Mercurial > repos > iuc > ncbi_eutils_efetch
annotate eutils.py @ 7:796d694b41dc draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit b399ac5996d8225353d3abaff58eb986da5545d7"
author | iuc |
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date | Wed, 06 Oct 2021 08:00:25 +0000 |
parents | c09fcbe4b16a |
children | 6c4b39080ed7 |
rev | line source |
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1
0fc65a60436f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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1 import json |
0
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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2 import os |
2
0977ec0f3ba8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
iuc
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3 from io import StringIO |
1
0fc65a60436f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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4 |
0
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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5 from Bio import Entrez |
1
0fc65a60436f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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6 |
0
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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7 Entrez.tool = "GalaxyEutils_1_0" |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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8 BATCH_SIZE = 200 |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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9 |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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10 |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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11 class Client(object): |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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12 |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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13 def __init__(self, history_file=None, user_email=None, admin_email=None): |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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14 self.using_history = False |
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c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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15 self.using_parsedids = False |
0
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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16 |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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17 if user_email is not None and admin_email is not None: |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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18 Entrez.email = ';'.join((admin_email, user_email)) |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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19 elif user_email is not None: |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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20 Entrez.email = user_email |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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21 elif admin_email is not None: |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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22 Entrez.email = admin_email |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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23 else: |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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24 Entrez.email = os.environ.get('NCBI_EUTILS_CONTACT', None) |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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25 |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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26 if Entrez.email is None: |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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27 raise Exception("Cannot continue without an email; please set " |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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28 "administrator email in NCBI_EUTILS_CONTACT") |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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29 |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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30 if history_file is not None: |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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31 with open(history_file, 'r') as handle: |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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32 data = json.loads(handle.read()) |
3
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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33 # esearch |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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34 if 'QueryKey' in data: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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35 self.query_key = data['QueryKey'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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36 self.webenv = data['WebEnv'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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37 self.query_keys = [] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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38 self.query_keys += [data['QueryKey']] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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39 self.using_history = True |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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40 elif 'query_key' in data: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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41 self.query_key = data['query_key'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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42 self.webenv = data['WebEnv'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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43 self.query_keys = [] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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44 self.query_keys += [data['query_key']] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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45 self.using_history = True |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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46 elif 'esearchresult' in data: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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47 self.query_key = data['esearchresult']['querykey'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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48 self.webenv = data['esearchresult']['webenv'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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49 self.query_keys = [] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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50 self.query_keys += [data['esearchresult']['querykey']] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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51 self.using_history = True |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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52 # elink |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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53 elif 'linksets' in data: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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54 # elink for cmd=neighbor_history |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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55 if 'linksetdbhistories' in data['linksets'][0]: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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56 self.webenv = data['linksets'][0]['webenv'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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57 self.query_key = data['linksets'][0]['linksetdbhistories'][0]['querykey'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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58 self.using_history = True |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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59 # elink for cmd=neighbor|neighbor_score |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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60 elif 'linksetdbs' in data['linksets'][0]: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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61 self.using_parsedids = True |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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62 # elink for neighbor |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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63 if isinstance(data['linksets'][0]['linksetdbs'][0]['links'][0], str): |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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64 self.idstr = ','.join(data['linksets'][0]['linksetdbs'][0]['links']) |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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65 # elink for neighbor_score |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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66 else: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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67 self.idstr = ','.join(map(lambda x: x['id'], data['linksets'][0]['linksetdbs'][0]['links'])) |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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68 if 'linksetdbhistories' in data['linksets'][0]: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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69 self.webenv = data['linksets'][0]['webenv'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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70 self.query_keys = [] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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71 for query in data['linksets'][0]['linksetdbhistories']: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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72 if 'querykey' in query: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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73 self.query_keys += [query['querykey']] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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74 else: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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75 print("No match") |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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76 print(data) |
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77 |
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78 def get_history(self): |
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79 if self.using_history: |
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80 return { |
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81 'query_key': self.query_key, |
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82 'WebEnv': self.webenv, |
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83 } |
3
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84 elif self.using_parsedids: |
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85 return { |
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86 'id': self.idstr, |
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87 } |
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88 else: |
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89 return {} |
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90 |
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91 def get_histories(self): |
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92 histories = [] |
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93 for key in self.query_keys: |
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94 histories += [{'WebEnv': self.webenv, 'query_key': key}] |
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95 return histories |
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96 |
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97 def post(self, database, **payload): |
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98 return json.dumps(Entrez.read(Entrez.epost(database, **payload)), indent=4) |
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99 |
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100 def fetch(self, db, ftype=None, **payload): |
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101 os.makedirs("downloads") |
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102 |
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103 if 'id' in payload: |
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104 summary = self.id_summary(db, payload['id']) |
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105 elif 'WebEnv' not in payload or 'query_key' not in payload: |
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106 summary = self.history_summary(db) |
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107 else: |
3
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108 summary = payload |
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109 |
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110 count = len(summary) |
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111 payload['retmax'] = BATCH_SIZE |
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112 |
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113 # This may be bad. I'm not sure yet. I think it will be ... but UGH. |
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114 for i in range(0, count, BATCH_SIZE): |
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115 payload['retstart'] = i |
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116 file_path = os.path.join('downloads', 'EFetch Results Chunk %s.%s' % (i, ftype)) |
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117 with open(file_path, 'w') as handle: |
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118 handle.write(Entrez.efetch(db, **payload).read()) |
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119 |
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120 def id_summary(self, db, id_list): |
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121 payload = { |
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122 'db': db, |
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123 'id': id_list, |
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124 } |
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125 return Entrez.read(Entrez.esummary(**payload)) |
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126 |
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127 def history_summary(self, db): |
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128 if not self.using_history: |
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129 raise Exception("History must be available for this method") |
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130 |
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131 payload = { |
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132 'db': db, |
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133 'query_key': self.query_key, |
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134 'WebEnv': self.webenv, |
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135 } |
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136 return Entrez.read(Entrez.esummary(**payload)) |
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137 |
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138 def summary(self, **payload): |
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139 return Entrez.esummary(**payload).read() |
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140 |
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141 def link(self, **payload): |
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142 return Entrez.elink(**payload).read() |
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143 |
3
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144 def extract_history_from_xml_file(self, xml_file): |
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145 history = {} |
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146 with open(xml_file, 'r') as handle: |
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147 xml_str = handle.read() |
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148 history = self.extract_history_from_xml(xml_str) |
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149 return history |
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150 |
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151 def extract_history_from_xml(self, xml_str): |
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152 try: |
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153 parsed_data = Entrez.read(StringIO(xml_str)) |
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154 history = {} |
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155 gotit = 0 |
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156 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
2
diff
changeset
|
157 # New code doesn't work for esearch input to elink - Parsing esearch output (reading an xml history) does not work as an elink input payload, which needs 'QueryKey'. Notably, if parsing elink output as input to elink, conversion of xml 'QueryKey' to 'query_key' is needed for some reason. Also Notably, efetch returned results using the 'QueryKey' key |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
2
diff
changeset
|
158 # For esearch xml history results |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
159 if 'QueryKey' in parsed_data: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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160 history['query_key'] = parsed_data['QueryKey'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
161 gotit += 1 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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162 if 'WebEnv' in parsed_data: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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|
163 history['WebEnv'] = parsed_data['WebEnv'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
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|
164 gotit += 1 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
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165 # For elink xml history results |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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166 if gotit < 2: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
