/lib/galaxy/jobs/actions/post.py
Python | 422 lines | 414 code | 5 blank | 3 comment | 11 complexity | 1dc61a4aaf4c894bea57c4bf275dfc37 MD5 | raw file
1import datetime 2import logging 3from galaxy.util import send_mail 4from galaxy.util.json import to_json_string 5 6log = logging.getLogger( __name__ ) 7 8# DBTODO This still needs refactoring and general cleanup. 9 10def get_form_template(action_type, title, content, help, on_output = True ): 11 if on_output: 12 form = """ 13 if (pja.action_type == "%s"){ 14 p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'> %s <br/> on " + pja.output_name + "\ 15 <div style='float: right;' class='buttons'><img src='/static/images/history-buttons/delete_icon.png'></div></div><div class='toolFormBody'>"; 16 %s 17 p_str += "</div><div class='toolParamHelp'>%s</div></div>"; 18 }""" % (action_type, title, content, help) 19 else: 20 form = """ 21 if (pja.action_type == "%s"){ 22 p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + "</span><div class='toolFormTitle'> %s \ 23 <div style='float: right;' class='buttons'><img src='/static/images/history-buttons/delete_icon.png'></div></div><div class='toolFormBody'>"; 24 %s 25 p_str += "</div><div class='toolParamHelp'>%s</div></div>"; 26 }""" % (action_type, title, content, help) 27 return form 28 29# def get_field(action, argument, i_type, label = None): 30# fstr = '' 31# fname = """pja__"+pja.output_name+"__%s__%s""" % (action, argument) 32# if label: 33# fstr += """<label for='pja__"+pja.output_name+"__ColumnSetAction__chromCol'>Chrom Column</label>""" 34# fstr += """<input type='text' value=" + chromCol + " name='pja__"+pja.output_name+"__ColumnSetAction__chromCol'/>""" 35 36class DefaultJobAction(object): 37 name = "DefaultJobAction" 38 verbose_name = "Default Job" 39 40 @classmethod 41 def execute(cls, app, sa_session, action, job, replacement_dict = None): 42 pass 43 44 @classmethod 45 def get_config_form(cls, trans): 46 return "<p>Default Job Action Config Form</p>" 47 48 @classmethod 49 def get_short_str(cls, pja): 50 if pja.action_arguments: 51 return "%s -> %s" % (pja.action_type, pja.action_arguments) 52 else: 53 return "%s" % pja.action_type 54 55 56class EmailAction(DefaultJobAction): 57 name = "EmailAction" 58 verbose_name = "Email Notification" 59 60 @classmethod 61 def execute(cls, app, sa_session, action, job, replacement_dict): 62 if action.action_arguments and action.action_arguments.has_key('host'): 63 host = action.action_arguments['host'] 64 else: 65 host = 'usegalaxy.org' 66 frm = 'galaxy-noreply@%s' % host 67 to = job.user.email 68 subject = "Galaxy workflow step notification '%s'" % (job.history.name) 69 outdata = ', '.join(ds.dataset.display_name() for ds in job.output_datasets) 70 body = "Your Galaxy job generating dataset '%s' is complete as of %s." % (outdata, datetime.datetime.now().strftime( "%I:%M" )) 71 try: 72 send_mail( frm, to, subject, body, app.config ) 73 except Exception, e: 74 log.error("EmailAction PJA Failed, exception: %s" % e) 75 76 @classmethod 77 def get_config_form(cls, trans): 78 form = """ 79 p_str += "<label for='pja__"+pja.output_name+"__EmailAction'>There are no additional options for this action. You will be emailed upon job completion.</label>\ 80 <input type='hidden' value='%s' name='pja__"+pja.output_name+"__EmailAction__host'/><input type='hidden' name='pja__"+pja.output_name+"__EmailAction'/>"; 81 """ % trans.request.host 82 return get_form_template(cls.name, cls.verbose_name, form, "This action will send an email notifying you when the job is done.", on_output = False) 83 84 @classmethod 85 def get_short_str(cls, pja): 86 if pja.action_arguments and pja.action_arguments.has_key('host'): 87 return "Email the current user from server %s when this job is complete." % pja.action_arguments['host'] 88 else: 89 return "Email the current user when this job is complete." 90 91 92class ChangeDatatypeAction(DefaultJobAction): 93 name = "ChangeDatatypeAction" 94 verbose_name = "Change Datatype" 95 @classmethod 96 def execute(cls, app, sa_session, action, job, replacement_dict): 97 for dataset_assoc in job.output_datasets: 98 if action.output_name == '' or dataset_assoc.name == action.output_name: 99 app.datatypes_registry.change_datatype( dataset_assoc.dataset, action.action_arguments['newtype']) 100 101 @classmethod 102 def get_config_form(cls, trans): 103 dt_list = "" 104 dtnames = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems()] 105 dtnames.sort() 106 for dt_name in dtnames: 107 dt_list += """<option id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype__%s' value='%s'>%s</option>""" % (dt_name, dt_name, dt_name) 108 ps = """ 109 p_str += "<label for='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>New Datatype:</label>\ 110 <select id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype' name='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>\ 111 %s\ 112 </select>"; 113 if (pja.action_arguments !