From c1228d71ab04252d84a6ee31d9928491bf7906dd Mon Sep 17 00:00:00 2001 From: semal Date: Mon, 6 Nov 2017 16:09:37 +0800 Subject: [PATCH] Init repo --- Controller/__init__.py | 0 Controller/get_mesh_code.py | 88 ++++++++ Controller/get_omim_tables.py | 51 +++++ Controller/get_transcripts.py | 53 +++++ Controller/process_mesh_code_result.py | 47 +++++ Controller/pubmed_controller.py | 267 +++++++++++++++++++++++++ LICENSE | 21 ++ README.md | 13 ++ blueprints/__init__.py | 0 blueprints/mesh.py | 36 ++++ blueprints/pubmed.py | 56 ++++++ config.py | 3 + generate_book.py | 46 +++++ requirements.txt | 26 +++ scrapy.cfg | 5 + sql/create_tables.sql | 6 + static/css/bootstrap.min.css | 5 + static/css/custom.css | 3 + static/js/bootstrap-table-zh-CN.min.js | 7 + static/js/bootstrap-table.min.js | 8 + static/js/bootstrap.file-input.js | 129 ++++++++++++ static/js/bootstrap.min.js | 7 + static/js/jquery.min.js | 5 + templates/base.html | 82 ++++++++ templates/download-transcripts.html | 11 + templates/index.html | 23 +++ templates/mesh/mesh_index.html | 54 +++++ templates/pubmed/formula_search.html | 28 +++ templates/pubmed/pmid_abstract.html | 44 ++++ web_server.py | 39 ++++ 30 files changed, 1163 insertions(+) create mode 100644 Controller/__init__.py create mode 100644 Controller/get_mesh_code.py create mode 100644 Controller/get_omim_tables.py create mode 100644 Controller/get_transcripts.py create mode 100644 Controller/process_mesh_code_result.py create mode 100644 Controller/pubmed_controller.py create mode 100644 LICENSE create mode 100644 README.md create mode 100644 blueprints/__init__.py create mode 100644 blueprints/mesh.py create mode 100644 blueprints/pubmed.py create mode 100644 config.py create mode 100644 generate_book.py create mode 100644 requirements.txt create mode 100644 scrapy.cfg create mode 100644 sql/create_tables.sql create mode 100644 static/css/bootstrap.min.css create mode 100644 static/css/custom.css create mode 100644 static/js/bootstrap-table-zh-CN.min.js create mode 100644 static/js/bootstrap-table.min.js create mode 100644 static/js/bootstrap.file-input.js create mode 100644 static/js/bootstrap.min.js create mode 100644 static/js/jquery.min.js create mode 100644 templates/base.html create mode 100644 templates/download-transcripts.html create mode 100644 templates/index.html create mode 100644 templates/mesh/mesh_index.html create mode 100644 templates/pubmed/formula_search.html create mode 100644 templates/pubmed/pmid_abstract.html create mode 100644 web_server.py diff --git a/Controller/__init__.py b/Controller/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/Controller/get_mesh_code.py b/Controller/get_mesh_code.py new file mode 100644 index 0000000..0141ae3 --- /dev/null +++ b/Controller/get_mesh_code.py @@ -0,0 +1,88 @@ +# coding=utf-8 +import multiprocessing +from time import sleep +import requests +import bs4 +import sys +from w3lib.html import remove_tags +import json + + +def get_mesh(phenotype): + """ + 模拟https://www.nlm.nih.gov/mesh/2016/mesh_browser/MBrowser.html页面的表单提交，获取数据。 + """ + try: + if phenotype.startswith('https://'): + r = requests.get(phenotype) + else: + url = 'https://www.nlm.nih.gov/cgi/mesh/2016/MB_cgi' + exact_submit = { + 'term': '%s' % phenotype, + 'exact': 'Find Exact Term' + } + # session = requests.session() + r = requests.post(url, data=exact_submit) + soup = bs4.BeautifulSoup(r.text, 'html.parser') + tags = soup.find_all("tr") + mesh_heading = '' + tree_numbers = [] + notes = [] + unique_id = '' + heading_mapped_to = {} + for tag in tags: + th = remove_tags(str(tag.find('th'))) + td = remove_tags(str(tag.find('td'))) + if th.strip() == 'MeSH Heading' or th.strip() == 'Name of Substance': + mesh_heading = td + elif th.strip() == 'Tree Number': + tree_numbers.append(td) + elif 'Note' in th: + notes.append(td) + elif th.strip() == 'Heading Mapped to': + # heading_mapped_to[td.strip()] = get_mesh(td.strip().replace('*', '')) + heading_mapped_to[td.strip()] = get_mesh( + 'https://www.nlm.nih.gov%s' % tag.find('a')['href'] + ) + elif th.strip() == 'Unique ID': + unique_id = td + record = { + 'phenotype': phenotype, + 'mesh_heading': mesh_heading, + 'tree_numbers': tree_numbers, + 'note': ';'.join(notes), + 'unique_id': unique_id, + 'heading_mapped_to': heading_mapped_to + } + return record + except: + sleep(10) + return { + 'phenotype': phenotype, + 'mesh_heading': 'error', + 'tree_numbers': 'error', + 'note': 'error', + 'unique_id': 'error', + 'heading_mapped_to': 'error', + } + + +def read_search_phenotypes(fp): + phenotypes = [] + with open(fp) as fi: + for line in fi: + if line.strip() == '': + continue + phenotypes.append(line.strip()) + return phenotypes + + +def batch(fp): + phenotypes = read_search_phenotypes(fp) + pool = multiprocessing.Pool(100) + result = pool.map(get_mesh, phenotypes) + json.dump(result, open('output/mesh_code_result.json', 'w')) + + +if __name__ == '__main__': + batch(sys.argv[1]) diff --git a/Controller/get_omim_tables.py b/Controller/get_omim_tables.py new file mode 100644 