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4468 lines (3499 loc) · 163 KB
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import io
import os
import re
import csv
import copy
import json
import yaml
import base64
import random
import string
import logging
import bashlex
import tarfile
import zipfile
import networkx as nx
import importlib
try:
import zlib
compression = zipfile.ZIP_DEFLATED
except (ImportError, AttributeError):
compression = zipfile.ZIP_STORED
import argparse
from collections import defaultdict
from pprint import pprint
from itertools import product
logging.basicConfig(level=logging.DEBUG)
class OBC_Executor_Exception(Exception):
'''
'''
pass
def detect_circles(graph, start, end):
'''
https://stackoverflow.com/questions/40833612/find-all-cycles-in-a-graph-implementation
'''
fringe = [(start, [])]
while fringe:
state, path = fringe.pop()
if path and state == end:
yield path
continue
for next_state in graph[state]:
if next_state in path:
continue
fringe.append((next_state, path+[next_state]))
bash_patterns = {
'parse_json' : r'''
function obc_parse_json()
{
echo $1 | \
sed -e "s/.*$2\":[ ]*\"\([^\"]*\)\".*/\1/"
}
''' + '\n', # https://stackoverflow.com/a/26655887/5626738
'curl_send_json': '''curl -s --header "Content-Type: application/json" --request POST -d '{json}' {url}''',
'command_to_variable': '''{variable}=$({command})''',
'string_contains': '''
if [[ ${variable} == *'{string}'* ]]; then
{contains_yes}
else
{contains_no}
fi
''',
'fail': 'echo "{error_message}"\nexit 1\n',
'update_server_status': r'''
function update_server_status()
{
if [[ $obc_current_token =~ ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$ ]]; then
local command="curl {insecure}-s --header \"Content-Type: application/json\" --request POST -d '{\"token\": \"$obc_current_token\", \"status\": \"$1\"}' {server}/report/"
local c=$(eval "$command")
if [[ $c == *'"success": true'* ]]; then
obc_current_token=$(obc_parse_json "$c" "token")
echo obc_current_token=\"${obc_current_token}\" > ${OBC_WORK_PATH}/obc_current_token.sh
else
if [[ $c == *'"success": false'* ]]; then
obc_error_message=$(obc_parse_json "$c" "error_message")
echo "Server Return Error: $obc_error_message"
# exit 1
else
echo "Server does not respond, or unknown error"
# exit 1
fi
fi
else
:
fi
}
''',
'base64_decode': r'''
function obc_base64_decode() {
echo $1 | base64 --decode
}
''',
'validate': r'''
function obc_validate() {
local command="$(obc_base64_decode $1)"
eval $command
}
''',
'init_report': r'''
if [ -n "${OBC_WORK_PATH}" ] ; then
export OBC_REPORT_PATH=${OBC_WORK_PATH}/${OBC_NICE_ID}.html
export OBC_REPORT_DIR=${OBC_WORK_PATH}/${OBC_NICE_ID}
mkdir -p ${OBC_REPORT_DIR}
echo "OBC: Report filename: ${OBC_REPORT_PATH}"
cat > ${OBC_REPORT_PATH} << OBCENDOFFILE
<!DOCTYPE html>
<html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
</head>
<body>
<p>
OpenBio Server: <a href="${OBC_SERVER}">${OBC_SERVER}</a> <br>
Workflow: <a href="${OBC_SERVER}/w/${OBC_WORKFLOW_NAME}/${OBC_WORKFLOW_EDIT}">${OBC_WORKFLOW_NAME}/${OBC_WORKFLOW_EDIT}</a> <br>
<p>
<h3>Intermediate Variables:</h3>
