Mercurial > repos > iuc > ncbi_eutils_efetch
comparison eutils.py @ 9:6c4b39080ed7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 41f5eb8e0aee5b779d618b5178098c4be89a9ef1
| author | iuc |
|---|---|
| date | Mon, 23 Jan 2023 10:37:57 +0000 |
| parents | c09fcbe4b16a |
| children |
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| 8:c5ff15011115 | 9:6c4b39080ed7 |
|---|---|
| 174 if gotit < 2: | 174 if gotit < 2: |
| 175 raise Exception("Could not find WebEnv in xml response") | 175 raise Exception("Could not find WebEnv in xml response") |
| 176 except Exception as e: | 176 except Exception as e: |
| 177 print("Error parsing...") | 177 print("Error parsing...") |
| 178 print(xml_str) | 178 print(xml_str) |
| 179 raise(e) | 179 raise e |
| 180 | 180 |
| 181 return history | 181 return history |
| 182 | 182 |
| 183 def extract_histories_from_xml_file(self, xml_file): | 183 def extract_histories_from_xml_file(self, xml_file): |
| 184 histories = [] | 184 histories = [] |
| 219 if gotit == 0 and gotenv == 0: | 219 if gotit == 0 and gotenv == 0: |
| 220 raise Exception("Could not find WebEnv in xml response") | 220 raise Exception("Could not find WebEnv in xml response") |
| 221 except Exception as e: | 221 except Exception as e: |
| 222 print("Error parsing...") | 222 print("Error parsing...") |
| 223 print(xml_str) | 223 print(xml_str) |
| 224 raise(e) | 224 raise e |
| 225 | 225 |
| 226 return histories | 226 return histories |
| 227 | 227 |
| 228 def search(self, **payload): | 228 def search(self, **payload): |
| 229 return Entrez.esearch(**payload).read() | 229 return Entrez.esearch(**payload).read() |