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