<ul>
<!-- {{INTERMEDIATE_VARIABLE}} -->
</ul>
<p>
<h3>Output Variables:</h3>
<ul>
<!-- {{OUTPUT_VARIABLE}} -->
</ul>
</body>
</html>
OBCENDOFFILE
fi
''',
'function_REPORT': r'''
export OBC_REPORT_PATH=${OBC_WORK_PATH}/${OBC_NICE_ID}.html
export OBC_REPORT_DIR=${OBC_WORK_PATH}/${OBC_NICE_ID}
function REPORT() {
if [ -n "${OBC_WORK_PATH}" ] ; then
local VAR=$1
local TIMENOW=$(date)
local WHOCALLEDME=$(caller 0 | awk '{print $2}')
if [ -z $3 ] ; then
local TAG=INTERMEDIATE_VARIABLE
else
local TAG=$3
fi
if [ ${TAG} == "INTERMEDIATE_VARIABLE" ] ; then
local EXTRA="${TIMENOW}. Called from: ${WHOCALLEDME}"
else
local EXTRA=""
fi
local FILEKIND=$(file "${2}")
# echo "OBC: FILE RESULT ${FILEKIND}"
if [[ $FILEKIND == *"PNG image data"* ]]; then
local NEWFILENAME=${OBC_REPORT_DIR}/$(basename ${2})
local LOCALFILENAME=${OBC_NICE_ID}/$(basename ${2})
cp ${2} ${NEWFILENAME}
local HTML="<li>${EXTRA} ${VAR}: <br><img src=\"${LOCALFILENAME}\"></li>\\\\n <!-- {{${TAG}}} -->\\\\n"
elif [[ $FILEKIND == *"PDF document"* ]]; then
local NEWFILENAME=${OBC_REPORT_DIR}/$(basename ${2})
local LOCALFILENAME=${OBC_NICE_ID}/$(basename ${2})
cp ${2} ${NEWFILENAME}
local HTML="<li>${EXTRA} ${VAR}: <br><a href=\"${LOCALFILENAME}\">${LOCALFILENAME}</a></li>\\\\n <!-- {{${TAG}}} -->\\\\n"
elif [[ -f ${2} ]] ; then
local NEWFILENAME=${OBC_REPORT_DIR}/$(basename ${2})
local LOCALFILENAME=${OBC_NICE_ID}/$(basename ${2})
cp ${2} ${NEWFILENAME}
local HTML="<li>${EXTRA} ${VAR}: <br><a href=\"${LOCALFILENAME}\">${LOCALFILENAME}</a></li>\\\\n <!-- {{${TAG}}} -->\\\\n"
else
local VALUE=$(echo "${2}" | sed 's/&/\\\&/g; s/</\\\</g; s/>/\\\>/g; s/"/\\\"/g; s/'"'"'/\\\'/g')
local HTML="<li>${EXTRA} ${VAR}=${VALUE}</li>\\\\n <!-- {{${TAG}}} -->\\\\n"
fi
sed -i -e "s|<\!-- {{${TAG}}} -->|${HTML}|" ${OBC_REPORT_PATH}
sed 's/\\n/\
/g' ${OBC_REPORT_PATH} > ${OBC_REPORT_PATH}.tmp
mv ${OBC_REPORT_PATH}.tmp ${OBC_REPORT_PATH}
fi
}
''',
'final_report': r'''
OBC_REPORT_TGZ=${OBC_WORK_PATH}/${OBC_NICE_ID}.tgz
#echo "RUNNING: "
#echo "tar zcf ${OBC_REPORT_TGZ} -C ${OBC_WORK_PATH} ${OBC_NICE_ID}.html ${OBC_NICE_ID}/"
tar zcf ${OBC_REPORT_TGZ} -C ${OBC_WORK_PATH} ${OBC_NICE_ID}.html ${OBC_NICE_ID}/
''',
'function_PARALLEL': r'''
function PARALLEL() {
local line_counter=0
local PIDS=() #
if [[ $2 == *$'\n'* ]] ; then
while IFS= read -r line; do
if [[ -z "${line// }" ]] ; then
continue # Ignore empty lines
fi
let "line_counter=line_counter+1"
if [ $line_counter -eq 1 ] ; then
IFS=',' read -ra header <<< "$line"
local header_length=${#header[@]}
let "header_length_0=header_length-1"
continue
fi
IFS=',' read -ra line_splitted <<< "$line"
local line_length=${#line_splitted[@]}
if [ $header_length -ne $line_length ] ; then
OBC_ERROR="Line:${line_counter} ${line} contains ${line_length} fields whereas the header has ${header_length} fields."
return
fi
# Set parameters
for i in $(seq 0 ${header_length_0})
do
declare "${header[${i}]}=${line_splitted[${i}]}"
done
#echo "Calling step: $1"
eval ${1} &
P=$!
PIDS=("${PIDS[@]}" ${P})
done <<< "$2"
else
for var in "$@" ; do
#echo ${var}
eval ${var} &
P=$!