== undefined && pja.action_arguments.newtype !== undefined){ 114 p_str += "<scrip" + "t type='text/javascript'>$('#pja__" + pja.output_name + "__ChangeDatatypeAction__newtype').val('" + pja.action_arguments.newtype + "');</scrip" + "t>"; 115 } 116 """ % dt_list 117 # Note the scrip + t hack above. Is there a better way? 118 return get_form_template(cls.name, cls.verbose_name, ps, 'This action will change the datatype of the output to the indicated value.') 119 120 @classmethod 121 def get_short_str(cls, pja): 122 return "Set the datatype of output '%s' to '%s'" % (pja.output_name, pja.action_arguments['newtype']) 123 124 125class RenameDatasetAction(DefaultJobAction): 126 name = "RenameDatasetAction" 127 verbose_name = "Rename Dataset" 128 129 @classmethod 130 def execute(cls, app, sa_session, action, job, replacement_dict): 131 # Prevent renaming a dataset to the empty string. 132 if action.action_arguments and action.action_arguments.has_key('newname') and action.action_arguments['newname'] != '': 133 new_name = action.action_arguments['newname'] 134 135 # TODO: Unify and simplify replacement options. 136 # Add interface through workflow editor UI 137 138 # The following if statement will process a request to rename 139 # using an input file name. 140 # TODO: Replace all matching code with regex 141 # Proper syntax is #{input_file_variable | option 1 | option n} 142 # where 143 # input_file_variable = is the name of an module input variable 144 # | = the delimiter for added options. Optional if no options. 145 # options = basename, upper, lower 146 # basename = keep all of the file name except the extension 147 # (everything before the final ".") 148 # upper = force the file name to upper case 149 # lower = force the file name to lower case 150 # suggested additions: 151 # "replace" option so you can replace a portion of the name, 152 # support multiple #{name} in one rename action... 153 154 if new_name.find("#{") > -1: 155 to_be_replaced = "" 156 # This assumes a single instance of #{variable} will exist 157 start_pos = new_name.find("#{") + 2 158 end_pos = new_name.find("}") 159 to_be_replaced = new_name[start_pos:end_pos] 160 input_file_var = to_be_replaced 161 # Pull out the piped controls and store them for later 162 # parsing. 163 tokens = to_be_replaced.split("|") 164 operations = [] 165 if len(tokens) > 1: 166 input_file_var = tokens[0].strip() 167 for i in range(1, len(tokens)): 168 operations.append(tokens[i].strip()) 169 170 replacement = "" 171 # Lookp through inputs find one with "to_be_replaced" input 172 # variable name, and get the replacement name 173 for input_assoc in job.input_datasets: 174 if input_assoc.name == input_file_var: 175 replacement = input_assoc.dataset.name 176 177 # Do operations on replacement 178 # Any control that is not defined will be ignored. 179 # This should be moved out to a class or module function 180 for operation in operations: 181 # Basename returns everything prior to the final '.' 182 if operation == "basename": 183 fields = replacement.split(".") 184 replacement = fields[0] 185 if len(fields) > 1: 186 temp = "" 187 for i in range(1, len(fields) - 1): 188 temp += "." + fields[i] 189 replacement += temp 190 elif operation == "upper": 191 replacement = replacement.upper() 192 elif operation == "lower": 193 replacement = replacement.lower() 194 195 new_name = new_name.replace("#{%s}" % to_be_replaced, replacement) 196 197 if replacement_dict: 198 for k, v in replacement_dict.iteritems(): 199 new_name = new_name.replace("${%s}" % k, v) 200 for dataset_assoc in job.output_datasets: 201 if action.output_name == '' or dataset_assoc.name == action.output_name: 202 dataset_assoc.dataset.name = new_name 203 204 @classmethod 205 def get_config_form(cls, trans): 206 form = """ 207 if (pja.action_arguments && pja.action_arguments.newname){ 208 p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\ 209 <input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=\\"" + pja.action_arguments.newname.replace(/"/g, """) + "\\"/>"; 210 } 211 else{ 212 p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\ 213 <input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=''/>"; 214 } 215 """ 216 return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.") 