Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4_0/mira4_validator.py @ 39:bbf14bb9607b draft default tip

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
author peterjc
date Mon, 03 Jun 2019 13:29:00 -0400
parents cee8f9005e43
children
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cee8f9005e43 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b
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1 """Python code to validate parameters in the Galaxy XML definition."""
cee8f9005e43 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b
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2
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3 # Called from the Galaxy Tool XML file
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4 # import sys
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7 def validate_input(trans, error_map, param_values, page_param_map):
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cee8f9005e43 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 206259620376b322fc8ed99a6efdd3712f38764b
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8 """Validate the min_size/max_size user input, before execution."""
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9 err_list = []
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10 for read_group in param_values["read_group"]:
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11 err = dict()
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12 segments = read_group["segments"]
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13 if str(segments["type"]) != "paired":
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14 err_list.append(dict())
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15 continue
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16
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17 min_size = str(segments["min_size"]).strip()
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18 max_size = str(segments["max_size"]).strip()
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19 # sys.stderr.write("DEBUG min_size=%r, max_size=%r\n" % (min_size, max_size))
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21 # Somehow Galaxy seems to turn an empty field into string "None"...
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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22 if min_size == "None":
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23 min_size = ""
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24 if max_size == "None":
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25 max_size = ""
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27 if min_size == "" and max_size == "":
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28 # Both missing is good
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29 pass
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30 elif min_size == "":
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31 err["min_size"] = "Minimum size required if maximum size given"
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32 elif max_size == "":
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33 err["max_size"] = "Maximum size required if minimum size given"
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34
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35 if min_size:
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36 try:
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37 min_size_int = int(min_size)
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38 if min_size_int < 0:
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bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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39 err["min_size"] = (
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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40 "Minumum size must not be negative (%i)" % min_size_int
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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41 )
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42 min_size = None # Avoid doing comparison below
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43 except ValueError:
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44 err["min_size"] = "Minimum size is not an integer (%s)" % min_size
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56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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45 min_size = None # Avoid doing comparison below
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47 if max_size:
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48 try:
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49 max_size_int = int(max_size)
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50 if max_size_int < 0:
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bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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51 err["max_size"] = (
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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52 "Maximum size must not be negative (%i)" % max_size_int
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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53 )
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54 max_size = None # Avoid doing comparison below
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55 except ValueError:
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56 err["max_size"] = "Maximum size is not an integer (%s)" % max_size
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57 max_size = None # Avoid doing comparison below
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59 if min_size and max_size and min_size_int > max_size_int:
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60 msg = "Minimum size must be less than maximum size (%i vs %i)" % (
bbf14bb9607b planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
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61 min_size_int,
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62 max_size_int,
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63 )
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64 err["min_size"] = msg
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65 err["max_size"] = msg
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67 if err:
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68 err_list.append({"segments": err})
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69 else:
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70 err_list.append(dict())
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72 if any(err_list):
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73 # Return an error map only if any readgroup gave errors
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74 error_map["read_group"] = err_list