I am trying to use python and twill to automate a search on the PubMed Database, but right now I'm having problems getting one search to work. My base code looks like this:
from twill.commands import *
go("http://www.pubmed.com")
fv("1","term","macropahge")
showforms()
When I run that, I get this output:
Form name=EntrezForm (#1)
## ## __Name__________________ __Type___ __ID________ __Value__________________
1 None select database [] of []
2 None select database [] of ['gquery']
3 None select database [] of ['assembly']
4 None select database [] of ['bioproject']
5 None select database [] of ['biosample']
6 None select database [] of ['biosystems']
7 None select database [] of ['books']
8 None select database [] of ['clinvar']
9 None select database [] of ['clone']
10 None select database [] of ['cdd']
11 None select database [] of ['gap']
12 None select database [] of ['dbvar']
13 None select database [] of ['epigenomics']
14 None select database [] of ['nucest']
15 None select database [] of ['gene']
16 None select database [] of ['genome']
17 None select database [] of ['gds']
18 None select database [] of ['geoprofiles']
19 None select database [] of ['nucgss']
20 None select database [] of ['homologene']
21 None select database [] of ['medgen']
22 None select database [] of ['mesh']
23 None select database [] of ['ncbisearch']
24 None select database [] of ['nlmcatalog']
25 None select database [] of ['nuccore']
26 None select database [] of ['omim']
27 None select database [] of ['pmc']
28 None select database [] of ['popset']
29 None select database [] of ['probe']
30 None select database [] of ['protein']
31 None select database [] of ['proteinclusters']
32 None select database [] of ['pcassay']
33 None select database [] of ['pccompound']
34 None select database [] of ['pcsubstance']
35 None select database [] of ['pubmed']
36 None select database [] of ['pubmedhealth']
37 None select database [] of ['snp']
38 None select database [] of ['sra']
39 None select database [] of ['structure']
40 None select database [] of ['taxonomy']
41 None select database [] of ['toolkit']
42 None select database [] of ['toolkitall']
43 None select database [] of ['toolkitbook']
44 None select database [] of ['unigene']
45 term text term macropahge
46 1 None submi ... search
47 EntrezSystem2.PEntre ... hidden (None) home
48 EntrezSystem2.PEntre ... hidden (None)
49 EntrezSystem2.PEntre ... hidden (None) pubmed
50 EntrezSystem2.PEntre ... hidden (None) pubmed
51 EntrezSystem2.PEntre ... hidden (None)
52 EntrezSystem2.PEntre ... hidden (None)
53 EntrezSystem2.PEntre ... hidden (None)
54 EntrezSystem2.PEntre ... hidden (None)
55 EntrezSystem2.PEntre ... hidden (None)
56 EntrezSystem2.PEntre ... hidden (None)
57 EntrezSystem2.PEntre ... hidden (None)
58 EntrezSystem2.PEntre ... hidden (None)
59 EntrezSystem2.PEntre ... hidden (None)
60 EntrezSystem2.PEntre ... hidden (None)
61 EntrezSystem2.PEntre ... hidden (None)
62 p$a hidden p$a
63 p$l hidden p$l EntrezSystem2
64 p$st hidden p$st pubmed
65 SessionId hidden SessionId CE8B4A8E3C997DA1_0124SID
66 Snapshot hidden Snapshot /projects/entrez/pubmed/PubMedGroup@1.54
<generator object __call__ at 0x030B8170>
So I know my code is putting the search term in correctly, but when I submit, it does not work.
submit()
find("macrophage")
Traceback (most recent call last):
File "<pyshell#5>", line 1, in <module>
find("macrophage")
File "C:\Users\Ed\AppData\Roaming\Python\Python27\site-packages\twill\commands.py", line 239, in find
raise TwillAssertionError("no match to '%s'" % (what,))
TwillAssertionError: no match to 'macrophage'
So, I am submitting incorrectly or using the wrong submit box. I know the term macrophage will show up on the page when I search, so something is wrong in the submit step. Any help is appreciated. When I try garbage phrases like ";lkjasdlfkjasd", I expect "No items found" but I do not see that either.
