Client program

A simple HTTP client program (e.g., fetch ) can be pointed at an HTTP server, accept lines of input from a standard input stream, send them as messages to an HTTP server, accept replies from that server and then write them to a standard output stream. The fetch program becomes a serial filter for any such HTTP server (which is now acting as a network compute server). 

Fax 612-625-6817, e-mail gopher boombox.micro.umn.edu Internet client/server for a distributed information delivery system. Client program for workstations is available by anonymous ftp from boombox.micro.umn.edu (132.84.132.2). UNIX workstations VAX, IBM, Macintosh, PCs. 

Application Tier. In a multi-tier architecture, the collection of programs that run on the chemist s client or workstation machine. It is the tier of programs "closest" to the chemist in the architecture. Typically this may be a Web client program or other program with a GUI that allows the chemist to interact with the architecture. 

Four APIs to caBIO are available, each suitable for different client-programming environments Java, Perl, SOAP, and HTTP-XML. Domain objects represent... 

An introduction to SQL is provided in Chapter 3, but with an emphasis on examples relevant to chemical information rather than business information, which is often used in other books. Chapter 4 discusses some of the RDBMS that are available, namely Oracle, MySQL, and PostgreSQL. All of them use SQL to insert, delete, update, and select data. Chapter 5 shows ways in which client programs, including Web-based applications, are used to connect to the database server. Chapter 6 examines ways in which RDBMS are typically used to handle numerical and textual chemical information using relational tables. An example of using data files from the PubChem project is included. 

Chapter 12 discusses more fully the ways in which client programs can interface with the database. The intent is to show how you might integrate a relational database into an existing suite of programs or design and implement a new computer system for chemical information. 

Client programs are discussed in later chapters of this book. The structured query language (SQL) designed for creating, selecting, deleting, and updating the database is discussed in Chapter 3. 

The RDBMS is installed and runs on a computer that functions as a database server. Any SQL commands are executed on the server by the RDBMS. Functions written in SQL or in any of the procedural languages mentioned above are also executed by the RDBMS. This has the advantage that the data tables used by these SQL commands or procedural functions are under the control of the server. This is the most efficient way to access the data. The disadvantage is that the server may have many requests to handle from many users. Another way to operate on data tables is indirectly, using a client program typically (although not necessarily) run from another computer. 

There is a smaller set of tools that are typically run on the server. Any SQL commands and any procedural language functions are run on the server. In principle, there is complete flexibility of the server side tools, since in principle any computer program can be written in any computer language. Later chapters of this book show how the RDBMS server itself can be extended using server side programming to handle chemical information. These extensions may directly solve the needs of a particular project, but more importantly they increase the flexibility of the RDBMS to handle chemical information. Client programs can use the results of chemical searches and other computations as well. 

Another useful client program is R.6 It is used for statistical analysis of data and has some nice graphical capabilities as well. There is an add-on to R that uses ODBC to communicate with an RDBMS server.7 Consider the following R program. 

Many other useful client programs allow input of data using SQL. For example Spotfire8 and Pipeline Pilot9 allow data to be read for an RDBMS using ODBC. 

In each example, a simple SQL statement is used to select rows that match a particular substructure. The rows are then simply fetched and printed. These examples should serve as a starting point to understand how client programs communicate with an RDBMS server using SQL. The examples can also server as a basis for other more complex client programs. 

Selecting rows from a table is only one common operation needed for a client program to work with an RDBMS. In addition to a simple SQL select statement, other more complex select statements will become necessary as more complex client programs are developed. It is also important to see how to properly use the SQL Insert statement. Rather than showing examples in several computer languages, the use of more complex SQL statements is discussed in Chapter 12. 

The smiles to symbols and smile to bonds functions return arrays of values. In the sample output above, the smiles to bonds output has been truncated for easier viewing. Some client programs may expect this information as separate rows, as if they were records in a file. These arrays may be cast into that form by using a plpgsql function that returns elements of an array as rows. This is shown in the next section. 

Using Tables Instead of Files in Client Programs... 

A traditional client program reads from a molecular structure file and performs some computation that depends on the molecular structural data. This read(file) function reads particular columns or fields from the file. A different function would be necessary for each type of file format. A traditional client program can be modified to read molecular structure data from... 

The previous section shows how molecular structures stored in an RDBMS can be made available to client programs that traditionally read molecular structure files. The advantage of storing molecular structures in an RDBMS is that the information can be used from within the database, as well as by external clients. For example, it would be possible to search a table of molecular structures for three-dimensional overlap, much like it might be searched for substructure match. Of course, such search functions need to be written and installed as extensions to an RDBMS, just like the matches functions was done for substructure searches. This section shows some possible ways this might be accomplished. 

This chapter discusses ways in which more complex client applications can be written. These programs use SQL to select, insert, delete, or update tables in the database. Depending on the computer language used for the client program, a variety of interface libraries is available. 

One disadvantage of using client programs is that data must be transferred to and from the server. Depending on how much data is required, this can cause a client program to run less efficiently than a server function run as an extension of the RDBMS. 

Most new client programs will benefit from a judicious use of both new server-side SQL functions and new client functions. It is wise to carefully consider which operations are best done on the RDBMS server and which are done using a client program. There are several suggestions to consider in designing the best system for a project. 

Chapter 5 introduced ways in which client programs can be used with an RDBMS server. Some existing client programs, such as Excel and R,... 

When a client program selects data from an RDBMS table using SQL, there are several methods that can be used. The following Perl code illustrates some of these methods. 

The marvin sketch SQL function can be called from any client program using database access methods described in Chapter 5. The marvin sketch program can be modified to allow specification of the sketch applet size, loading an initial SMILES, or any other option provided by the Marvin sketch applet. 

This addition does not correct the issues with tautomers, but it does allow an easy way to detect tautomers in the database. Note also that alerting the user is the responsibility of the client program and is not performed in this trigger function or in any of the other constraints in the registration schema. 

If SMILES is used to store molecular structures in a relational database management system(RDBMS), it may be necessary to extract the symbol and bond information for some client programs that expect a connection table. The smiles to symbol and smiles to bonds function shown in the next sections allow the symbol and bond information in a SMILES to be extracted as an array. Some client programs may prefer to process this information in rows, as if they were records in a file. The following plpgsql functions can be used to present the array elements as rows. Two functions are shown ctable (connection table) and symbol coords. The symbol coords function requires an array of coordinates in addition to the symbols. 

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