217 218 @classmethod 219 def get_short_str(cls, pja): 220 # Prevent renaming a dataset to the empty string. 221 if pja.action_arguments and pja.action_arguments.has_key('newname') and pja.action_arguments['newname'] != '': 222 return "Rename output '%s' to '%s'." % (pja.output_name, pja.action_arguments['newname']) 223 else: 224 return "Rename action used without a new name specified. Output name will be unchanged." 225 226 227class HideDatasetAction(DefaultJobAction): 228 name = "HideDatasetAction" 229 verbose_name = "Hide Dataset" 230 231 @classmethod 232 def execute(cls, app, sa_session, action, job, replacement_dict): 233 for dataset_assoc in job.output_datasets: 234 if dataset_assoc.dataset.state != dataset_assoc.dataset.states.ERROR and ( action.output_name == '' or dataset_assoc.name == action.output_name ): 235 dataset_assoc.dataset.visible=False 236 237 @classmethod 238 def get_config_form(cls, trans): 239 return """ 240 if (pja.action_type == "HideDatasetAction"){ 241 p_str += "<input type='hidden' name='pja__"+pja.output_name+"__HideDatasetAction'/>"; 242 } 243 """ 244 @classmethod 245 def get_short_str(cls, pja): 246 return "Hide output '%s'." % pja.output_name 247 248class DeleteDatasetAction(DefaultJobAction): 249 # This is disabled for right now. Deleting a dataset in the middle of a workflow causes errors (obviously) for the subsequent steps using the data. 250 name = "DeleteDatasetAction" 251 verbose_name = "Delete Dataset" 252 253 @classmethod 254 def execute(cls, app, sa_session, action, job, replacement_dict): 255 for dataset_assoc in job.output_datasets: 256 if action.output_name == '' or dataset_assoc.name == action.output_name: 257 dataset_assoc.dataset.deleted=True 258 259 @classmethod 260 def get_config_form(cls, trans): 261 form = """ 262 p_str += "<label for='pja__"+pja.output_name+"__DeleteDatasetAction'>There are no additional options for this action. This dataset will be marked deleted.</label>\ 263 <input type='hidden' name='pja__"+pja.output_name+"__DeleteDatasetAction'/>"; 264 """ 265 return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.") 266 267 @classmethod 268 def get_short_str(cls, pja): 269 return "Delete this dataset after creation." 270 271 272 273class ColumnSetAction(DefaultJobAction): 274 name = "ColumnSetAction" 275 verbose_name = "Assign Columns" 276 @classmethod 277 def execute(cls, app, sa_session, action, job, replacement_dict): 278 for dataset_assoc in job.output_datasets: 279 if action.output_name == '' or dataset_assoc.name == action.output_name: 280 for k, v in action.action_arguments.items(): 281 if v != '': 282 # Try to use both pure integer and 'cX' format. 283 if v[0] == 'c': 284 v = v[1:] 285 v = int(v) 286 if v != 0: 287 setattr(dataset_assoc.dataset.metadata, k, v) 288 289 @classmethod 290 def get_config_form(cls, trans): 291 form = """ 292 if (pja.action_arguments !== undefined){ 293 (pja.action_arguments.chromCol === undefined) ? chromCol = "" : chromCol=pja.action_arguments.chromCol; 294 (pja.action_arguments.startCol === undefined) ? startCol = "" : startCol=pja.action_arguments.startCol; 295 (pja.action_arguments.endCol === undefined) ? endCol = "" : endCol=pja.action_arguments.endCol; 296 (pja.action_arguments.strandCol === undefined) ? strandCol = "" : strandCol=pja.action_arguments.strandCol; 297 (pja.action_arguments.nameCol === undefined) ? nameCol = "" : nameCol=pja.action_arguments.nameCol; 298 }else{ 299 chromCol = ''; 300 startCol = ''; 301 endCol = ''; 302 strandCol = ''; 303 nameCol = ''; 304 } 305 p_str += "<p>Leave any of these fields blank if they do not need to be set.</p>\ 306 <label for='pja__"+pja.output_name+"__ColumnSetAction__chromCol'>Chrom Column</label>\ 307 <input type='text' value='" + chromCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__chromCol'/>\ 308 <label for='pja__"+pja.output_name+"__ColumnSetAction__startCol'>Start Column</label>\ 309 <input type='text' value='" + startCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__startCol'/>\ 310 <label for='pja__"+pja.output_name+"__ColumnSetAction__endCol'>End Column</label>\ 311 <input type='text' value='" + endCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__endCol'/>\ 312 <label for='pja__"+pja.output_name+"__ColumnSetAction__strandCol'>Strand Column</label>\ 313 <input type='text' value='" + strandCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__strandCol'/>\ 314 <label for='pja__"+pja.output_name+"__ColumnSetAction__nameCol'>Name Column</label>\ 315 <input type='text' value='" + nameCol + "' name='pja__"+pja.output_name+"__ColumnSetAction__nameCol'/>\"; 316 """ 317 return get_form_template(cls.name, cls.verbose_name, form, "This action will set column assignments in the output dataset. Blank fields are ignored.") 