IDS=("${PIDS[@]}" ${P})
done
fi
wait "${PIDS[@]}"
OBC_ERROR=""
}
''',
}
r'''
A="
PARAM_1,PARAM_2
1,2
3,4
5,6
7,8
9,10
"
PARALLEL step_example "$A"
# a = re.findall(r'[\w]+=\"[\w\s,\.]+\"[\s]+PARALLEL[\s]+[\w]+[\s]+\"\$[\w]+\"', text)
PARALLEL step_example_1 step_example_2
'''
bash_patterns['get_json_value'] = '{variable}=$(obc_parse_json "${json_variable}" "{json_key}")'
# Global parameters
g = {
'silent': False,
'CLIENT_OBC_DATA_PATH': '/usr/local/airflow/REPORTS/DATA',
'CLIENT_OBC_TOOL_PATH': '/usr/local/airflow/REPORTS/TOOL',
'CLIENT_OBC_WORK_PATH': '/usr/local/airflow/REPORTS/WORK',
'possible_letters_nice_id': tuple(string.ascii_lowercase + string.digits),
}
def log_info(message):
'''
'''
if not g['silent']:
logging.info(message)
def setup_bash_patterns(args):
'''
Change some values of the bash patterns according to arg arguments
'''
bash_patterns['update_server_status'] = bash_patterns['update_server_status'].replace('{server}', args.server) # .format does not work since it contains "{"
bash_patterns['update_server_status'] = bash_patterns['update_server_status'].replace('{insecure}', '-k ' if args.insecure else '')
## Helper functions
def base64_encode(s):
'''
Takes a string and converts it to a base64 string
'''
return base64.b64encode(s.encode()).decode('ascii')
class Workflow:
'''
'''
WORKFLOW_TYPE = 'workflow'
INPUT_TYPE = 'input'
OUTPUT_TYPE = 'output'
STEP_TYPE = 'step'
TOOL_TYPE = 'tool'
# Variables that are assumed to be set from the environment
DEFAULT_INPUT_VARIABLES = [
'OBC_TOOL_PATH',
'OBC_DATA_PATH',
'OBC_WORK_PATH',
]
EXIT_ON_ERROR = True # Should the workflow exit on error?
def __init__(self,
workflow_filename=None,
workflow_object=None,
workflow_string=None,
askinput='JSON',
obc_server=None,
workflow_id=None,
):
'''
workflow_filename: the JSON filename of the workflow
workflow_object: The representation of the workflow
workflow_string: A string representation of the JSON workflow object (used in workflow upload)
askinput:
JSON: Ask for input during convertion to BASH
BASH: Ask for input in BASH
One of these should not be None
obc_server the server for which we are generating the script (if any)
workflow_id: The nice_id of the workflow
'''
# One of workflow_filename, workflow_object, workflow_string can be declared
declared = [x[0] for x in (
('workflow_filename', workflow_filename),
('workflow_object', workflow_object),
('workflow_string', workflow_string),
)
if x[1]
]
if len(declared) == 0:
raise OBC_Executor_Exception('None of workflow_filename, workflow_object, workflow_string have been declared')
if len(declared) > 1:
raise OBC_Executor_Exception(
f'Only one of workflow_filename, workflow_object, workflow_string can be declared. You declared: '
', '.join(declared)
)
self.workflow_filename = workflow_filename
self.workflow_object = workflow_object
self.workflow_string = workflow_string
self.askinput = askinput
self.obc_server = obc_server
self.workflow_id = workflow_id
self.parse_workflow_filename()
def __str__(self,):
'''
'''
return json.dumps(self.workflow, indent=4)
@staticmethod
def create_nice_id(length=8):
'''
Create a nice id
'''
return ''.join(random.sample(g['possible_letters_nice_id'], length))
def tool_bash_script_generator(self,):
'''
'''
tool_installation_order = self.get_tool_installation_order()
for tool in tool_installation_order:
yield tool
def get_tool_dependencies(self, tool):
'''
Returns the tools that this tool depends from
'''
def rec(tool):
ret = []
for tool_slash_id in tool['dependencies']:
tool_d = self.tool_slash_id_d[tool_slash_id]
ret.append(Workflow.get_tool_slash_id(tool_d))
ret.extend(rec(tool_d))
return ret
ret = set(rec(tool))
return [self.tool_slash_id_d[x] for x in ret]
def get_tool_dependent_variables(self, tool, include_this_tool=False):
'''
Get the variables for which this tool is dependent
include_this_tool: If True, include also the variables of this tool
'''
def recursion(tool, the_list):
for tool_slash_id in tool['dependencies']:
tool_d = self.tool_slash_id_d[tool_slash_id]
for variable in tool_d['variables']:
the_list.append((variable, tool_d))
recursion(tool_d, the_list)
the_list = []
recursion(tool, the_list)
if include_this_tool:
for variable in tool['variables']:
the_list.append((variable, tool))
return the_list
