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Patch 1: Adds a dataframe feature for a query#66

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yochannah merged 6 commits intointermine:devfrom
mbasil09:patch-1
Dec 20, 2019
Merged

Patch 1: Adds a dataframe feature for a query#66
yochannah merged 6 commits intointermine:devfrom
mbasil09:patch-1

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@mbasil09
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@mbasil09 mbasil09 commented Dec 13, 2019

solves #39

@mbasil09
PEP8 Update
68c7b63
@mbasil09
PEP8 Update
a72412b
@mbasil09
PEP8 Update
56794f7
@mbasil09
PEP8 Update
65fd0ec
@mbasil09
PEP8 Update
8fe05e6 
Someone had accidentally added an empty line.
@mbasil09
Added a dataframe feature
2e62758 
new method "dataframe" added, which returns a pandas dataframe

Usage:
query.dataframe()


optional arguments:
size: maximum results to return
start:  index of first result to be returned
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pep8speaks commented Dec 13, 2019

Hello @mbasil09! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

Line 104:12: E713 test for membership should be 'not in'
Line 154:80: E501 line too long (82 > 79 characters)
Line 272:40: W605 invalid escape sequence '\s'
Line 291:80: E501 line too long (109 > 79 characters)
Line 292:80: E501 line too long (85 > 79 characters)
Line 306:80: E501 line too long (101 > 79 characters)
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Line 522:80: E501 line too long (127 > 79 characters)
Line 575:13: E741 ambiguous variable name 'l'
Line 628:80: E501 line too long (101 > 79 characters)
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Line 912:80: E501 line too long (91 > 79 characters)
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Line 840:80: E501 line too long (87 > 79 characters)
Line 899:80: E501 line too long (91 > 79 characters)
Line 934:80: E501 line too long (84 > 79 characters)

Line 3:20: W605 invalid escape sequence '\w'
Line 3:23: W605 invalid escape sequence '.'
Line 3:27: W605 invalid escape sequence '\w'
Line 13:9: E722 do not use bare 'except'
Line 17:80: E501 line too long (84 > 79 characters)
Line 77:9: E722 do not use bare 'except'
Line 80:12: E713 test for membership should be 'not in'

Line 7:80: E501 line too long (82 > 79 characters)
Line 51:80: E501 line too long (87 > 79 characters)
Line 75:80: E501 line too long (131 > 79 characters)
Line 78:80: E501 line too long (81 > 79 characters)
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Line 111:80: E501 line too long (99 > 79 characters)
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Line 113:80: E501 line too long (87 > 79 characters)
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Line 295:80: E501 line too long (82 > 79 characters)
Line 296:80: E501 line too long (91 > 79 characters)
Line 298:80: E501 line too long (91 > 79 characters)
Line 309:36: W605 invalid escape sequence '\s'
Line 309:49: W605 invalid escape sequence '\s'
Line 310:39: W605 invalid escape sequence '\s'
Line 310:52: W605 invalid escape sequence '('
Line 310:55: W605 invalid escape sequence ')'
Line 310:58: W605 invalid escape sequence '\s'
Line 311:39: W605 invalid escape sequence '\s'
Line 311:50: W605 invalid escape sequence '\s'
Line 312:39: W605 invalid escape sequence '\s'
Line 312:50: W605 invalid escape sequence '\s'
Line 314:13: W605 invalid escape sequence '('
Line 314:15: W605 invalid escape sequence '\s'
Line 314:28: W605 invalid escape sequence '\s'
Line 314:32: W605 invalid escape sequence '\s'
Line 314:45: W605 invalid escape sequence '\s'
Line 314:48: W605 invalid escape sequence ')'
Line 332:80: E501 line too long (81 > 79 characters)
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Line 346:80: E501 line too long (90 > 79 characters)
Line 379:80: E501 line too long (80 > 79 characters)
Line 432:80: E501 line too long (99 > 79 characters)
Line 493:80: E501 line too long (80 > 79 characters)
Line 520:25: W605 invalid escape sequence '('
Line 520:37: W605 invalid escape sequence '\s'
Line 520:41: W605 invalid escape sequence ')'
Line 530:46: W605 invalid escape sequence '\s'
Line 650:45: W605 invalid escape sequence '\s'
Line 657:32: W605 invalid escape sequence '.'
Line 657:34: W605 invalid escape sequence '*'
Line 666:80: E501 line too long (102 > 79 characters)
Line 694:39: W605 invalid escape sequence '.'
Line 694:41: W605 invalid escape sequence '*'
Line 835:80: E501 line too long (92 > 79 characters)
Line 844:80: E501 line too long (93 > 79 characters)
Line 847:80: E501 line too long (82 > 79 characters)
Line 849:80: E501 line too long (83 > 79 characters)
Line 851:80: E501 line too long (88 > 79 characters)
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Line 862:80: E501 line too long (85 > 79 characters)
Line 867:80: E501 line too long (101 > 79 characters)
Line 871:80: E501 line too long (114 > 79 characters)
Line 875:80: E501 line too long (101 > 79 characters)
Line 876:80: E501 line too long (111 > 79 characters)
Line 885:80: E501 line too long (89 > 79 characters)
Line 896:80: E501 line too long (100 > 79 characters)
Line 1015:80: E501 line too long (88 > 79 characters)
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Line 1020:80: E501 line too long (84 > 79 characters)
Line 1023:80: E501 line too long (88 > 79 characters)
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Line 1064:80: E501 line too long (84 > 79 characters)
Line 1139:80: E501 line too long (83 > 79 characters)
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Line 1297:80: E501 line too long (89 > 79 characters)
Line 1309:80: E501 line too long (81 > 79 characters)
Line 1310:80: E501 line too long (92 > 79 characters)
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Line 1317:80: E501 line too long (94 > 79 characters)
Line 1332:80: E501 line too long (85 > 79 characters)
Line 1333:80: E501 line too long (93 > 79 characters)
Line 1334:80: E501 line too long (92 > 79 characters)
Line 1403:55: W291 trailing whitespace
Line 1422:80: E501 line too long (93 > 79 characters)
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Line 1435:80: E501 line too long (85 > 79 characters)
Line 1440:80: E501 line too long (83 > 79 characters)
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Line 1602:80: E501 line too long (86 > 79 characters)
Line 1608:80: E501 line too long (84 > 79 characters)
Line 1610:9: E741 ambiguous variable name 'l'
Line 1712:80: E501 line too long (132 > 79 characters)
Line 1715:80: E501 line too long (104 > 79 characters)
Line 1841:80: E501 line too long (92 > 79 characters)
Line 1846:80: E501 line too long (83 > 79 characters)
Line 1895:80: E501 line too long (102 > 79 characters)
Line 1904:80: E501 line too long (82 > 79 characters)
Line 1931:80: E501 line too long (80 > 79 characters)
Line 1932:80: E501 line too long (81 > 79 characters)

