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author siwaa
date Mon, 10 Jun 2024 18:49:34 +0000
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1 # Galaxy tools for GAMA platform
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3 Desc
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4 ====
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6 The **gama_tool.xml** tool runs a **GAMA Python client**
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7 interacting with **gama-server (Headless server)**
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8 concerning a **"Predator Prey" agent-based simulation**.
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9 It relies on the **gama.simg** container.
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11 See also :
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12 [containers](../containers) from where container gama.simg comes ;
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13 [use-containers](../use-containers) ;
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14 [../../README.md](../../README.md)
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16 The **gama_tool.xml** tool case has been written **from an existing example**
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17 (*same example as in [use-containers](../use-containers)*) :
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19 - example code of https://github.com/gitrdm/gama-client-python
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20 project
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21 - URL : https://github.com/gitrdm/gama-client-python?tab=readme-ov-file#example-code
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22 - more : see [../../README.md](../../README.md)
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24 The **gama_tool.xml** tool case is based on :
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25
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26 - A **"Predator Prey" agent-based model** of the **GAMA platform**.
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27 - A **Python program** (*MY_sequential_example.py*) interacting with
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28 the GAMA platform in headless mode, as a GAMA Python client to :
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29 - **drive the experiment** : initialization, parameters settings,
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30 running, pausing, running some more steps, stop.
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31 - **observe the experiment** : getting information values such as :
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32 cycle, nb_preys/nb_preys_init...
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34 Sources
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35 =======
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37 The reused existing files have been copied
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38 at **[src/originals](./src/originals)** folder so :
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39
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40 - **sequential_example.py**
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41 from gama-client-python/examples/sequential_example.py :
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42
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43 ```
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44 # examples
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45 cd src/originals
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46 mkdir TMP; cd TMP
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47 git clone https://github.com/gitrdm/gama-client-python.git
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48 cd ..
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49 cp -fr TMP/gama-client-python/examples .
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50 rm -fr TMP
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51 ```
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52
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53 - **predatorPrey.gaml** and **gama-headless.sh** from gama-platform/headless
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54 (gama-platform/headless/samples/predatorPrey/predatorPrey.gaml,
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55 gama-platform/headless/gama-headless.sh)
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56 by gama.simg :
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57
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58 ```
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59 # headless
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60 gama_SIMGPATH=../../../containers/gama.simg
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61 cd src/originals
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62 mkdir OPT
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63 singularity exec --bind ./OPT:/OPT $gama_SIMGPATH bash -c "cp -fr /opt/gama-platform /OPT/."
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64 cp -fr OPT/gama-platform/headless headless
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65 rm -fr OPT
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66 ```
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67
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68 Galaxy tool Inputs / Outputs
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69 ============================
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70
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71 **[gama_tool.xml](./gama_tool.xml) Inputs** :
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73 - **nb_preys_init** (integer)
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74 - **nb_predators_init** (integer)
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75 - **nb_more_steps** (integer)
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76
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77 **[gama_tool.xml](./gama_tool.xml) Outputs** :
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78
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79 - **results .txt file** produced while running the simulator
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80 (cf 'reflex save_result' into MY_predatorPrey.gaml).
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81 - **run_server .txt file** : gama-server screen display capture
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82 - **run_client .txt file** : gama-client screen display capture
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83
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84 Galaxy tool Code
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85 ================
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86
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87 The Galaxy tool **[src](./src) folder** contains :
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88
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89 - **[MY_sequential_example.py](./src/MY_sequential_example.py)** :
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90 **Python code**
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91
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92 - created from [src/originals/examples/sequential_example.py](./src/originals/examples/sequential_example.py)
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93 - modification : variables values for gama-server
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94 (*MY_SERVER_URL, MY_SERVER_PORT, GAML_FILE_PATH_ON_SERVER*),
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95 for experiment (*EXPERIMENT_NAME, MY_EXP_INIT_PARAMETERS*).
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96 - modification : added some "print"
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97
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98 - **[MY_predatorPrey.gaml](./src/MY_predatorPrey.gaml)** :
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99 **"Predator Prey" agent-based simulator** file
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100
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101 - created from [src/originals/headless/samples/predatorPrey/predatorPrey.gaml](./src/originals/headless/samples/predatorPrey/predatorPrey.gaml)
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102 - modification : added **'reflex save_result'** to save some results data
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103 into results.txt file.
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104
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105 - **[cmd_gama_headless.sh](./src/cmd_gama_headless.sh)** :
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106 **commands file** (Shell script)
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107 launching GAMA Headless gama-server *(by calling MY_gama-headless.sh)*
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108
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109 - **[cmd_python_client.sh](./src/cmd_python_client.sh)** :
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110 **commands file** (Shell script)
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111 launching Python program MY_sequential_example.py
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112
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113 - **[MY_gama-headless.sh](./src/MY_gama-headless.sh)** :
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114
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115 - created from [src/originals/headless/gama-headless.sh](./src/originals/headless/gama-headless.sh)
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116 - modify : setting **java.io.tmpdir** property
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117 (```-Djava.io.tmpdir=$MY_TEMP_DIR```),
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118 because of gama_tool.xml running error :
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119 ```
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120 javax.imageio.IIOException: Can't create cache file!
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121 at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:361)
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122 ....
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123 Caused by: java.nio.file.FileSystemException: /tmp/imageio10268746820164254686.tmp: Read-only file system
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124 ....
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125 SLF4J: No SLF4J providers were found.
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126 SLF4J: Defaulting to no-operation (NOP) logger implementation
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127 SLF4J: See http://www.slf4j.org/codes.html#noProviders for further details.
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128 ```
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129
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130 *Default temporary directory for Linux is /tmp. The JVM automatically
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131 sets the temporary directory path as a system property. It can be
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132 changed by setting the java.io.tmpdir property to the desired
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133 path when starting the JVM.*
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134
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135 Local run by 'planemo serve'
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136 ============================
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137
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138 **Installs** :
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139
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140 - Install Singularity : singularity version 3.8.5
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141
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142 - Install Galaxy code :
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143 ```
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144 cd ~/DEVS
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145 git clone https://github.com/galaxyproject/galaxy.git
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146 ```
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147
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148 Note : Galaxy requiring at least singularity 3.7
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149 (cf singularity exec : --no-mount option)
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150
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151 - Install Planemo into a Python virtualenv :
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152 ```
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153 pip3 install --upgrade pip wheel setuptools virtualenv
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154 python3 -m venv _venv_planemo
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155 source _venv_planemo/bin/activate
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156
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157 python3 -m pip install planemo
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158 ```
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159
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160 **Use** :
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161
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162 ```
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163 source _fab/_venv_planemo/bin/activate
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164 ```
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165
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166 - Survey :
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167 ```
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168 htop
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169 ```
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170
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171 - Check tool syntax :
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172 ```
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173 planemo lint --report_level all --fail_level error gama_tool.xml
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174 ```
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175
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176 - Run tool :
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177 ```
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178 make serveGAMA
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179 ```
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180
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181 => http://127.0.0.1:9090
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182
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183 Use those Galaxy tools
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184 ======================
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185
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186 See [use-tools](../use-tools).
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187
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188