index 0000000..ccf15dc --- /dev/null +++ b/Controller/get_omim_tables.py @@ -0,0 +1,51 @@ +import os +import multiprocessing + + +def run(gene): + fn_list = os.listdir('result') + if '%s.tsv' % gene not in fn_list: + os.system( + 'aria2c --header="Cookie:donation-popup=true; ' + 'sessionid=o5tznyomgtr5x70wmej8hlyg4sck0k8z; _ga=GA1.2.801700580.1476441682" ' + '"https://omim.org/search/?index=geneMap&search=%s&start=1&limit=10000&format=tab" ' + '-o result/%s.tsv' % (gene, gene) + ) + + +def get_genes(): + genes = [] + with open('/home/jjiang/omim.txt') as fi: + for line in fi: + genes.append(line.strip()) + return genes + + +def multi_run(): + genes = get_genes() + pool = multiprocessing.Pool(100) + pool.map(run, genes) + + +def get_all_records(): + genes = get_genes() + for gene in genes: + with open('result/%s.tsv' % gene) as fi: + for line in fi: + if line.startswith('Gene Map Search'): + continue + try: + if gene in line.split('\t')[2]: + yield line + except IndexError: + continue + + +def generate_all(): + with open('all_record.tsv', 'w') as fo: + for line in get_all_records(): + fo.write(line) + + +if __name__ == '__main__': + generate_all() diff --git a/Controller/get_transcripts.py b/Controller/get_transcripts.py new file mode 100644 index 0000000..854a01a --- /dev/null +++ b/Controller/get_transcripts.py @@ -0,0 +1,53 @@ +import os +import urllib2 + +import bs4 + + +def get_ENST(enst_number): + cmd = 'wget "http://www.ensembl.org/Homo_sapiens/Export/Output/Transcript?db=core;flank3_display=0;' \ + 'flank5_display=0;output=fasta;t=%s;param=cdna;param=coding;param=peptide;param=utr5;param=utr3;' \ + 'param=exon;param=intron;genomic=unmasked;_format=Text" -O %s.fa' % (enst_number, enst_number) + os.system(cmd) + with open('%s.fa' % enst_number) as fi: + seq = fi.read() + os.system('rm %s.fa' % enst_number) + return seq + + +def get_uuid(nm_number): + url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=%s' % nm_number + response = urllib2.urlopen(url) + soup = bs4.BeautifulSoup(response.read(), 'html.parser') + id_list = [str(s).replace('', '').replace('', '') for s in soup('id')] + if len(id_list) == 1: + return id_list[0] + else: + return None + + +def get_NM(nm_number): + uuid = get_uuid(nm_number) + if uuid is None: + return '' + cmd = 'wget "https://www.ncbi.nlm.nih.gov//sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&' \ + 'report=fasta&sort=&id=%s&from=begin&to=end&maxplex=1" -O %s.fa' % (uuid, nm_number) + os.system(cmd) + with open('%s.fa' % nm_number) as fi: + seq = fi.read() + os.system('rm %s.fa' % nm_number) + return seq + + +def get_transcripts(accession_list): + seq_list = [] + for accession in accession_list: + if accession.startswith('ENST'): + seq_list.append(get_ENST(accession)) + elif accession.startswith('NM'): + seq_list.append(get_NM(accession)) + return '\n'.join(seq_list) + + +if __name__ == '__main__': + print get_uuid('NM_002944') diff --git a/Controller/process_mesh_code_result.py b/Controller/process_mesh_code_result.py new file mode 100644 index 0000000..0108ee9 --- /dev/null +++ b/Controller/process_mesh_code_result.py @@ -0,0 +1,47 @@ +import json +import csv +import sys + +reload(sys) +sys.setdefaultencoding('utf8') + + +def get_tree_numbers(rec): + tree_nums = [] + if rec['tree_numbers'] != 'error' and len(rec['tree_numbers']) > 0: + return rec['tree_numbers'] + elif rec['heading_mapped_to'] != 'error' and len(rec['heading_mapped_to'].keys()) > 0: + for k, v in rec['heading_mapped_to'].items(): + tree_nums.extend(get_tree_numbers(v)) + return tree_nums + else: + return tree_nums + + +def process(): + with open('output/mesh_code_result.json') as fi: + result = json.load(fi) + + tree_number_max_count = max([len(get_tree_numbers(record)) for record in result]) + + with open('output/mesh_code_result.csv', 'w') as fo: + writer = csv.writer(fo) + header_row = ['Phenotype', 'MeSH Heading/Name of Substance'] + header_row.extend(['Tree Number'] * tree_number_max_count) + header_row.append('Notes') + header_row.append('Heading Mapped to') + writer.writerow(header_row) + for record in result: + row = [record['phenotype'].strip(), record['mesh_heading'].strip()] + tree_numbers = get_tree_numbers(record) + empty = [''] * (tree_number_max_count - len(tree_numbers)) + for tn in tree_numbers: + row.append(tn.strip()) + for e in empty: + row.append(e) + row.append(record['note'].strip()) + row.append( + ';'.join(record['heading_mapped_to'].keys()) + if record['heading_mapped_to'] != 'error' else 'error' + ) + writer.writerow(row) diff --git a/Controller/pubmed_controller.py b/Controller/pubmed_controller.py new file mode 100644 index 0000000..2665cf4 --- /dev/null +++ b/Controller/pubmed_controller.py @@ -0,0 +1,267 @@ +import csv +import json +import multiprocessing +import os +import sqlite3 +import sys +import urllib2 +import bs4 + +reload(sys) +sys.setdefaultencoding('utf8') + + +def connect_db(): + conn = sqlite3.connect('db.sqlite') + return conn + + +def get_unique_snps(): + cursor = connect_db().execute('SELECT * FROM