def parse_workflow_filename(self, ):
'''
Parse and perform sanity tests
'''
if self.workflow_filename:
try:
with open(self.workflow_filename) as f:
self.workflow = json.load(f)
except FileNotFoundError:
raise OBC_Executor_Exception(f'File {self.workflow_filename} does not exist')
except json.decoder.JSONDecodeError as e:
raise OBC_Executor_Exception(f'File {self.workflow_filename} does not seem to be in JSON format. Error: {str(e)}')
elif self.workflow_string:
try:
self.workflow = json.loads(self.workflow_string)
except json.decoder.JSONDecodeError as e:
raise OBC_Executor_Exception(f'Could not parse workflow_string as JSON. Error: {str(e)}')
elif self.workflow_object:
self.workflow = self.workflow_object
self.input_parameters = self.get_input_parameters()
self.root_workflow = self.get_root_workflow()
self.root_workflow_id = self.root_workflow['id']
self.root_step = self.get_root_step()
self.root_inputs_outputs = self.get_input_output_from_workflow(self.root_workflow)
self.output_parameters = self.root_inputs_outputs['outputs']
self.nice_id = self.workflow['nice_id'] # The nice ID from the server
self.nice_id_local = Workflow.create_nice_id() # A local nice ID
if self.nice_id: # The id from the JSON
self.nice_id_global = self.nice_id
elif self.workflow_id: # The id from the executor
self.nice_id_global = self.workflow_id
else:
self.nice_id_global = self.nice_id_local # The id created in this class
self.current_token = self.workflow['token']
log_info('Workflow Name: {} Edit: {} Report: {}'.format(
self.root_workflow['name'], self.root_workflow['edit'], self.nice_id,
))
# Apply some integrity checks
for node in self.node_iterator():
# Every node has a type
assert 'type' in node
# Every node has a id
assert 'id' in node
# Every node has a belongto
assert 'belongto' in node
# Assert proper fields and types in belongto
if not node['belongto'] is None:
assert 'name' in node['belongto']
assert 'edit' in node['belongto']
assert type(node['belongto']['name']) is str
assert type(node['belongto']['edit']) is int
# Check that that there are no circular dependencies
self.check_tool_dependencies_for_circles();
# Check that all root input are set
self.input_parameter_values = {}
self.input_unset_variables = [] # IDs of variables that have not be set by any step
log_info('Checking for input values.')
for root_input_node in self.root_inputs_outputs['inputs']:
var_set = False
for arg_input_name, arg_input_value in self.input_parameters.items():
if arg_input_value is None:
break
if arg_input_name == root_input_node['id']:
log_info(' {}={}'.format(root_input_node['id'], arg_input_value))
self.input_parameter_values[root_input_node['id']] = {'value': arg_input_value, 'description': root_input_node['description']}
var_set = True
break
if not var_set:
self.input_unset_variables.append(root_input_node);
user_message = Workflow.create_input_parameter_message(root_input_node['id'], root_input_node['description'])
if self.askinput == 'JSON':
local_input_parameter = input(user_message)
self.input_parameter_values[root_input_node['id']] = {'value': local_input_parameter, 'description': root_input_node['description']}
elif self.askinput == 'BASH':
pass # Do nothing
elif self.askinput == 'NO':
log_info('Warning: Input Parameter {} ({}) has not been set by any step.'.format(root_input_node['id'], root_input_node['description']))
# Set None values
self.input_parameter_values[root_input_node['id']] = {'value': None, 'description': root_input_node['description']}
# Check that all output_parameterss will be eventually set
for root_output_node in self.root_inputs_outputs['outputs']:
found_output_filling_step = False
for step_node in self.node_iterator():
if not self.is_step(step_node):
continue
if root_output_node['id'] in step_node['outputs']:
found_output_filling_step = True
continue
if not found_output_filling_step and (not self.askinput in ['BASH']):
# If askinput = BASH don't raise exception
message = 'Output {} ({}) is not set by any step!'.format(root_output_node['id'], root_output_node['description'])
raise OBC_Executor_Exception(message)
# Confirm that all main workflows have exactly one main step
# Confirm that all sub workflows have exactly one sub main step
for workflow in self.get_all_workflows():
