We Keep Coding

Extracting Author name from XML tags using ElelemtTree

Following is the link to access the XML document:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=%2726161999%27&retmode=xml
I'm trying to extract the author Name which includes Lastname+Forename and make a string with only author name. I'm only being able to extract the details separately.
Following is the code that I have tried
r = requests.get(
'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id='26161999'&retmode=xml')
root = et.fromstring(r.content)
for elem in root.findall(".//ForeName"):
elem_ = elem.text
auth_name = list(elem_.split(" "))
authordata.append(auth_name)
val = [item if isinstance(item, str) else " ".join(item) for item in authordata] #flattening the list since its a nested list, converting nested list into string
seen = set()
val = [x for x in val if x not in seen and not seen.add(x)]
author= ' '.join(val)
print(author)
The output obtained from the above code is:
Elisa Riccardo Mirco Laura Valentina Antonio Sara Carla Borri Barbara
The expected output is a combination of firstname + Lastname:
Elisa Oppici Riccardo Montioli Mirco Dindo Laura Maccari Valentina Porcari Antonio Lorenzetto Chellini Sara Carla Borri Voltattorni Barbara Cellini

From your question I understand that you want a concatenation of ForeName and LastName for each author. You can achieve that by querying directly for those fields for each Author element in the tree and concatenate the corresponding text fields:
import xml.etree.ElementTree as et
import requests
r = requests.get(
'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id="26161999"&retmode=xml'
)
root = et.fromstring(r.content)
author_names = []
for author in root.findall(".//Author"):
fore_name = author.find('ForeName').text
last_name = author.find('LastName').text
author_names.append(fore_name + ' ' + last_name)
print(author_names)
# or to get your exact output format:
print(' '.join(author_names))

Error when creating dictionaries from text files

I've been working on a function which will update two dictionaries (similar authors, and awards they've won) from an open text file. The text file looks something like this:
Brabudy, Ray
Hugo Award
Nebula Award
Saturn Award
Ellison, Harlan
Heinlein, Robert
Asimov, Isaac
Clarke, Arthur
Ellison, Harlan
Nebula Award
Hugo Award
Locus Award
Stephenson, Neil
Vonnegut, Kurt
Morgan, Richard
Adams, Douglas
And so on. The first name is an authors name (last name first, first name last), followed by awards they may have won, and then authors who are similar to them. This is what I've got so far:
def load_author_dicts(text_file, similar_authors, awards_authors):
name_of_author = True
awards = False
similar = False
for line in text_file:
if name_of_author:
author = line.split(', ')
nameA = author[1].strip() + ' ' + author[0].strip()
name_of_author = False
awards = True
continue
if awards:
if ',' in line:
awards = False
similar = True
else:
if nameA in awards_authors:
listawards = awards_authors[nameA]
listawards.append(line.strip())
else:
listawards = []
listawards.append(line.strip()
awards_authors[nameA] = listawards
if similar:
if line == '\n':
similar = False
name_of_author = True
else:
sim_author = line.split(', ')
nameS = sim_author[1].strip() + ' ' + sim_author[0].strip()
if nameA in similar_authors:
similar_list = similar_authors[nameA]
similar_list.append(nameS)
else:
similar_list = []
similar_list.append(nameS)
similar_authors[nameA] = similar_list
continue
This works great! However, if the text file contains an entry with just a name (i.e. no awards, and no similar authors), it screws the whole thing up, generating an IndexError: list index out of range at this part Zname = sim_author[1].strip()+" "+sim_author[0].strip() )
How can I fix this? Maybe with a 'try, except function' in that area?
Also, I wouldn't mind getting rid of those continue functions, I wasn't sure how else to keep it going. I'm still pretty new to this, so any help would be much appreciated! I keep trying stuff and it changes another section I didn't want changed, so I figured I'd ask the experts.

How about doing it this way, just to get the data in, then manipulate the dictionary any ways you want.
test.txt contains your data
Brabudy, Ray
Hugo Award
Nebula Award
Saturn Award
Ellison, Harlan
Heinlein, Robert
Asimov, Isaac
Clarke, Arthur
Ellison, Harlan
Nebula Award
Hugo Award
Locus Award
Stephenson, Neil
Vonnegut, Kurt
Morgan, Richard
Adams, Douglas
And my code to parse it.
award_parse.py
data = {}
name = ""
awards = []
f = open("test.txt")
for l in f:
# make sure the line is not blank don't process blank lines
if not l.strip() == "":
# if this is a name and we're not already working on an author then set the author
# otherwise treat this as a new author and set the existing author to a key in the dictionary
if "," in l and len(name) == 0:
name = l.strip()
elif "," in l and len(name) > 0:
# check to see if recipient is already in list, add to end of existing list if he/she already
# exists.
if not name.strip() in data:
data[name] = awards
else:
data[name].extend(awards)
name = l.strip()
awards = []
# process any lines that are not blank, and do not have a ,
else:
awards.append(l.strip())
f.close()
for k, v in data.items():
print("%s got the following awards: %s" % (k,v))

read txt file into dictionary

I have the following type of document, where each person might have a couple of names and an associated description of features:
New person
name: ana
name: anna
name: ann
feature: A 65-year old woman that has no known health issues but has a medical history of Schizophrenia.
New person
name: tom
name: thomas
name: thimoty
name: tommy
feature: A 32-year old male that is known to be deaf.
New person
.....
What I would like is to read this file in a python dictionary, where each new person is id-ed.
i.e. Person with ID 1 will have the names ['ann','anna','ana']
and will have the feature ['A 65-year old woman that has no known health issues but has a medical history of Schizophrenia.' ]
Any suggestions?