complete_res') + snps = [] + for row in cursor: + sub_snps = row[1].split(',') + snps.extend(sub_snps) + snps = list(set(snps)) + + with open('unique_snps.txt', 'w') as fo: + for snp in snps: + if snp == '': + continue + fo.write(snp.strip() + '\n') + + +def get_formulas_in_db(): + conn = connect_db() + cursor = conn.execute('SELECT formula FROM formulas') + formulas = [] + for row in cursor: + formulas.append(row[0]) + return formulas + + +def get_formula_id(formula): + conn = connect_db() + cursor = conn.execute( + 'SELECT formula_id FROM formulas WHERE formula = "%s"' % formula.replace('"', '""') + ) + formula_id = None + for row in cursor: + formula_id = row[0] + return formula_id + + +def get_complete_res_by_formula(formula): + conn = connect_db() + print 'Searching pubmeb...' + pmid_list = search_pubmed(formula) + print len(pmid_list), 'Got it!' + cursor = conn.execute( + 'SELECT pmid, mutations, title, abstract FROM complete_res ' + 'WHERE pmid IN (%s)' % ','.join(["'%s'" % pmid for pmid in pmid_list]) + ) + records = [] + for row in cursor: + snps = ', '.join(list(set([snp.strip() for snp in row[1].split(',')]))) + records.append([row[0], snps, row[2], row[3]]) + return records + + +def get_pmid_list_in_db(table='pubmed_papers'): + conn = connect_db() + cursor = conn.execute('SELECT pmid FROM %s' % table) + pmid_list = [] + for row in cursor: + pmid_list.append(row[0]) + return pmid_list + + +def scrapy_pmid_abstract(pmid_list): + print 'Start get pmid in db...' + pmid_in_db = get_pmid_list_in_db() + print 'Got', len(pmid_in_db), 'in database.', 'Start remove db including pmids...' + # pmids = ','.join([pmid for pmid in pmid_list if pmid not in pmid_in_db]) + pmid_list = list(set(pmid_list).difference(set(pmid_in_db))) + pmids = ','.join(pmid_list) + print 'Left', len(pmids.split(',')), 'Scrapy them!' + if pmids == '': + return 'Exist!' + os.system('rm pubmed_abstract.json') + os.system( + 'scrapy crawl fetch_pubmed_abstract -a pmids="%s" ' + '-o pubmed_abstract.json -t json' % pmids + ) + with open('pubmed_abstract.json') as fi: + res = fi.read() + if res.strip() == '': + return 'Got nothing!' + else: + return 'Got something!' + + +def insert_formula(formula): + os.system( + '(echo insert into formulas \\(formula\\) values \\(\\"%s\\"\\)\\;) ' + '| sqlite3 db.sqlite' % formula + ) + + +def insert_abstract(): + conn = connect_db() + with open('pubmed_abstract.json') as fi: + res = json.load(fi) + for rec in res: + if 'pmid' in rec.keys(): + pmid = rec['pmid'].strip() + title = rec['title'].strip().replace('"', '""') + abstract = rec['abstract'].replace('"', '""') if 'abstract' in rec.keys() else '' + abstract = abstract.strip() if abstract is not None else '' + conn.execute( + 'insert into pubmed_papers (pmid, title, abstract) ' + 'VALUES ("%s", "%s", "%s")' % (pmid, title, abstract) + ) + conn.commit() + conn.close() + + +def get_abstract_in_db(pmid_list): + conn = connect_db() + cursor = conn.execute('SELECT pmid, abstract FROM pubmed_papers') + abstract_list = [] + new_pmid_list = [] + for row in cursor: + if row[0] in pmid_list: + new_pmid_list.append(row[0]) + abstract_list.append(row[1]) + return new_pmid_list, abstract_list + + +def extract_snps_sub(args): + file_names = os.listdir('result') + print args[0] + os.system( + 'java -cp seth-1.3-jar-with-dependencies.jar ' + 'seth.ner.wrapper.SETHNERAppMut "%s" >result/%s.seth' % (args[0], args[1]) + ) + + +def clean_seth_files(pmid_list): + pmid_fn_list = ['%s.seth' % pi for pi in pmid_list] + fo = csv.writer(open('mentioned_snps.csv', 'w')) + for fn in os.listdir('result'): + if not fn.endswith('.seth'): + continue + if fn not in pmid_fn_list: + continue + snps = [] + with open('result/%s' % fn) as fi: + for line in fi: + if line.startswith('MutationMention'): + snps.append(line.split(',')[4].split('=')[1]) + fo.writerow( + [fn.split('.')[0], ','.join(snps)] + ) + + +def extract_snps(formula): + pmid_list = search_pubmed(formula) + print 'Get pmid in database...' + pmid_list_in_db = get_pmid_list_in_db('mentioned_snps') + # pmid_list = [pmid for pmid in pmid_list if pmid not in pmid_list_in_db] + pmid_list = list(set(pmid_list).difference(pmid_list_in_db)) + print 'Get abstract from database...' + pmid_list, abstract_list = get_abstract_in_db(pmid_list) + os.chdir('lib/seth') + pool = multiprocessing.Pool(10) + queue = [] + print 'Generating seth list...' + for abstract, pmid in zip(abstract_list, pmid_list): + queue.append((abstract, pmid)) + print 'Start extracting snps...' + pool.map(extract_snps_sub, queue) + print 'Cleaning seth files' + clean_seth_files(pmid_list) + os.chdir('../..') + conn = connect_db() + with open('lib/seth/mentioned_snps.csv') as fi: + reader = csv.reader(fi) + for row in reader: + pmid, mutations = row[0], row[1] + conn.execute( + 'REPLACE INTO mentioned_snps (pmid, mutations) ' + 'VALUES ("%s", "%s")' % (pmid, mutations) + ) + conn.commit() + conn.close() + + +def get_formulas(): + conn = connect_db() + formulas = [] + cursor = conn.execute('SELECT formula FROM formulas;') + for