# Is this the main workflow?
if self.is_root_workflow(workflow):
main_counter = sum(step['main'] for step in self.get_steps_from_workflow(workflow))
main_str = 'MAIN'
else:
main_counter = sum(step['sub_main'] for step in self.get_steps_from_workflow(workflow))
main_str = 'SUB'
if main_counter == 0:
message = '{} Workflow {} has 0 main steps'.format(main_str, workflow['id'])
raise OBC_Executor_Exception(message)
if main_counter > 1:
message = '{} Workflow {} has more than one ({}) main steps'.format(main_str, workflow['id'], main_counter)
raise OBC_Executor_Exception(message)
# Create a dictionary. Keys are tool slash id. values are tools
self.tool_slash_id_d = {self.get_tool_slash_id(tool):tool for tool in self.tool_iterator()}
# Create a dictionary. Keys are tool slash ids. Values are lists of the slash ids of their dependencies
self.tool_run_afters = {self.get_tool_dash_id(t, no_dots=True): [self.get_tool_dash_id(self.tool_slash_id_d[x], no_dots=True) for x in t['dependencies']] for t in self.tool_iterator()}
# Create a dictionary. Keys are tool ids. Values are tuples: (variables from which they depend from, dependent tool)
# This does not contain the variables of the tool that is the key
self.tool_dependent_variables = {self.get_tool_dash_id(tool, no_dots=True):self.get_tool_dependent_variables(tool) for tool in self.tool_iterator()}
# Create a dictionary. Keys are tool ids. Values are tuples: (variables from which they depend from, dependent tool)
# It also contains the variables of the tool that is the key
self.tool_variables = {self.get_tool_dash_id(tool, no_dots=True):self.get_tool_dependent_variables(tool, include_this_tool=True) for tool in self.tool_iterator()}
# Create a dictionary. Keys are tool variable ids . Values are the tools in which they belong.
self.tool_variables_ids = {self.get_tool_bash_variable(tool, tool_variable['name']):tool for tool in self.tool_iterator() for tool_variable in tool['variables']}
# Create a dictionary. Keys are step ids. Values are tool objects
self.step_ids = {step['id']:step for step in self.step_iterator()}
# Create a dictionary. Keys are input ids. Values are input objects
self.input_ids = {inp['id']:inp for inp in self.inputs_iterator()}
# Create a dictionary. Keys a output ids. Values are output objects
self.output_ids = {outp['id']:outp for outp in self.outputs_iterator()}
self.set_step_reads_sets()
def set_step_reads_sets(self,):
'''
The 'inputs' and 'outputs' fields for every step does NOT contain which variables are set and read respectively.
It contains which variables are **referred**
Here we make an assumption:
If a step refers to an input variable and they belong to the same workflow, then the step READS the variable
If a step refers to an output variable and they belong to the same workflow, then the step SETS the variable
'''
# keys are input ids. Values are the steps who set these values
self.input_setters = defaultdict(list)
# Keys are output ids. Values are the steps who set htese values
self.output_setters = defaultdict(list)
for step in self.step_iterator():
step['inputs_reads'] = []
step['inputs_sets'] = []
step['outputs_sets'] = []
step['outputs_reads'] = []
for step_input in step['inputs']:
input_node = self.input_ids[step_input]
if input_node['belongto'] == step['belongto']:
#print ('Step: {} Reads: {}'.format(step['id'], step_input))
step['inputs_reads'].append(step_input)
else:
step['inputs_sets'].append(step_input)
self.input_setters[step_input].append(step['id'])
for step_output in step['outputs']:
output_node = self.output_ids[step_output]
if output_node['belongto'] == step['belongto']:
#print ('Step: {} Sets: {}'.format(step['id'], step_output))
step['outputs_sets'].append(step_output)
self.output_setters[step_output].append(step['id'])
else:
step['outputs_reads'].append(step_output)
def check_tool_dependencies_for_circles(self,):
'''
'''
# Get all tools
all_tools = [node for node in self.node_iterator() if self.is_tool(node)]
# Contruct the tool graph
graph = {self.get_tool_slash_id(tool): tool['dependencies'] for tool in all_tools}
for tool_id in graph.keys():
circles = detect_circles(graph, tool_id, tool_id)
try:
circle = next(circles)
except StopIteration as e:
pass # This is supposed to happen
else:
message = 'Found circular tool dependency!'
