Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4_0/mira4_validator.py @ 34:0785a6537f3e draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 6405ba93fcec7ea93452bf54d559c7507ee7a57c
author peterjc
date Wed, 07 Jun 2017 12:33:39 -0400
parents 56b421d59805
children cee8f9005e43
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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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1 # Called from the Galaxy Tool XML file
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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2 # import sys
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5 def validate_input(trans, error_map, param_values, page_param_map):
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6 """Validates the min_size/max_size user input, before execution."""
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7 err_list = []
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8 for read_group in param_values["read_group"]:
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9 err = dict()
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10 segments = read_group["segments"]
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11 if str(segments["type"]) != "paired":
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12 err_list.append(dict())
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13 continue
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14
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15 min_size = str(segments["min_size"]).strip()
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16 max_size = str(segments["max_size"]).strip()
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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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17 # sys.stderr.write("DEBUG min_size=%r, max_size=%r\n" % (min_size, max_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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19 # 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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20 if min_size == "None":
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21 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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22 if max_size == "None":
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23 max_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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25 if min_size == "" and max_size == "":
56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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26 # Both missing is good
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27 pass
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28 elif min_size == "":
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29 err["min_size"] = "Minimum size required if maximum size given"
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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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30 elif max_size == "":
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31 err["max_size"] = "Maximum size required if minimum size given"
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33 if min_size:
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34 try:
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35 min_size_int = int(min_size)
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36 if min_size_int < 0:
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37 err["min_size"] = "Minumum size must not be negative (%i)" % min_size_int
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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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38 min_size = None # Avoid doing comparison below
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39 except ValueError:
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40 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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parents: 25
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41 min_size = None # Avoid doing comparison below
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43 if max_size:
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44 try:
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45 max_size_int = int(max_size)
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56b421d59805 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
peterjc
parents: 25
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46 if max_size_int < 0:
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47 err["max_size"] = "Maximum size must not be negative (%i)" % max_size_int
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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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48 max_size = None # Avoid doing comparison below
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49 except ValueError:
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50 err["max_size"] = "Maximum size is not an integer (%s)" % max_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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parents: 25
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51 max_size = None # Avoid doing comparison below
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53 if min_size and max_size and min_size_int > max_size_int:
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54 msg = "Minimum size must be less than maximum size (%i vs %i)" % (min_size_int, max_size_int)
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55 err["min_size"] = msg
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56 err["max_size"] = msg
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57
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58 if err:
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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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parents: 25
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59 err_list.append({"segments": err})
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60 else:
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61 err_list.append(dict())
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63 if any(err_list):
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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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64 # Return an error map only if any readgroup gave errors
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65 error_map["read_group"] = err_list