row in cursor: + formulas.append(row[0]) + return formulas + + +def search_pubmed(search_formula): + """ + Using search_formula to search papers though pubmed e-search api. + + Parameters + ----------- + search_formula : str + search term, like "?term=breast+cancer+china+chinese+human+mutation" + + Returns + -------- + pmid_list : list + list of pmid + """ + pmid_list = [] + base_url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' + url = '/'.join([base_url, search_formula]) + retstart = 0 + retmax = 5000 + size = retmax + print 'Start soup it...' + while size == retmax: + print len(pmid_list) + joined_url = '%s&retstart=%d&retmax=%d' % (url, retstart, retmax) + print joined_url + response = urllib2.urlopen(joined_url) + soup = bs4.BeautifulSoup(response.read(), 'html.parser') + id_list = [str(s).replace('', '').replace('', '') for s in soup('id')] + size = len(id_list) + pmid_list.extend(id_list) + retstart += retmax + print 'Soup finished!' + return pmid_list + + +def generate_csv_by_formula(formula): + pmid_list = search_pubmed(formula) + os.system('rm output/mentioned_snps.csv') + conn = connect_db() + cursor = conn.execute( + 'select pmid, mutations, title, abstract from complete_res ' + 'where pmid in (%s)' % ','.join(["'%s'" % pmid for pmid in pmid_list]) + ) + with open('output/mentioned_snps.csv', 'w') as fo: + csv_writer = csv.writer(fo) + csv_writer.writerow(['pmid', 'mutations', 'title', 'abstract']) + for row in cursor: + csv_writer.writerow(row) + + # os.system( + # 'sqlite3 -header -csv db.sqlite "select pmid, mutations ' + # 'from complete_res where pmid IN (%s);" ' + # '>mentioned_snps.csv' % ','.join(["'%s'" % pmid for pmid in pmid_list]) + # ) + + +if __name__ == '__main__': + search_pubmed( + '?term=%28chinese%5BTitle%2FAbstract%5D+OR+CHN%5BTitle%2FAbstract%5D+OR+Korea*%5BTitle%2FAbstract%5D+OR+Japan*%5BTitle%2FAbstract%5D+OR+China%5BTitle%2FAbstract%5D+OR+Taiwan*%5BTitle%2FAbstract%5D+OR+Singapore*%5BTitle%2FAbstract%5D+OR+Asian*%5BTitle%2FAbstract%5D%29+AND+%28single+nucleotide+polymorphism*%5BTitle%2FAbstract%5D+OR+SNP*%5BTitle%2FAbstract%5D+OR+variant*%5BTitle%2FAbstract%5D+OR+polymorphism*%5BTitle%2FAbstract%5D%29+AND+%28association*%5BTitle%2FAbstract%5D+OR+gwas%5BTitle%2FAbstract%5D+OR+genome+wide+association*%5BTitle%2FAbstract%5D+OR+genome-wide+association*%5BTitle%2FAbstract%5D+OR+genome-wide+meta-analysis*%5BTitle%2FAbstract%5D+OR+meta+analysis*%5BTitle%2FAbstract%5D+OR+meta-analysis*%5BTitle%2FAbstract%5D+OR+replication*%5BTitle%2FAbstract%5D%29+AND+%22humans%22%5BMeSH+Terms%5D' + ) + # insert_abstract() diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..246f5e5 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2016 GENOWISE + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..a3d8b7d --- /dev/null +++ b/README.md @@ -0,0 +1,13 @@ +## 目的 +DataFetch作为一个获取数据的爬虫程序，要满足公司所有数据抓取需求。对其他项目的进行提供数据支持。 +DataFetch也是一个独立的项目，将使用Scrapy框架进行开发。另外会提供一些接口服务来被其他人使用。 + + +## 需要支持的功能 +1. 从PubMed上搜索和批量下载文献的摘要。 +2. 从GWASdb上搜索和增量下载。 + + +## 现在的需求 +1. 芯片设计需要额外的20万个位点，我们希望*从文献中抓取到相关的位点信息*。包括位点的位置信息（可以是 +dbsnp号，可以是genomic location），位点相关的表型，位点的P值。 diff --git a/blueprints/__init__.py b/blueprints/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/blueprints/mesh.py b/blueprints/mesh.py new file mode 100644 index 0000000..43d9bdf --- /dev/null +++ b/blueprints/mesh.py @@ -0,0 +1,36 @@ +from flask import Blueprint, render_template, request, redirect, url_for, send_file +from werkzeug import secure_filename +from config import APP_FOLDER +from Controller.get_mesh_code import batch +from Controller.process_mesh_code_result import process + +mesh = Blueprint('mesh', __name__, template_folder='%s/templates/mesh' % APP_FOLDER) + + +@mesh.route('/upload_mesh_phenotypes', methods=['POST']) +def upload_phenotypes(): + print 'Start upload phenotypes file...' + upload_file = request.files['phenotypes'] + if upload_file: + print 'Found upload file!' + filename = secure_filename(upload_file.filename) + upload_file.save('upload/%s' % filename) + print 'Saved file!' + print 'Start get mesh code...' + batch('upload/%s' % filename) + print 'Done!' + process() + return 'output/mesh_code_result.csv' + + +@mesh.route('/download_result') +def download_mesh_result(): + return send_file( + 'output/mesh_code_result.csv', as_attachment=True, + attachment_filename='mesh_code_result.csv' + ) + + +@mesh.route('/mesh_classifier', methods=['GET']) +def mesh_index(): + return render_template('mesh_index.html') diff --git a/blueprints/pubmed.py b/blueprints/pubmed.py new file mode 100644 index 0000000..76aab27 --- /dev/null +++ b/blueprints/pubmed.py @@ -0,0 +1,56 @@ +from flask import Blueprint, render_template, request, redirect, url_for, send_file +from Controller.pubmed_controller import get_formulas, search_pubmed, scrapy_pmid_abstract, \ + insert_formula, insert_abstract, get_complete_res_by_formula, extract_snps, \ + generate_csv_by_formula +from config import APP_FOLDER + +pubmed = Blueprint('pubmed', __name__, template_folder='%s/templates/pubmed' % APP_FOLDER) + + +@pubmed.route('/pubmed_search') +def