Line 49:80: E501 line too long (126 > 79 characters)
Line 54:80: E501 line too long (111 > 79 characters)
Line 58:80: E501 line too long (82 > 79 characters)

Line 38:80: E501 line too long (89 > 79 characters)
Line 51:80: E501 line too long (88 > 79 characters)
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Line 89:80: E501 line too long (80 > 79 characters)
Line 172:17: E722 do not use bare 'except'
Line 183:21: E722 do not use bare 'except'

Line 58:80: E501 line too long (80 > 79 characters)
Line 82:9: E741 ambiguous variable name 'l'
Line 92:9: E741 ambiguous variable name 'l'
Line 101:9: E741 ambiguous variable name 'l'
Line 113:9: E741 ambiguous variable name 'l'
Line 117:80: E501 line too long (88 > 79 characters)
Line 157:9: E741 ambiguous variable name 'l'
Line 161:80: E501 line too long (88 > 79 characters)
Line 172:9: E741 ambiguous variable name 'l'
Line 179:9: E741 ambiguous variable name 'l'
Line 188:9: E741 ambiguous variable name 'l'
Line 200:9: E741 ambiguous variable name 'l'
Line 215:9: E741 ambiguous variable name 'l'
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Line 241:9: E741 ambiguous variable name 'l'
Line 253:9: E741 ambiguous variable name 'l'
Line 264:9: E741 ambiguous variable name 'l'
Line 279:9: E741 ambiguous variable name 'l'
Line 300:80: E501 line too long (82 > 79 characters)
Line 302:80: E501 line too long (80 > 79 characters)
Line 330:80: E501 line too long (85 > 79 characters)
Line 356:80: E501 line too long (93 > 79 characters)
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Line 445:80: E501 line too long (90 > 79 characters)
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Line 516:80: E501 line too long (90 > 79 characters)
Line 524:80: E501 line too long (93 > 79 characters)
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Line 13:9: E265 block comment should start with '# '
Line 14:9: E265 block comment should start with '# '
Line 15:9: E265 block comment should start with '# '

Line 109:80: E501 line too long (91 > 79 characters)
Line 193:9: E722 do not use bare 'except'

