1 //
2 // interactengine.cpp
3 // Mothur
4 //
5 // Created by Sarah Westcott on 10/21/19.
6 // Copyright © 2019 Schloss Lab. All rights reserved.
7 //
8
9 #include "interactengine.hpp"
10 #include "batchengine.hpp"
11
12 /***********************************************************************/
13
InteractEngine(string tpath,map<string,string> ev)14 InteractEngine::InteractEngine(string tpath, map<string, string> ev) : Engine(tpath) {
15
16 if (m->getLogFileName() == "") {
17 time_t ltime = time(NULL); /* calendar time */
18 string outputPath = current->getOutputDir();
19 //if (outputPath == "") { outputPath = current->getDefaultPath(); }
20 string logFileName = outputPath + "mothur." + toString(ltime) + ".logfile";
21 m->setLogFileName(logFileName, false);
22 m->mothurOut("\n");
23 }
24 setEnvironmentVariables(ev);
25 }
26
27 /***********************************************************************/
28
~InteractEngine()29 InteractEngine::~InteractEngine(){}
30
31 /***********************************************************************/
32 //This function allows the user to input commands one line at a time until they quit.
33 //If the command is garbage it does nothing.
getInput()34 bool InteractEngine::getInput(){
35 try {
36 string input = "";
37 string commandName = "";
38 string options = "";
39 int quitCommandCalled = 0;
40
41 while(quitCommandCalled != 1){
42
43 input = getCommand();
44
45 if (m->getControl_pressed()) { input = "quit()"; }
46
47 //allow user to omit the () on the quit command
48 if (input == "quit") { input = "quit()"; }
49 if (input == "help") { input = "help()"; }
50
51 CommandOptionParser parser(input);
52 commandName = parser.getCommandString();
53
54 options = parser.getOptionString();
55
56 if (commandName != "") {
57 numCommandsRun++;
58 m->setExecuting(true);
59 m->resetCommandErrors();
60
61 //executes valid command
62 m->setChangedSeqNames(true);
63
64 Command* command = cFactory->getCommand(commandName, options);
65 quitCommandCalled = command->execute();
66 delete command;
67
68 //if we aborted command
69 if (quitCommandCalled == 2) { m->mothurOut("[ERROR]: did not complete " + commandName + ".\n"); }
70
71 m->setControl_pressed(false);
72 m->setExecuting(false);
73
74 }else { m->mothurOut("[ERROR]: Invalid.\n"); }
75 }
76 return true;
77 }
78 catch(exception& e) {
79 m->errorOut(e, "InteractEngine", "getInput");
80 exit(1);
81 }
82 }
83 /***********************************************************************/
getCommand()84 string InteractEngine::getCommand() {
85 try {
86 string returnCommand = "";
87 #if defined NON_WINDOWS
88 #ifdef USE_READLINE
89 char* nextCommand = NULL;
90 nextCommand = readline("\nmothur > ");
91
92 if(nextCommand != NULL) { add_history(nextCommand); }
93 else{ //^D causes null string and we want it to quit mothur
94 nextCommand = strdup("quit()");
95 }
96
97 m->mothurOutJustToLog("\nmothur > " + toString(nextCommand) + "\n");
98 returnCommand = nextCommand;
99 free(nextCommand);
100
101 #else
102 m->mothurOut("\nmothur > ");
103 getline(cin, returnCommand);
104 m->mothurOut("\n");
105 m->mothurOutJustToLog("\nmothur > " + toString(returnCommand) + "\n");
106 #endif
107 #else
108 m->mothurOut("\nmothur > ");
109 getline(cin, returnCommand);
110 m->mothurOut("\n");
111 m->mothurOutJustToLog(toString(returnCommand) + "\n");
112 #endif
113
114 //allow user to omit the () on the help and quit commands
115 if (returnCommand == "quit") { returnCommand = "quit()"; }
116 if (returnCommand == "help") { returnCommand = "help()"; }
117 if (returnCommand == "") { return returnCommand; }
118
119 string type = findType(returnCommand);
120
121 if (type == "environment") {
122 //set environmental variables
123 string key, value; value = returnCommand;
124 util.splitAtEquals(key, value);
125
126 map<string, string>::iterator it = environmentalVariables.find(key);
127 if (it == environmentalVariables.end()) { environmentalVariables[key] = value; }
128 else { it->second = value; }
129
130 m->mothurOut("Setting environment variable " + key + " to " + value + "\n");
131
132 returnCommand = getCommand();
133
134 }else if (type == "batch") {
135 m->mothurOutClearBuffer();
136 m->mothurOut("/*****************************************************************************/\n");
137
138 BatchEngine newBatchEngine(path, returnCommand, environmentalVariables);
139
140 if (newBatchEngine.getOpenedBatch()) {
141 bool bail = false;
142 while(!bail) { bail = newBatchEngine.getInput(); }
143 }
144 m->mothurOutClearBuffer();
145 m->mothurOut("/*****************************************************************************/\n");
146
147 returnCommand = getCommand();
148 }else { //assume command, look for environmental variables to replace
149
150 int evPos = returnCommand.find_first_of('$');
151 if (evPos == string::npos) { }//no '$' , nothing to do
152 else { replaceVariables(returnCommand); }
153 }
154
155 if (m->getDebug()) {
156 double ramUsed, total;
157 ramUsed = util.getRAMUsed(); total = util.getTotalRAM();
158 m->mothurOut("RAM used: " + toString(ramUsed/(double)GIG) + " Gigabytes. Total Ram: " + toString(total/(double)GIG) + " Gigabytes.\n\n");
159 }
160
161 return returnCommand;
162 }
163 catch(exception& e) {
164 m->errorOut(e, "InteractEngine", "getCommand");
165 exit(1);
166 }
167 }
168 /***********************************************************************/
169