formula_search(): + formulas = get_formulas() + return render_template('formula_search.html', formulas=formulas) + + +@pubmed.route('/get_result', methods=['POST', 'GET']) +def get_result(): + formula = request.form.get('formula') + print 'Search pubmed...' + pmid_list = search_pubmed(formula) + print 'Got', len(pmid_list), 'from pubmed!' + res = scrapy_pmid_abstract(pmid_list) + print res + if res == 'Got nothing!': + return redirect(url_for('pubmed.formula_search')) + if res == 'Exist!': + return redirect(url_for('pubmed.view_pmid_abstract', formula=formula)) + print 'Insert formula...' + insert_formula(formula) + print 'Insert abstract...' + insert_abstract() + return redirect(url_for('pubmed.view_pmid_abstract', formula=formula)) + + +@pubmed.route('/formula/') +def view_pmid_abstract(formula): + records = get_complete_res_by_formula(formula) + return render_template('pmid_abstract.html', records=records, formula=formula) + + +@pubmed.route('/extract_snps', methods=['POST']) +def snps_extraction(): + formula = request.form.get('formula') + print 'Start extracting snps...' + extract_snps(formula) + return redirect(url_for('pubmed.view_pmid_abstract', formula=formula)) + + +@pubmed.route('/download_snps', methods=['POST']) +def download_snps(): + formula = request.form.get('formula') + generate_csv_by_formula(formula) + return send_file( + 'output/mentioned_snps.csv', as_attachment=True, + attachment_filename='mentioned_snps.csv' + ) diff --git a/config.py b/config.py new file mode 100644 index 0000000..2176359 --- /dev/null +++ b/config.py @@ -0,0 +1,3 @@ +import os + +APP_FOLDER = os.path.dirname(os.path.realpath(__file__)) diff --git a/generate_book.py b/generate_book.py new file mode 100644 index 0000000..eaa987d --- /dev/null +++ b/generate_book.py @@ -0,0 +1,46 @@ +# coding=utf-8 +import os +import sys + +reload(sys) +sys.setdefaultencoding('utf8') +import json + +fo = open(sys.argv[1]) +res = json.load(fo) +fo.close() +try: + os.mkdir('%s' % res[0]['book_title']) +except OSError: + pass + +fa = open('%s.md' % res[0]['book_title'], 'w') +fa.write("""title: %s +date: 2012-05-07 13:01:05 +category: + - 小说 +tag: + - %s +--- +""" % (res[0]['book_title'], res[0]['book_title'])) +for k in sorted(res, key=lambda x: int(x['chapter_order'])): + chapter_name = '第{:d}章 {chapter_name}'.format( + int(k['chapter_order']), + chapter_name=k['chapter_name'].split()[-1] + ) + fo = open('%s/%s.md' % (k['book_title'], chapter_name), 'w') + pre = """title: %s +categories: + - 小说 + - %s +tag: + - %s +date: 2012-05-07 12:01:05 +show: hide +--- +""" % (chapter_name, k['book_title'], k['book_title']) + fo.write(pre) + for p in k['chapter_content']: + fo.write('%s\n\n' % p.strip()) + fo.close() + fa.write('## [%s](../%s/%s)\n\n' % (chapter_name, k['book_title'], chapter_name)) diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..ed5fed4 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,26 @@ +bs4 +requests +attrs==16.2.0 +cffi==1.8.3 +cryptography==1.5.2 +cssselect==0.9.2 +enum34==1.1.6 +idna==2.1 +ipaddress==1.0.17 +lxml==3.6.4 +parsel==1.0.3 +pip==8.1.2 +pyasn1==0.1.9 +pyasn1-modules==0.0.8 +pycparser==2.14 +PyDispatcher==2.0.5 +pyOpenSSL==16.1.0 +queuelib==1.4.2 +Scrapy==1.2.0 +service-identity==16.0.0 +setuptools==28.3.0 +six==1.10.0 +Twisted==16.4.1 +w3lib==1.15.0 +wheel==0.30.0a0 +zope.interface==4.3.2 diff --git a/scrapy.cfg b/scrapy.cfg new file mode 100644 index 0000000..6b2ec7c --- /dev/null +++ b/scrapy.cfg @@ -0,0 +1,5 @@ +[settings] +default = data_fetch.settings + +[deploy] +project = data_fetch \ No newline at end of file diff --git a/sql/create_tables.sql b/sql/create_tables.sql new file mode 100644 index 0000000..1b42f78 --- /dev/null +++ b/sql/create_tables.sql @@ -0,0 +1,6 @@ +CREATE TABLE pubmed_papers ( + id TEXT PRIMARY KEY UNIQUE, + pmid TEXT, + title TEXT, + abstract TEXT +); \ No newline at end of file diff --git a/static/css/bootstrap.min.css b/static/css/bootstrap.min.css new file mode 100644 index 0000000..b6fe4e0 --- /dev/null +++ b/static/css/bootstrap.min.css @@ -0,0 +1,5 @@ +/*! + * Bootstrap v3.3.1 (http://getbootstrap.com) + * Copyright 2011-2014 Twitter, Inc. + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) + *//*! normalize.css v3.0.2 | MIT License | git.io/normalize */html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,menu,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background-color:transparent}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}dfn{font-style:italic}h1{margin:.67em 0;font-size:2em}mark{color:#000;background:#ff0}small{font-size:80%}sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:1em 40px}hr{height:0;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box}pre{overflow:auto}code,kbd,pre,samp{font-family:monospace,monospace;font-size:1em}button,input,optgroup,select,textarea{margin:0;font:inherit;color:inherit}button{overflow:visible}button,select{text-transform:none}button,html input[type=button],input[type=reset],input[type=submit]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0}input{line-height:normal}input[type=checkbox],input[type=radio]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;padding:0}input[type=number]::-webkit-inner-spin-button,input[type=number]::-webkit-outer-spin-button{height:auto}input[type=search]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield}input[type=search]::-webkit-search-cancel-button,input[type=search]::-webkit-search-decoration{-webkit-appearance:none}fieldset{padding:.35em .625em .75em;margin:0 2px;border:1px solid silver}legend{padding:0;border:0}textarea{overflow:auto}optgroup{font-weight:700}table{border-spacing:0;border-collapse:collapse}td,th{padding:0}/*! 