-
Notifications
You must be signed in to change notification settings - Fork 5
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
019a1e4
commit b656a9f
Showing
7 changed files
with
225 additions
and
19 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,197 @@ | ||
| import cProfile | ||
| import re | ||
| import os | ||
| from pymongo import MongoClient | ||
| from htmlmin.minify import html_minify | ||
| from settings import APP_JSON, APP_MOL2, APP_ARTICLES | ||
| from difflib import SequenceMatcher as SM | ||
| import ujson as json | ||
| from Levenshtein import ratio | ||
| #import json | ||
|
|
||
| Masses = dict(H=1.01, He=4.00, Li=6.94, Be=9.01, B=10.81, C=12.01, | ||
| N=14.01, O=16.00, F=19.00, Ne=20.18, Na=22.99, Mg=24.31, | ||
| Al=26.98, Si=28.09, P=30.97, S=32.07, Cl=35.45, Ar=39.95, | ||
| K=39.10, Ca=40.08, Sc=44.96, Ti=47.87, V=50.94, Cr=52.00, | ||
| Mn=54.94, Fe=55.85, Co=58.93, Ni=58.69, Cu=63.55, Zn=65.39, | ||
| Ga=69.72, Ge=72.61, As=74.92, Se=78.96, Br=79.90, Kr=83.80, | ||
| Rb=85.47, Sr=87.62, Y=88.91, Zr=91.22, Nb=92.91, Mo=95.94, | ||
| Tc=98.00, Ru=101.07, Rh=102.91, Pd=106.42, Ag=107.87, | ||
| Cd=112.41, In=114.82, Sn=118.71, Sb=121.76, Te=127.60, | ||
| I=126.90, Xe=131.29, Cs=132.91, Ba=137.33, La=138.91, | ||
| Ce=140.12, Pr=140.91, Nd=144.24, Pm=145.00, Sm=150.36, | ||
| Eu=151.96, Gd=157.25, Tb=158.93, Dy=162.50, Ho=164.93, | ||
| Er=167.26, Tm=168.93, Yb=173.04, Lu=174.97, Hf=178.49, | ||
| Ta=180.95, W=183.84, Re=186.21, Os=190.23, Ir=192.22, | ||
| Pt=195.08, Au=196.97, Hg=200.59, Tl=204.38, Pb=207.2, | ||
| Bi=208.98, Po=209.00, At=210.00, Rn=222.00, Fr=223.00, | ||
| Ra=226.00, Ac=227.00, Th=232.04, Pa=231.04, U=238.03, | ||
| Np=237.00, Pu=244.00, Am=243.00, Cm=247.00, Bk=247.00, | ||
| Cf=251.00, Es=252.00, Fm=257.00, Md=258.00, No=259.00, | ||
| Lr=262.00, Rf=261.00, Db=262.00, Sg=266.00, Bh=264.00, | ||
| Hs=269.00, Mt=268.00) | ||
|
|
||
|
|
||
| def chunks(l, n): | ||
| """ Yield successive n-sized chunks from l. | ||
| """ | ||
| for i in xrange(0, len(l), n): | ||
| yield l[i:i + n] | ||
|
|
||
| def similar(x, f, m0, query): | ||
| #print x | ||
| #if isinstance(x, list): | ||
| # score_list = map(lambda z: similar(z, f, m0, query), x) | ||
| # return sum(score_list) | ||
| #else: | ||
| # if x in query: | ||
| if query in x: | ||
| score = 10 + ratio(x.encode('utf8', 'ignore'), query.encode('utf8', 'ignore')) + m0 / formula2mass(f) | ||
| else: | ||
| score = ratio(x.encode('utf8', 'ignore'), query.encode('utf8', 'ignore')) + m0 / formula2mass(f) | ||
| return score | ||
|
|
||
| def formula2mass(f): | ||
| s = re.findall('([A-Z][a-z]?)([0-9]*)', f) | ||
| compoundweight = 0 | ||
| for element, count in s: | ||
| count = int(count or '1') | ||
| compoundweight += Masses[element] * count | ||
| return compoundweight | ||
| # element_pat = re.compile("([A-Z][a-z]?)(\d*)") | ||
| # sum_weight = 0 | ||
| # for (element_name, count) in element_pat.findall("CH3COOH"): | ||
| # if count == "": | ||
| # count = 1 | ||
| # else: | ||
| # count = int(count) | ||
| # sum_weight += Masses[element_name] * count | ||
| # return sum_weight | ||
|
|
||
| def get_json_data_file(key_first_two, key): | ||
| try: | ||
| # Loads the JSON file relevant to the InChI key requested | ||
| with open(os.path.join(APP_JSON, key_first_two + '/' + key + '.json')) as j: | ||
| return json.load(j) | ||
| except IOError: | ||
| # If we don't have the key, flash | ||
| return False | ||
|
|
||
| def browse(query="water", searchType="name", page_num="1"): | ||
|
|
||
| # Get the page number that is passed in | ||
| # If negative, make it positive | ||
| # If no page number is passed in, assume it is 1 | ||
| try: | ||
| page_num = abs(int(page_num)) | ||
| except ValueError: | ||
| page_num = 1 | ||
|
|
||
| # If there was no query searched for, flash and go to home | ||
| if query == "-1": | ||
| flash( | ||