message += '\n' + ' --> '.join(circle)
raise OBC_Executor_Exception(message)
def check_step_calls_for_circles(self,):
'''
'''
#Construct the step graph
graph = {step['id']: step['steps'] for step in self.step_iterator()}
for step_id in graph.keys():
circles = detect_circles(graph, step_id, step_id)
try:
circle = next(circles)
except StopIteration as e:
pass
else:
circle_str = ' --> '.join(circle)
return circle_str
return ''
def get_token_set_bash_commands(self, ):
'''
'''
return 'obc_current_token="{}"'.format(self.current_token)
def show_basic_info(self,):
'''
self.root_workflow['name'], self.root_workflow['edit'], self.nice_id,
'''
ret = '\n'
ret += 'OBC_WORKFLOW_NAME="{}"\n'.format(self.root_workflow['name'])
ret += 'OBC_WORKFLOW_EDIT={}\n'.format(self.root_workflow['edit'])
ret += 'OBC_NICE_ID="{}"\n'.format(self.nice_id_global)
ret += 'OBC_SERVER="{}"\n'.format(self.obc_server)
ret += 'echo "OBC: Workflow name: ${OBC_WORKFLOW_NAME}"\n'
ret += 'echo "OBC: Workflow edit: ${OBC_WORKFLOW_EDIT}"\n'
ret += f'echo "OBC: Workflow report: {self.nice_id}"\n'
ret += f'echo "OBC: Server URL: {self.obc_server}"\n'
ret += '\n'
return ret
def get_input_parameters_read_bash_commands(self, ):
'''
Bash commands for reading input/output
'''
ret = '\n'
if self.input_unset_variables:
# Read unset variables from the command line
# https://github.com/kantale/OpenBioC/issues/154
ret += Workflow.read_arguments_from_commandline([x['id'] for x in self.input_unset_variables])
# Check if the variable has been read from command line. If not halt execution and prompt for a value
for unset_variable in self.input_unset_variables:
ret += 'if [ -z ${{{}+x}} ]; then\n'.format(unset_variable['id']) # https://stackoverflow.com/questions/3601515/how-to-check-if-a-variable-is-set-in-bash
ret += ' echo "{}"\n'.format(Workflow.create_input_parameter_message(unset_variable['id'], unset_variable['description']))
ret += ' read -p "{}=" {}\n'.format(unset_variable['id'], unset_variable['id'])
ret += 'fi\n'
return ret
@staticmethod
def create_input_parameter_message(variable_id, variable_description):
'''
Message to display when input variable has not been set.
'''
return 'OBC: Input parameter: {} ({}) has not been set by any step. Enter value: '.format(variable_id, variable_description)
@staticmethod
def read_arguments_from_commandline(arguments):
'''
Help from: https://stackoverflow.com/questions/192249/how-do-i-parse-command-line-arguments-in-bash
'''
ret = ''
ret += 'for i in "$@"\n'
ret += 'do\n'
ret += 'case $i in\n'
for variable_id in arguments:
ret += ' --{VARIABLE_ID}=*)\n'.format(VARIABLE_ID=variable_id)
ret += ' {VARIABLE_ID}="${{i#*=}}"\n'.format(VARIABLE_ID=variable_id)
ret += ' shift\n'
ret += ' ;;\n'
ret += ' *)\n'
ret += ' ;;\n'
ret += 'esac\n'
ret += 'done\n\n'
return ret
def get_tool_bash_commands(self, tool,
validation=True,
update_server_status=True,
read_variables_from_command_line=False,
variables_json_filename=None,
variables_sh_filename_read=None,
variables_sh_filename_write=None,
):
'''
update_server_status: boolean, should we update the server status?
variables_json_filename: Create a json file that contains the values of the variables (if None it does not create it)
read_variables_from_command_line: Assume that this is running from a cammand line file.sh script. Read the arguments from command line
variables_sh_filename_read: If it is set (list), then read all variables from all files in the list
variables_sh_filename_write: If it is set (string), then create a bash filename with all variables
'''
log_info('Building installation bash commands for: {}'.format(tool['label']))
tool_id = Workflow.get_tool_dash_id(tool, no_dots=True)
# Add Bash commands
ret = '### BASH INSTALLATION COMMANDS FOR TOOL: {}\n'.format(tool['label'])
ret += 'echo "OBC: INSTALLING TOOL: {}"\n'.format(tool['label'])
if update_server_status:
ret += Workflow.bash_tool_installation_started(tool) + '\n'
if read_variables_from_command_line:
arguments = [Workflow.get_tool_bash_variable(dependent_tool, dependent_variable['name'])
for dependent_variable, dependent_tool in self.tool_dependent_variables[tool_id]]
ret += Workflow.read_arguments_from_commandline(arguments)
if variables_sh_filename_read:
for filename in variables_sh_filename_read:
ret += '### READING VARIABLES FROM {}\n'.format(filename)
ret += '. {}\n\n'.format(filename)
# Do we exit on commands?
if Workflow.EXIT_ON_ERROR:
tool['installation_commands'] = f'\nset -e\n{tool["installation_commands"]}\nset +x\n'