Line 32:80: E501 line too long (91 > 79 characters)
Line 41:13: E722 do not use bare 'except'
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Line 80:80: E501 line too long (89 > 79 characters)
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Line 263:80: E501 line too long (81 > 79 characters)
Line 272:80: E501 line too long (81 > 79 characters)
Line 295:14: E741 ambiguous variable name 'l'
Line 339:9: E722 do not use bare 'except'
Line 342:80: E501 line too long (120 > 79 characters)
Line 357:80: E501 line too long (88 > 79 characters)
Line 363:80: E501 line too long (84 > 79 characters)
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Line 523:80: E501 line too long (83 > 79 characters)
Line 534:80: E501 line too long (85 > 79 characters)
Line 569:44: E711 comparison to None should be 'if cond is None:'
Line 570:45: E711 comparison to None should be 'if cond is not None:'
Line 571:48: E711 comparison to None should be 'if cond is None:'
Line 586:80: E501 line too long (84 > 79 characters)
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Line 616:80: E501 line too long (111 > 79 characters)
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Line 712:80: E501 line too long (86 > 79 characters)
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Line 815:80: E501 line too long (99 > 79 characters)
Line 835:80: E501 line too long (988 > 79 characters)
Line 847:80: E501 line too long (859 > 79 characters)
Line 852:33: E711 comparison to None should be 'if cond is not None:'
Line 855:80: E501 line too long (83 > 79 characters)
Line 868:34: E711 comparison to None should be 'if cond is not None:'
Line 871:80: E501 line too long (84 > 79 characters)
Line 886:80: E501 line too long (192 > 79 characters)
Line 895:80: E501 line too long (104 > 79 characters)
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Line 912:38: E711 comparison to None should be 'if cond is not None:'
Line 913:80: E501 line too long (80 > 79 characters)
Line 927:80: E501 line too long (236 > 79 characters)
Line 928:80: E501 line too long (228 > 79 characters)
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Line 1149:80: E501 line too long (88 > 79 characters)
Line 1230:80: E501 line too long (100 > 79 characters)
Line 1232:80: E501 line too long (107 > 79 characters)
Line 1241:34: W601 .has_key() is deprecated, use 'in'
Line 1242:34: W601 .has_key() is deprecated, use 'in'
Line 1243:38: W601 .has_key() is deprecated, use 'in'
Line 1250:80: E501 line too long (82 > 79 characters)
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Line 23:80: E501 line too long (101 > 79 characters)
Line 27:80: E501 line too long (146 > 79 characters)
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Line 33:80: E501 line too long (101 > 79 characters)
Line 56:80: E501 line too long (89 > 79 characters)
Line 62:80: E501 line too long (163 > 79 characters)
Line 66:80: E501 line too long (159 > 79 characters)
Line 76:80: E501 line too long (97 > 79 characters)
Line 77:80: E501 line too long (80 > 79 characters)
Line 78:80: E501 line too long (80 > 79 characters)
Line 79:80: E501 line too long (80 > 79 characters)
Line 87:9: E722 do not use bare 'except'
Line 98:80: E501 line too long (161 > 79 characters)
Line 102:80: E501 line too long (174 > 79 characters)
Line 106:80: E501 line too long (158 > 79 characters)
Line 107:80: E501 line too long (113 > 79 characters)
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Line 127:80: E501 line too long (158 > 79 characters)
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Line 151:80: E501 line too long (92 > 79 characters)
Line 154:80: E501 line too long (135 > 79 characters)
Line 163:80: E501 line too long (109 > 79 characters)
Line 167:80: E501 line too long (110 > 79 characters)

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mbasil09 commented Dec 13, 2019

closes #39

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mbasil09 commented Dec 13, 2019

@yochannah @julie-sullivan
Try this. If you find some errors, do tell me, I'll try to fix those.

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yochannah commented Dec 13, 2019

@mbasil09 Thanks! I'll take a look at the functionality imminently. Do you think it's safe to ignore the long lines here and assume they'll be fixed in your other PR?

@yochannah yochannah self-requested a review December 13, 2019 11:52
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mbasil09 commented Dec 13, 2019

@yochannah
Please ignore the PEP8 bot here.
I am solving those queries in #65.

yochannah
yochannah approved these changes Dec 20, 2019
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query.dataframe() works as expected, returning a pandas dataframe, and the original iterator methods still work as they used to, preserving backwards compatibilty. @mbasil09 - this is perfect, thank you!

@yochannah yochannah merged commit 7060545 into intermine:dev Dec 20, 2019
@mbasil09 mbasil09 deleted the patch-1 branch December 20, 2019 19:18
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@mbasil09 @pep8speaks @yochannah