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(max-width:991px){.hidden-sm{display:none!important}}@media (min-width:992px) and (max-width:1199px){.hidden-md{display:none!important}}@media (min-width:1200px){.hidden-lg{display:none!important}}.visible-print{display:none!important}@media print{.visible-print{display:block!important}table.visible-print{display:table}tr.visible-print{display:table-row!important}th.visible-print,td.visible-print{display:table-cell!important}}.visible-print-block{display:none!important}@media print{.visible-print-block{display:block!important}}.visible-print-inline{display:none!important}@media print{.visible-print-inline{display:inline!important}}.visible-print-inline-block{display:none!important}@media print{.visible-print-inline-block{display:inline-block!important}}@media print{.hidden-print{display:none!important}} \ No newline at end of file diff --git a/static/css/custom.css b/static/css/custom.css new file mode 100644 index 0000000..bc055b8 --- /dev/null +++ b/static/css/custom.css @@ -0,0 +1,3 @@ +body { + line-height: 2; +} \ No newline at end of file diff --git a/static/js/bootstrap-table-zh-CN.min.js b/static/js/bootstrap-table-zh-CN.min.js new file mode 100644 index 0000000..e903fdf --- /dev/null +++ b/static/js/bootstrap-table-zh-CN.min.js @@ -0,0 +1,7 @@ +/* +* bootstrap-table - v1.10.1 - 2016-02-17 +* https://github.com/wenzhixin/bootstrap-table +* Copyright (c) 2016 zhixin wen +* Licensed MIT License +*/ +!function(a){"use strict";a.fn.bootstrapTable.locales["zh-CN"]={formatLoadingMessage:function(){return"正在努力地加载数据中，请稍候……"},formatRecordsPerPage:function(a){return"每页显示 "+a+" 条记录"},formatShowingRows:function(a,b,c){return"显示第 "+a+" 到第 "+b+" 条记录，总共 "+c+" 条记录"},formatSearch:function(){return"搜索"},formatNoMatches:function(){return"没有找到匹配的记录"},formatPaginationSwitch:function(){return"隐藏/显示分页"},formatRefresh:function(){return"刷新"},formatToggle:function(){return"切换"},formatColumns:function(){return"列"}},a.extend(a.fn.bootstrapTable.defaults,a.fn.bootstrapTable.locales["zh-CN"])}(jQuery); \ No newline at end of file diff --git a/static/js/bootstrap-table.min.js b/static/js/bootstrap-table.min.js new file mode 100644 index 0000000..3fe39fc --- /dev/null +++ b/static/js/bootstrap-table.min.js @@ -0,0 +1,8 @@ +/* +* bootstrap-table - v1.10.1 - 2016-02-17 +* https://github.com/wenzhixin/bootstrap-table +* Copyright (c) 2016 zhixin wen +* Licensed MIT License +*/ +!function(a){"use strict";var b=null,c=function(a){var b=arguments,c=!0,d=1;return a=a.replace(/%s/g,function(){var a=b[d++];return"undefined"==typeof a?(c=!1,""):a}),c?a:""},d=function(b,c,d,e){var f="";return a.each(b,function(a,b){return b[c]===e?(f=b[d],!1):!0}),f},e=function(b,c){var d=-1;return a.each(b,function(a,b){return b.field===c?(d=a,!1):!0}),d},f=function(b){var c,d,e,f=0,g=[];for(c=0;cd;d++)g[c][d]=!1;for(c=0;ce;e++)g[c+e][k]=!0;for(e=0;j>e;e++)g[c][k+e]=!0}},g=function(){if(null===b){var c,d,e=a("

").addClass("fixed-table-scroll-inner"),f=a("

").addClass("fixed-table-scroll-outer");f.append(e),a("body").append(f),c=e[0].offsetWidth,f.css("overflow","scroll"),d=e[0].offsetWidth,c===d&&(d=f[0].clientWidth),f.remove(),b=c-d}return b},h=function(b,d,e,f){var g=d;if("string"==typeof d){var h=d.split(".");h.length>1?(g=window,a.each(h,function(a,b){g=g[b]})):g=window[d]}return"object"==typeof g?g:"function"==typeof g?g.apply(b,e):!g&&"string"==typeof d&&c.apply(this,[d].concat(e))?c.apply(this,[d].concat(e)):f},i=function(b,c,d){var e=Object.getOwnPropertyNames(b),f=Object.getOwnPropertyNames(c),g="";if(d&&e.length!==f.length)return!1;for(var h=0;h-1&&b[g]!==c[g])return!1;return!0},j=function(a){return"string"==typeof a?a.replace(/&/g,"&").replace(//g,">").replace(/"/g,""").replace(/'/g,"'").replace(/`/g,"`"):a},k=function(b){var c=0;return b.children().each(function(){c0||navigator.userAgent.match(/Trident.*rv\:11\./))},o=function(b,c){this.options=c,this.$el=a(b),this.$el_=this.