# We are adding the installation commands in parenthesis.
# By doing so, we are isolating the raw installation commands with the rest pre- and post- commands
ret += '(\n:\n' + tool['installation_commands'] + '\n)\n' # Add A bash no-op command (:) to avoid empty installation instructions
if Workflow.EXIT_ON_ERROR:
ret += 'EXITCODE=$?\n'
ret += 'if [ $EXITCODE -ne 0 ] ; then\n'
ret += ' echo OBC: INSTALLATION OF TOOL: {} FAILED\n'.format(tool['label'])
ret += ' exit $EXITCODE\n'
ret += 'fi\n'
ret += 'echo "OBC: INSTALLATION OF TOOL: {} . COMPLETED"\n'.format(tool['label'])
ret += '### END OF INSTALLATION COMMANDS FOR TOOL: {}\n\n'.format(tool['label'])
if validation:
# Add Bash validation commands
ret += '### BASH VALIDATION COMMANDS FOR TOOL: {}\n'.format(tool['label'])
ret += 'echo "OBC: VALIDATING THE INSTALLATION OF THE TOOL: {}"\n'.format(tool['label'])
#ret += tool['validation_commands'] + '\n'
#validation_script_filename = tool['label'].replace('/', '__') + '__validation.sh'
#ret += "cat > {} << ENDOFFILE\n".format(validation_script_filename) # Add 'ENDOFFILE' in single quotes to have raw input
if Workflow.EXIT_ON_ERROR:
tool['validation_commands'] = f'\nset -e\n{tool["validation_commands"]}\nset +e\n'
ret += '(\n:\n' + tool['validation_commands'] + '\n)\n' # Run validation commands in a dedicated environment () . Add A bash no-op command (:) to avoid empty installation instructions
#ret += 'ENDOFFILE\n\n'
#ret += 'chmod +x {}\n'.format(validation_script_filename)
#ret += './{}\n'.format(validation_script_filename)
ret += 'EXITCODE=$?\n'
ret += 'if [ $EXITCODE -eq 0 ] ; then\n'
ret += ' echo "OBC: VALIDATION FOR TOOL: {} SUCCEEDED"\n'.format(tool['label'])
ret += 'else\n'
ret += ' echo "OBC: VALIDATION FOR TOOL: {} FAILED"\n'.format(tool['label'])
if Workflow.EXIT_ON_ERROR:
ret += ' exit $EXITCODE\n'
ret += 'fi\n\n'
ret += '### END OF VALIDATION COMMANDS FOR TOOL: {}\n\n'.format(tool['label'])
if update_server_status:
ret += Workflow.bash_tool_installation_finished(tool) + '\n'
ret += '### SETTING TOOL VARIABLES FOR: {}\n'.format(tool['label'])
for tool_variable in tool['variables']:
tool_bash_variable=self.get_tool_bash_variable(tool, tool_variable['name'])
ret += 'export {}="{}" # {} \n'.format(tool_bash_variable, tool_variable['value'], tool_variable['description'])
ret += 'echo "OBC: SET {}=\\"${}\\" <-- {} "\n'.format(tool_bash_variable, tool_bash_variable, tool_variable['description'])
ret += '### END OF SETTING TOOL VARIABLES FOR: {}\n\n'.format(tool['label'])
if variables_json_filename:
ret += '### CREATING JSON FILE WITH TOOL VARIABLES\n'
ret += "cat > {} << ENDOFFILE\n".format(variables_json_filename) # Add 'ENDOFFILE' for raw input
ret += Workflow.get_tool_bash_variables_json(tool) + '\n'
ret += 'ENDOFFILE\n\n'
if variables_sh_filename_write:
ret += '### CREATING BASH WITH TOOL VARIABLES\n'
ret += "cat > {} << ENDOFFILE\n".format(variables_sh_filename_write)
for tool_variable in tool['variables']:
tool_bash_variable=self.get_tool_bash_variable(tool, tool_variable['name'])
ret +='{VAR}="{VALUE}"\n'.format(VAR=tool_bash_variable, VALUE=tool_variable['value'])
ret += 'ENDOFFILE\n'
return ret
@staticmethod
def get_edge_id(source_id, target_id):
return f'{source_id}..{target_id}'
def get_input_bash_commands(self,):
'''
'''
ret = '### SET ROOT WORKFLOW INPUT PARAMETERS\n'
for variable, data in self.input_parameter_values.items():
ret += '{}="{}" # {}\n'.format(variable, data['value'], data['description'])
ret += '### END OF SET ROOT WORKFLOW INPUT PARAMETERS'
return ret
def get_output_bash_commands(self,):
ret = '### PRINT OUTPUT PARAMETERS\n'
ret += 'echo "OBC: Output Variables:"\n'
for output_parameter in self.output_parameters:
ret += 'echo "OBC: {} = ${{{}}}"\n'.format(output_parameter['id'], output_parameter['id'])
ret += 'REPORT {} ${{{}}} OUTPUT_VARIABLE \n'.format(output_parameter['id'], output_parameter['id'])
ret += '### END OF PRINTING OUTPUT PARAMETERS\n'
return ret
def get_step_bash_commands(self, ):
'''
TODO: CREATE AN ORDERING ACCORDING TO WORKFLOWS!