Assuming that your input file is lo.txt. It can be added to dictionary this way:
file = open('lo.txt')
final_data = []
feature = []
names = []
for line in file.readlines():
if ("feature") in line:
data = line.replace("\n","").split(":")
feature=data[1]
final_data.append({
'names': names,
'feature': feature
})
names = []
feature = []
if ("name") in line:
data = line.replace("\n","").split(":")
names.append(data[1])
print final_data

Something like this might work
result = {}
f = open("document.txt")
contents = f.read()
info = contents.split('==== new person ===')
for i in range(len(info)):
info[i].split('\n')
names = []
features = []
for j in range(len(info[i])):
info[i][j].split(':')
if info[i][j][0] == 'name':
names.append(info[i][j][1])
else:
features.append(info[i][j][1])
result[i] = {'names': names,'features': features}
print(result)
This should give you something like:
{0: {'names': ['ana', 'anna', 'ann'], features:['...', '...']}}
e.t.c

Here is code that may work for you:
f = open("documents.txt").readlines()
f = [i.strip('\n') for i in f]
final_condition = f[len(f)-1]
f.remove(final_condition)
names = [i.split(":")[1] for i in f]
the_dict = {}
the_dict["names"] = names
the_dict["features"] = final_condition
print the_dict
All it does is split the names at ":" and take the last element of the resulting list (the names) and keep it for the list names.

Looping over a list within a dict

I'm new to python, so bear with me.
I have a dict containing lists:
ophav = {'ill': ['Giunta, John'], 'aut': ['Fox, Gardner', 'Doe, John'], 'clr': ['Mumle, Mads'], 'trl': ['Cat, Fat']}
The key names ('ill', 'aut', ...) and the number of items in the lists will be different on each run of the script.
I'd love to do something like:
opfmeta = []
for key, person in ophav.items():
opfmeta.append('<dc:creator role="' + key + '">' + person + '</dc:creator>')
I know this is not working ("cannot concatenate 'str' and 'list' objects") - I have to loop over the list within the dict somehow. How do I do that?
Edit: I need separate entries for each person, like:
<dc:creator role="ill">Fox, Gardner</dc:creator>
<dc:creator role="ill">Doe, John</dc:creator>

You can do that using ' & '.join():
opfmeta = []
for key, person in ophav.items():
opfmeta.append('<dc:creator role="' + key + '">' + ' & '.join(person) + '</dc:creator>')
This will join all the elements of the list together with the specified delimiter (in this case ' & ') so your result will something like this:
<dc:creator role="ill">Fox, Gardner & Doe, John</dc:creator>
You can check out the full working demonstration HERE
Answer to your updated question:
ophav = {'ill': ['Giunta, John'], 'aut': ['Fox, Gardner', 'Doe, John'], 'clr': ['Mumle, Mads'], 'trl': ['Cat, Fat']}
opfmeta = []
for key, person in ophav.items():
for i in person:
opfmeta.append('<dc:creator role="' + key + '">' + i + '</dc:creator>')
for i in opfmeta:
print i
[OUTPUT]
<dc:creator role="ill">Giunta, John</dc:creator>
<dc:creator role="aut">Fox, Gardner</dc:creator>
<dc:creator role="aut">Doe, John</dc:creator>
<dc:creator role="clr">Mumle, Mads</dc:creator>
<dc:creator role="trl">Cat, Fat</dc:creator>
NEW DEMO

Split a file into a list

This is what I have so far:
EX1 = open('ex1.txt')
EX1READ = EX1.read()
X1READ.splitlines(0)
['jk43:23 Marfield Lane:Plainview:NY:10023',
'axe99:315 W. 115th Street, Apt. 11B:New York:NY:10027',
'jab44:23 Rivington Street, Apt. 3R:New York:NY:10002',
'ap172:19 Boxer Rd.:New York:NY:10005',
'jb23:115 Karas Dr.:Jersey City:NJ:07127',
'jb29:119 Xylon Dr.:Jersey City:NJ:07127',
'ak9:234 Main Street:Philadelphia:PA:08990']
I'd like to be able to just grab the userId from this list and print it alphabetized. Any hints would be great.

userIds = []
EX1 = open('ex1.txt')
X1READ = EX1.readlines()
for line in X1READ:
useridname = line.split(" ")[0].split(":")[0];
userid = line.split(" ")[0].split(":")[1]
userIds.append([useridname, userid])
I'm sure there are more Pythonic ways to do this, but my method will return an list of lists, where each child list in the parent list is formatted like this:
["jk43", "23"]
So to get the first user id and id number, you'd do this:
firstUserId = userIds[0][0] + ": " + userIds[0][1]
Which would output
"jk43: 23"
To sort the list of IDs, you'd do something like this:
userIds = sorted(userIds, key = id: id[0])

Assuming the part before the first ":" is the userID you could do it in a more pythonic way like that:
with open("ex1.txt") as f:
lines = f.readlines()
userIDs = [l.split(":",1)[0] for l in lines]
print "\n".join(sorted(userIDs))

This does it:
IDs=[]
with open('ex1.txt', 'rb') as f:
for line in f:
IDs.append(line.split(':')[0])
print sorted(IDs)
Prints:
['ak9', 'ap172', 'axe99', 'jab44', 'jb23', 'jb29', 'jk43']
If your user id's like jk43:23 use IDs.append(line.split(' ')[0]) and that prints:
['ak9:234', 'ap172:19', 'axe99:315', 'jab44:23', 'jb23:115', 'jb29:119', 'jk43:23']
If your user ids are the number only, use IDs.append(int(line.split(' ')[0].split(':')[1])) which prints:
[19, 23, 23, 115, 119, 234, 315]