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167 if 'LinkSetDbHistory' in parsed_data[0]: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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changeset
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168 if 'QueryKey' in parsed_data[0]['LinkSetDbHistory'][0]: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
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169 history['query_key'] = parsed_data[0]['LinkSetDbHistory'][0]['QueryKey'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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170 gotit += 1 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
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171 if 'WebEnv' in parsed_data[0]: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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172 history['WebEnv'] = parsed_data[0]['WebEnv'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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173 gotit += 1 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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174 if gotit < 2: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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175 raise Exception("Could not find WebEnv in xml response") |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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176 except Exception as e: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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177 print("Error parsing...") |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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178 print(xml_str) |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
179 raise(e) |
0
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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180 |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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181 return history |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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182 |
3
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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183 def extract_histories_from_xml_file(self, xml_file): |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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184 histories = [] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
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185 with open(xml_file, 'r') as handle: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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186 xml_str = handle.read() |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
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187 histories = self.extract_histories_from_xml(xml_str) |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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188 return histories |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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|
189 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
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190 def extract_histories_from_xml(self, xml_str): |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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191 try: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
192 parsed_data = Entrez.read(StringIO(xml_str)) |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
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193 histories = [] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
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194 gotit = 0 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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changeset
|
195 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
2
diff
changeset
|
196 # New code doesn't work for esearch input to elink - Parsing esearch output (reading an xml history) does not work as an elink input payload, which needs 'QueryKey'. Notably, if parsing elink output as input to elink, conversion of xml 'QueryKey' to 'query_key' is needed for some reason. Also Notably, efetch returned results using the 'QueryKey' key |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
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197 # For esearch xml history results |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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changeset
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198 if 'QueryKey' in parsed_data: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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199 tmp_hist = {} |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
2
diff
changeset
|
200 tmp_hist['query_key'] = parsed_data['QueryKey'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
201 gotit += 1 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
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202 if 'WebEnv' in parsed_data: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
203 tmp_hist['WebEnv'] = parsed_data['WebEnv'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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204 gotit += 1 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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205 if gotit == 2: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
206 histories += [tmp_hist] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
207 # For elink xml history results |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
208 else: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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changeset
|
209 gotenv = 0 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
210 if 'LinkSetDbHistory' in parsed_data[0]: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
2
diff
changeset
|
211 for query in parsed_data[0]['LinkSetDbHistory']: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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changeset
|
212 tmp_hist = {} |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
213 if 'WebEnv' in parsed_data[0]: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
214 tmp_hist['WebEnv'] = parsed_data[0]['WebEnv'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
2
diff
changeset
|
215 if 'QueryKey' in query: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
216 tmp_hist['query_key'] = query['QueryKey'] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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changeset
|
217 histories += [tmp_hist] |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
218 gotit += 1 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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219 if gotit == 0 and gotenv == 0: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
220 raise Exception("Could not find WebEnv in xml response") |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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|
221 except Exception as e: |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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changeset
|
222 print("Error parsing...") |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
223 print(xml_str) |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
changeset
|
224 raise(e) |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
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|
225 |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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changeset
|
226 return histories |
c09fcbe4b16a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
iuc
parents:
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diff
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|
227 |
0
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
228 def search(self, **payload): |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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changeset
|
229 return Entrez.esearch(**payload).read() |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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changeset
|
230 |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
231 def info(self, **kwargs): |
71bcf87a7031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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|
232 return Entrez.einfo(**kwargs).read() |
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233 |
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234 def gquery(self, **kwargs): |
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235 return Entrez.egquery(**kwargs).read() |
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236 |
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237 def citmatch(self, **kwargs): |
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238 return Entrez.ecitmatch(**kwargs).read() |
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239 |
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240 @classmethod |
3
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241 def jsonstring2jsondata(cls, json_str): |
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242 json_handle = StringIO(json_str) |
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243 json_data = json.loads(json_handle.read()) |
