structure is broadly used in a module, it is declared near the start of the module, just after the module opening comment and any includes. This is followed by broadly used module local (static) variables. Less broadly used structs and variables may be grouped with the functions they are used with. If a module is used by other modules, it will be represented in a header file. In the majority of cases one .h file corresponds to one .c file. Typically the opening comment is duplicated in .h and .c files, as are the public structure and function declarations and opening comments. In general we try, with mixed success, to keep modules less than 2000 lines. Sadly many of the Genome Browser specific modules are currently quite long. On the bright side the vast majority of the library modules are reasonably sized. PREVENTING SQL-INJECTION In order to prevent SQL-Injection (sqli), we use primarily a special function called sqlSafef() to construct properly escaped SQL strings. The main article about preventing sqli is found here on genomewiki: http://genomewiki.ucsc.edu/index.php/Sql_injection_protection There are several other related and supporting functions to defeat sqli. The function reference is found here: http://genomewiki.ucsc.edu/index.php/Sql-injection_safe_functions ====================================================================