$el.clone(),this.timeoutId_=0,this.timeoutFooter_=0,this.init()};o.DEFAULTS={classes:"table table-hover",locale:void 0,height:void 0,undefinedText:"-",sortName:void 0,sortOrder:"asc",striped:!1,columns:[[]],data:[],dataField:"rows",method:"get",url:void 0,ajax:void 0,cache:!0,contentType:"application/json",dataType:"json",ajaxOptions:{},queryParams:function(a){return a},queryParamsType:"limit",responseHandler:function(a){return a},pagination:!1,onlyInfoPagination:!1,sidePagination:"client",totalRows:0,pageNumber:1,pageSize:10,pageList:[10,25,50,100],paginationHAlign:"right",paginationVAlign:"bottom",paginationDetailHAlign:"left",paginationPreText:"‹",paginationNextText:"›",search:!1,searchOnEnterKey:!1,strictSearch:!1,searchAlign:"right",selectItemName:"btSelectItem",showHeader:!0,showFooter:!1,showColumns:!1,showPaginationSwitch:!1,showRefresh:!1,showToggle:!1,buttonsAlign:"right",smartDisplay:!0,escape:!1,minimumCountColumns:1,idField:void 0,uniqueId:void 0,cardView:!1,detailView:!1,detailFormatter:function(){return""},trimOnSearch:!0,clickToSelect:!1,singleSelect:!1,toolbar:void 0,toolbarAlign:"left",checkboxHeader:!0,sortable:!0,silentSort:!0,maintainSelected:!1,searchTimeOut:500,searchText:"",iconSize:void 0,iconsPrefix:"glyphicon",icons:{paginationSwitchDown:"glyphicon-collapse-down icon-chevron-down",paginationSwitchUp:"glyphicon-collapse-up icon-chevron-up",refresh:"glyphicon-refresh icon-refresh",toggle:"glyphicon-list-alt icon-list-alt",columns:"glyphicon-th icon-th",detailOpen:"glyphicon-plus icon-plus",detailClose:"glyphicon-minus icon-minus"},rowStyle:function(){return{}},rowAttributes:function(){return{}},onAll:function(){return!1},onClickCell:function(){return!1},onDblClickCell:function(){return!1},onClickRow:function(){return!1},onDblClickRow:function(){return!1},onSort:function(){return!1},onCheck:function(){return!1},onUncheck:function(){return!1},onCheckAll:function(){return!1},onUncheckAll:function(){return!1},onCheckSome:function(){return!1},onUncheckSome:function(){return!1},onLoadSuccess:function(){return!1},onLoadError:function(){return!1},onColumnSwitch:function(){return!1},onPageChange:function(){return!1},onSearch:function(){return!1},onToggle:function(){return!1},onPreBody:function(){return!1},onPostBody:function(){return!1},onPostHeader:function(){return!1},onExpandRow:function(){return!1},onCollapseRow:function(){return!1},onRefreshOptions:function(){return!1},onResetView:function(){return!1}},o.LOCALES=[],o.LOCALES["en-US"]=o.LOCALES.en={formatLoadingMessage:function(){return"Loading, please wait..."},formatRecordsPerPage:function(a){return c("%s records per page",a)},formatShowingRows:function(a,b,d){return c("Showing %s to %s of %s rows",a,b,d)},formatDetailPagination:function(a){return c("Showing %s rows",a)},formatSearch:function(){return"Search"},formatNoMatches:function(){return"No matching records found"},formatPaginationSwitch:function(){return"Hide/Show pagination"},formatRefresh:function(){return"Refresh"},formatToggle:function(){return"Toggle"},formatColumns:function(){return"Columns"},formatAllRows:function(){return"All"}},a.extend(o.DEFAULTS,o.LOCALES["en-US"]),o.COLUMN_DEFAULTS={radio:!1,checkbox:!1,checkboxEnabled:!0,field:void 0,title:void 0,titleTooltip:void 0,"class":void 0,align:void 0,halign:void 0,falign:void 0,valign:void 0,width:void 0,sortable:!1,order:"asc",visible:!0,switchable:!0,clickToSelect:!0,formatter:void 0,footerFormatter:void 0,events:void 0,sorter:void 0,sortName:void 0,cellStyle:void 0,searchable:!0,searchFormatter:!0,cardVisible:!0},o.EVENTS={"all.bs.table":"onAll","click-cell.bs.table":"onClickCell","dbl-click-cell.bs.table":"onDblClickCell","click-row.bs.table":"onClickRow","dbl-click-row.bs.table":"onDblClickRow","sort.bs.table":"onSort","check.bs.table":"onCheck","uncheck.bs.table":"onUncheck","check-all.bs.table":"onCheckAll","uncheck-all.bs.table":"onUncheckAll","check-some.bs.table":"onCheckSome","uncheck-some.bs.table":"onUncheckSome","load-success.bs.table":"onLoadSuccess","load-error.bs.table":"onLoadError","column-switch.bs.table":"onColumnSwitch","page-change.bs.table":"onPageChange","search.bs.table":"onSearch","toggle.bs.table":"onToggle","pre-body.bs.table":"onPreBody","post-body.bs.table":"onPostBody","post-header.bs.table":"onPostHeader","expand-row.bs.table":"onExpandRow","collapse-row.bs.table":"onCollapseRow","refresh-options.bs.table":"onRefreshOptions","reset-view.bs.table":"onResetView"},o.prototype.init=function(){this.initLocale(),this.initContainer(),this.initTable(),this.initHeader(),this.initData(),this.initFooter(),this.initToolbar(),this.initPagination(),this.initBody(),this.initSearchText(),this.initServer()},o.prototype.initLocale=function(){if(this.options.locale){var b=this.options.locale.split(/-|_/);b[0].toLowerCase(),b[1]&&b[1].toUpperCase(),a.fn.bootstrapTable.locales[this.options.locale]?a.extend(this.options,a.fn.bootstrapTable.locales[this.options.locale]):a.fn.bootstrapTable.locales[b.join("-")]?a.extend(this.options,a.fn.bootstrapTable.locales[b.join("-")]):a.fn.bootstrapTable.locales[b[0]]&&a.extend(this.options,a.fn.bootstrapTable.locales[b[0]])}},o.prototype.initContainer=function(){this.$container=a(['
','
',"top"===this.options.paginationVAlign||"both"===this.options.paginationVAlign?'
':"",'
','
','
','
',this.options.formatLoadingMessage(),"
","
",'
',"bottom"===this.options.paginationVAlign||"both"===this.options.paginationVAlign?'