318 319 @classmethod 320 def get_short_str(cls, pja): 321 return "Set the following metadata values:<br/>" + "<br/>".join(['%s : %s' % (k, v) for k, v in pja.action_arguments.iteritems()]) 322 323 324class SetMetadataAction(DefaultJobAction): 325 name = "SetMetadataAction" 326 # DBTODO Setting of Metadata is currently broken and disabled. It should not be used (yet). 327 328 @classmethod 329 def execute(cls, app, sa_session, action, job, replacement_dict): 330 for data in job.output_datasets: 331 data.set_metadata( action.action_arguments['newtype'] ) 332 333 @classmethod 334 def get_config_form(cls, trans): 335 # dt_list = "" 336 # mdict = {} 337 # for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems(): 338 # for mn, mt in dtype_value.metadata_spec.items(): 339 # if mt.visible: 340 # mdict[mt.desc] = mt.param.get_html(value= mn).replace('"', "'").strip().replace('\n','') 341 # for k, v in mdict.items(): 342 # dt_list += "<p><strong>" + k + ":</strong><br/>" + v + "</p>" 343 # form = """ 344 # p_str += "%s"; 345 # """ % dt_list 346 # return get_form_template('SetMetadataAction', 'Set Metadata', form, "This action will change metadata for the dataset.") 347 form = """ 348 p_str += "<p>Leave any of these fields blank if they do not need to be set.</p><label for='pja__"+pja.output_name+"__SetMetadataAction__chromCol'>Chrom Column</label>\ 349 <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__chromCol'/>\ 350 <label for='pja__"+pja.output_name+"__SetMetadataAction__startCol'>Start Column</label>\ 351 <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__startCol'/>\ 352 <label for='pja__"+pja.output_name+"__SetMetadataAction__endCol'>End Column</label>\ 353 <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__endCol'/>\ 354 <label for='pja__"+pja.output_name+"__SetMetadataAction__comment_lines'>Comment Lines</label>\ 355 <input type='text' name='pja__"+pja.output_name+"__SetMetadataAction__comment_lines'/>\ 356 "; 357 """ 358 return get_form_template(cls.name, cls.verbose_name, form, "This action will set metadata in the output dataset.") 359 360 361 362class ActionBox(object): 363 364 actions = { "RenameDatasetAction" : RenameDatasetAction, 365 "HideDatasetAction" : HideDatasetAction, 366 "ChangeDatatypeAction": ChangeDatatypeAction, 367 "ColumnSetAction" : ColumnSetAction, 368 "EmailAction" : EmailAction, 369 # "SetMetadataAction" : SetMetadataAction, 370 # "DeleteDatasetAction" : DeleteDatasetAction, 371 } 372 public_actions = ['RenameDatasetAction', 'ChangeDatatypeAction', 'ColumnSetAction', 'EmailAction'] 373 immediate_actions = ['ChangeDatatypeAction', 'RenameDatasetAction'] 374 375 @classmethod 376 def get_short_str(cls, action): 377 if action.action_type in ActionBox.actions: 378 return ActionBox.actions[action.action_type].get_short_str(action) 379 else: 380 return "Unknown Action" 381 382 @classmethod 383 def handle_incoming(cls, incoming): 384 npd = {} 385 for key, val in incoming.iteritems(): 386 if key.startswith('pja'): 387 sp = key.split('__') 388 ao_key = sp[2] + sp[1] 389 # flag / output_name / pjatype / desc 390 if not ao_key in npd: 391 npd[ao_key] = {'action_type' : sp[2], 392 'output_name' : sp[1], 393 'action_arguments' : {}} 394 if len(sp) > 3: 395 if sp[3] == 'output_name': 396 npd[ao_key]['output_name'] = val 397 else: 398 npd[ao_key]['action_arguments'][sp[3]] = val 399 else: 400 # Not pja stuff. 401 pass 402 return to_json_string(npd) 403 404 @classmethod 405 def get_add_list(cls): 406 addlist = "<select id='new_pja_list' name='new_pja_list'>" 407 for action in ActionBox.public_actions: 408 addlist += "<option value='%s'>%s</option>" % (ActionBox.actions[action].name, ActionBox.actions[action].verbose_name) 409 addlist += "</select>" 410 return addlist 411 412 @classmethod 413 def get_forms(cls, trans): 414 forms = "" 415 for action in ActionBox.actions: 416 forms += ActionBox.actions[action].get_config_form(trans) 417 return forms 418 419 @classmethod 420 def execute(cls, app, sa_session, pja, job, replacement_dict = None): 421 if ActionBox.actions.has_key(pja.action_type): 422 ActionBox.actions[pja.action_type].execute(app, sa_session, pja, job, replacement_dict)