'''
ret = '### SETTING BASH FUNCTIONS FOR STEPS\n\n'
for a_node in self.node_iterator():
if not self.is_step(a_node):
continue
ret += '# STEP: {}\n'.format(a_node['id'])
ret += '{} () {{\n'.format(a_node['id'])
ret += "OBC_WHOCALLEDME=$(caller 0 | awk '{print $2}') \n"
ret += 'if [ ${OBC_WHOCALLEDME} == "PARALLEL" ] ; then \n '
ret += " OBC_WHOCALLEDME=$(caller 1 | awk '{print $2}') \n"
ret += "fi\n"
ret += 'echo "OBC: CALLING STEP: {} CALLER: $OBC_WHOCALLEDME"\n'.format(a_node['id']) #
ret += 'update_server_status "step started {} $OBC_WHOCALLEDME"\n'.format(a_node['id'])
ret += a_node['bash'] + '\n'
ret += 'update_server_status "step finished {}"\n'.format(a_node['id'])
ret += '}\n'
ret += '### END OF SETTING BASH FUNCTIONS FOR STEPS\n'
return ret
def get_main_step_bash_commands(self,):
'''
'''
ret = '### CALLING MAIN STEP\n'
ret += '{}\n'.format(self.root_step['id'])
ret += '### END OF CALLING MAIN STEP\n'
return ret
@staticmethod
def get_tool_slash_id(tool):
'''
'''
return '/'.join([tool['name'], tool['version'], str(tool['edit'])])
@staticmethod
def get_tool_dash_id(tool, no_dots=False):
'''
'''
ret = '__'.join([tool['name'], tool['version'], str(tool['edit'])])
if no_dots:
ret = ret.replace('.', '_')
return ret
@staticmethod
def get_tool_cytoscape_id(tool, no_dots=True):
'''
'''
return f'{Workflow.get_tool_dash_id(tool, no_dots=no_dots)}__2'
@staticmethod
def create_tool_from_cytoscape_id(cytoscape_tool_id):
'''
'''
s = cytoscape_tool_id.split('__')
return {
'name': s[0],
'version': s[1],
'edit': int(s[2]),
}
@staticmethod
def get_tool_vars_filename(tool):
'''
'''
return Workflow.get_tool_vars_filename_tool_id(Workflow.get_tool_dash_id(tool, no_dots=True))
@staticmethod
def get_tool_vars_filename_tool_id(tool_id):
'''
'''
return '{TOOL_ID}_VARS.sh'.format(TOOL_ID=tool_id)
@staticmethod
def get_tool_bash_variable(tool, variable_name):
'''
'''
return '{}__{}'.format(Workflow.get_tool_dash_id(tool, no_dots=True), variable_name)
@staticmethod
def get_tool_bash_variables_json(tool):
'''
'''
d = {Workflow.get_tool_bash_variable(tool, tool_variable['name']): tool_variable['value'] for tool_variable in tool['variables']}
return json.dumps(d, indent=4)
@staticmethod
def tool_label_to_object(tool_label):
'''
The inverse of get_tool_slash_id
'''
name, version, edit = tool_label.split('/')
return {
'name': name,
'version': version,
'edit': int(edit),
}