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244 return json_data |
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245 |
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246 @classmethod |
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247 def jsonfile2UIlist(cls, json_file): |
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248 merged_ids = [] |
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249 with open(json_file, 'r') as handle: |
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250 json_data = json.loads(handle.read()) |
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251 for id in cls.jsondata2UIlist(json_data): |
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252 merged_ids += [id] |
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253 return merged_ids |
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254 |
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255 @classmethod |
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256 def jsondata2UIlist(cls, json_data): |
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257 merged_ids = [] |
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258 |
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259 # Always prioritize the result links as opposed to the search links |
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260 # elink - retrieves linked IDs for cmd=neighbor|neighbor_score only |
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261 if 'linksets' in json_data: |
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262 for lnk in json_data['linksets'][0]['linksetdbs']: |
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263 if 'links' in lnk: |
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264 for id in lnk['links']: |
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265 # elink for neighbor |
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266 if isinstance(id, str): |
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267 merged_ids.append(id) |
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268 # elink for neighbor_score |
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269 else: |
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270 merged_ids.append(id['id']) |
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271 # esearch |
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272 elif 'esearchresult' in json_data: |
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273 for id in json_data['esearchresult']['idlist']: |
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274 merged_ids += [id] |
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275 |
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276 return merged_ids |
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277 |
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278 @classmethod |
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279 def xmlfile2UIlist(cls, xml_file): |
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280 merged_ids = [] |
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281 with open(xml_file, 'r') as handle: |
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282 xml_data = Entrez.read(handle) |
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283 for id in cls.xmldata2UIlist(xml_data): |
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284 merged_ids += [id] |
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285 return merged_ids |
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286 |
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287 @classmethod |
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288 def xmlstring2UIlist(cls, xml_str): |
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289 merged_ids = [] |
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290 xml_data = Entrez.read(StringIO(xml_str)) |
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291 for id in cls.xmldata2UIlist(xml_data): |
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292 merged_ids += [id] |
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293 return merged_ids |
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294 |
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295 @classmethod |
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296 def xmldata2UIlist(cls, xml_data): |
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297 merged_ids = [] |
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298 |
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299 try: |
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300 # Always prioritize the result links as opposed to the search links |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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301 # elink - retrieves linked IDs for cmd=neighbor|neighbor_score only |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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302 if 'LinkSetDb' in xml_data[0]: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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303 for lnk in xml_data[0]['LinkSetDb'][0]['Link']: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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304 # elink for neighbor |
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305 if isinstance(lnk, str): |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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306 merged_ids.append(lnk) |
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307 # elink for neighbor_score |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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308 else: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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309 merged_ids.append(lnk['Id']) |
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310 # esearch |
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311 elif 'IdList' in xml_data: |
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312 for id in xml_data['IdList']: |
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313 merged_ids += [id] |
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314 # If it was not elink output, we will end up here |
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315 except Exception: |
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316 # esearch |
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317 if 'IdList' in xml_data: |
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318 for id in xml_data['IdList']: |
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319 merged_ids += [id] |
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320 |
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321 return merged_ids |
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322 |
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323 @classmethod |
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324 def parse_ids(cls, id_list, id, history_file, xml_file, json_file): |
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325 """Parse IDs passed on --cli or in a file passed to the cli |
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326 """ |
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327 merged_ids = [] |
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328 if id is not None: |
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329 for pid in id.replace('__cn__', ',').replace('\n', ',').split(','): |
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330 if pid is not None and len(pid) > 0: |
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331 merged_ids.append(pid) |
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332 |
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333 if id_list is not None: |
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334 with open(id_list, 'r') as handle: |
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335 merged_ids += [x.strip() for x in handle.readlines()] |
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336 |
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337 if xml_file is not None: |
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338 tmp_ids = cls.xmlfile2UIlist(xml_file) |
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339 for id in tmp_ids: |
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340 merged_ids += [id] |
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341 |
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342 if json_file is not None: |
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343 tmp_ids = cls.jsonfile2UIlist(json_file) |
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344 for id in tmp_ids: |
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345 merged_ids += [id] |
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346 |
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347 return merged_ids |
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348 |
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349 @classmethod |
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350 def getVersion(cls): |
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351 """Return the biopython version |
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352 """ |
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353 import Bio |
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354 return Bio.__version__ |