| "You didn't search for anything! You have been redirected to the home page.", 'redirect') | ||
| return "" | ||
|
|
||
| # Initialize the Mongo client | ||
| client = MongoClient() | ||
| db = client.test | ||
|
|
||
| results = [] | ||
|
|
||
| # Do a text search for the passed in query | ||
| if searchType == 'formula': | ||
| query = query.upper() | ||
| elif searchType == 'tag': | ||
| searchType = 'tags' | ||
| elif searchType == 'synonym': | ||
| searchType = 'synonyms' | ||
| elif searchType == 'inchi': | ||
| searchType = 'inchikey' | ||
| query = query.upper() | ||
| if query in redirect_table.keys(): | ||
| query = redirect_table[query] | ||
| cursor = db.molecules.find({str(searchType): str(query)}).limit(500) | ||
|
|
||
| # Append all dicts in the cursor to a results array | ||
| for i in cursor: | ||
| i["mol2url"] = i["inchikey"][:2] + "/" + i["inchikey"] | ||
| i["json_data"] = get_json_data_file(i["inchikey"][:2], i["inchikey"]) | ||
| results.append(i) | ||
|
|
||
| if len(results) == 0: | ||
| cursor = db.molecules.find({"$text": {"$search": str(query)}}) | ||
| for i in cursor: | ||
| i["mol2url"] = i["inchikey"][:2] + "/" + i["inchikey"] | ||
| try: | ||
| i["json_data"] = get_json_data_file(i["inchikey"][:2], i["inchikey"]) | ||
| results.append(i) | ||
| except: | ||
| if len(list(cursor)) == 0: | ||
| rendered_html = "<html><body></body></html>" | ||
| min_html = html_minify(rendered_html.encode('utf8')) | ||
| return min_html | ||
|
|
||
|
|
||
| # Find lightest molecule to normalize mass-based search | ||
| temp = sorted( | ||
| map(lambda x: x["formula"], results), key=lambda x: formula2mass(x)) | ||
| lightest = formula2mass(temp[0]) if temp else 1e12 | ||
|
|
||
| results = sorted(results, key=lambda x: similar( | ||
| x[searchType], x['formula'], lightest, str(query)), reverse=True) | ||
|
|
||
| # If there is only one result, show that molecule page directly | ||
| total_results = len(results) | ||
| if total_results == 1: | ||
| return "" | ||
|
|
||
| # Split the reults array into chunks of 50 each for search pagination - 50 for AJAX (May want to change) | ||
| tempArr = list(chunks(results, 100)) | ||
|
|
||
| # The number of pages is just the total number of chunks | ||
| num_pages = len(tempArr) | ||
|
|
||
| # If the number of pages is more than 0, return the N-1th page to the template | ||
| # If the number of pages is 0, that means there are no results, so results = None | ||
| # If an index that doesn't exist is accessed (user manually making a URL query), | ||
| # then just go to the first page of results | ||
| try: | ||
| if num_pages > 0: | ||
| results = tempArr[page_num - 1] | ||
| else: | ||
| results = None | ||
| except IndexError: | ||
| results = tempArr[0] | ||
|
|
||
| page = {'id': "page-browse"} | ||
|
|
||
| # This is to tell the front-end which page the user is on | ||
| # If no page_num was passed in and there are multiple pages, first page is active | ||
| # Else if no page_num was passed in and there is one page, make active -1 to hide pager | ||
| # If the user passes is a page_num greater than the number of pages, then first page | ||
| # Else the active page is just whatever page the user is on | ||
| if page_num == -1 and num_pages > 1: | ||
| active = 1 | ||
| elif page_num == -1 and num_pages == 1: | ||
| active = -1 | ||
| else: | ||
| if page_num > num_pages: | ||
| active = 1 | ||
| else: | ||
| active = page_num | ||
|
|
||
| rendered_html = "<html><body></body></html>" | ||
| min_html = html_minify(rendered_html.encode('utf8')) | ||
| return min_html | ||
|
|
||
| import cProfile, pstats, StringIO | ||
| pr = cProfile.Profile() | ||
| pr.enable() | ||
| browse("acid", "name", "1") | ||
| pr.disable() | ||
| s = StringIO.StringIO() | ||
| sortby = 'tottime' | ||
| ps = pstats.Stats(pr, stream=s).sort_stats(sortby) | ||
| ps.print_stats() | ||
| print s.getvalue() |