Mercurial > repos > bgruening > cp_cellprofiler

annotate cp_common_functions.py @ 4:fca368c99299 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 705efdd46afce6cbb44c87d8249566ebd528b230"
author bgruening
date Fri, 29 May 2020 18:16:51 -0400
parents 78a16d8c8d5e
children e917a2424690
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1 INDENTATION = " "
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2 LINE_NUM_MODULES = 4
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4 def get_json_value(json_input, keys_path):
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5 """Returns the value specified in keys_path (using dot notation) or an empty string if the key doesn't exist"""
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6 if not isinstance(json_input, dict):
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7 return ""
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8 keys = keys_path.split(".")
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9 try:
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10 value = json_input[keys[0]]
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11 for key in keys[1:]:
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12 value = value[key]
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13 return value
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14 except KeyError:
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15 return ""
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18 def concat_conditional(a, b):
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19 if a == "" or b == "":
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20 return ""
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21 else:
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22 return f"{a}_{b}"
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25 def get_total_number_of_modules(pipeline_lines):
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26 """Gets the number of modules from the header of the previous pipeline"""
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27 number_of_modules = pipeline_lines[LINE_NUM_MODULES].strip().split(':')[1]
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28 return int(number_of_modules)
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31 def get_pipeline_lines(input_pipeline):
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32 """Returns a list with the lines in the .cppipe file"""
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33 with open(input_pipeline) as f:
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34 lines = f.readlines()
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35 return lines
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38 def update_module_count(pipeline_lines, count):
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39 """Updates the number of modules in the .cppipe header"""
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40 module_count_entry = pipeline_lines[LINE_NUM_MODULES].strip().split(':')[0]
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41 pipeline_lines[4] = f"{module_count_entry}:{count}\n"
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42 return pipeline_lines
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45 def write_pipeline(filename, lines_pipeline):
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46 """Writes the lines composing the pipeline into a file"""
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47 with open(filename, "w") as f:
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48 f.writelines(lines_pipeline)
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51 def build_header(module_name, module_number):
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52 """Creates the first line of a module given the name and module number"""
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53 result = "|".join([f"{module_name}:[module_num:{module_number}",
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54 "svn_version:\\'Unknown\\'",
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55 "variable_revision_number:4",
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56 "show_window:False",
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57 "notes:\\x5B\\x5D",
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58 "batch_state:array(\\x5B\\x5D, dtype=uint8)",
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59 "enabled:True",
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60 "wants_pause:False]\n"])
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61 return result