':"","
","
"].join("")),this.$container.insertAfter(this.$el),this.$tableContainer=this.$container.find(".fixed-table-container"),this.$tableHeader=this.$container.find(".fixed-table-header"),this.$tableBody=this.$container.find(".fixed-table-body"),this.$tableLoading=this.$container.find(".fixed-table-loading"),this.$tableFooter=this.$container.find(".fixed-table-footer"),this.$toolbar=this.$container.find(".fixed-table-toolbar"),this.$pagination=this.$container.find(".fixed-table-pagination"),this.$tableBody.append(this.$el),this.$container.after('
'),this.$el.addClass(this.options.classes),this.options.striped&&this.$el.addClass("table-striped"),-1!==a.inArray("table-no-bordered",this.options.classes.split(" "))&&this.$tableContainer.addClass("table-no-bordered")},o.prototype.initTable=function(){var b=this,c=[],d=[];this.$header=this.$el.find(">thead"),this.$header.length||(this.$header=a("").appendTo(this.$el)),this.$header.find("tr").each(function(){var b=[];a(this).find("th").each(function(){b.push(a.extend({},{title:a(this).html(),"class":a(this).attr("class"),titleTooltip:a(this).attr("title"),rowspan:a(this).attr("rowspan")?+a(this).attr("rowspan"):void 0,colspan:a(this).attr("colspan")?+a(this).attr("colspan"):void 0},a(this).data()))}),c.push(b)}),a.isArray(this.options.columns[0])||(this.options.columns=[this.options.columns]),this.options.columns=a.extend(!0,[],c,this.options.columns),this.columns=[],f(this.options.columns),a.each(this.options.columns,function(c,d){a.each(d,function(d,e){e=a.extend({},o.COLUMN_DEFAULTS,e),"undefined"!=typeof e.fieldIndex&&(b.columns[e.fieldIndex]=e),b.options.columns[c][d]=e})}),this.options.data.length||(this.$el.find(">tbody>tr").each(function(){var c={};c._id=a(this).attr("id"),c._class=a(this).attr("class"),c._data=l(a(this).data()),a(this).find("td").each(function(d){var e=b.columns[d].field;c[e]=a(this).html(),c["_"+e+"_id"]=a(this).attr("id"),c["_"+e+"_class"]=a(this).attr("class"),c["_"+e+"_rowspan"]=a(this).attr("rowspan"),c["_"+e+"_title"]=a(this).attr("title"),c["_"+e+"_data"]=l(a(this).data())}),d.push(c)}),this.options.data=d)},o.prototype.initHeader=function(){var b=this,d={},e=[];this.header={fields:[],styles:[],classes:[],formatters:[],events:[],sorters:[],sortNames:[],cellStyles:[],searchables:[]},a.each(this.options.columns,function(f,g){e.push(""),0==f&&!b.options.cardView&&b.options.detailView&&e.push(c('
',b.options.columns.length)),a.each(g,function(a,f){var g="",h="",i="",j="",k=c(' class="%s"',f["class"]),l=(b.options.sortOrder||f.order,"px"),m=f.width;if(void 0===f.width||b.options.cardView||"string"==typeof f.width&&-1!==f.width.indexOf("%")&&(l="%"),f.width&&"string"==typeof f.width&&(m=f.width.replace("%","").replace("px","")),h=c("text-align: %s; ",f.halign?f.halign:f.align),i=c("text-align: %s; ",f.align),j=c("vertical-align: %s; ",f.valign),j+=c("width: %s; ",!f.checkbox&&!f.radio||m?m?m+l:void 0:"36px"),"undefined"!=typeof f.fieldIndex){if(b.header.fields[f.fieldIndex]=f.field,b.header.styles[f.fieldIndex]=i+j,b.header.classes[f.fieldIndex]=k,b.header.formatters[f.fieldIndex]=f.formatter,b.header.events[f.fieldIndex]=f.events,b.header.sorters[f.fieldIndex]=f.sorter,b.header.sortNames[f.fieldIndex]=f.sortName,b.header.cellStyles[f.fieldIndex]=f.cellStyle,b.header.searchables[f.fieldIndex]=f.searchable,!f.visible)return;if(b.options.cardView&&!f.cardVisible)return;d[f.field]=f}e.push(""),e.push(c('
',b.options.sortable&&f.sortable?"sortable both":"")),g=f.title,f.checkbox&&(!b.options.singleSelect&&b.options.checkboxHeader&&(g=''),b.header.stateField=f.field),f.radio&&(g="",b.header.stateField=f.field,b.options.singleSelect=!0),e.push(g),e.push("
"),e.push('
'),e.push("
"),e.push("")}),e.push("")}),this.$header.html(e.join("")),this.$header.find("th[data-field]").each(function(){a(this).data(d[a(this).data("field")])}),this.$container.off("click",".th-inner").on("click",".th-inner",function(c){var d=a(this);return d.closest(".bootstrap-table")[0]!==b.$container[0]?!1:void(b.options.sortable&&d.parent().data().sortable&&b.onSort(c))}),this.$header.children().children().off("keypress").on("keypress",function(c){if(b.options.sortable&&a(this).data().sortable){var d=c.keyCode||c.which;13==d&&b.onSort(c)}}),!this.options.showHeader||this.options.cardView?(this.$header.hide(),this.$tableHeader.hide(),this.$tableLoading.css("top",0)):(this.$header.show(),this.$tableHeader.show(),this.$tableLoading.css("top",this.$header.outerHeight()+1),this.getCaret()),this.$selectAll=this.$header.find('[name="btSelectAll"]'),this.$selectAll.off("click").on("click",function(){var c=a(this).prop("checked");b[c?"checkAll":"uncheckAll"](),b.updateSelected()})},o.prototype.initFooter=function(){!this.options.showFooter||this.options.cardView?this.$tableFooter.hide():this.$tableFooter.show()},o.prototype.initData=function(a,b){this.data="append"===b?this.data.concat(a):"prepend"===b?[].concat(a).concat(this.data):a||this.options.data,this.options.data="append"===b?this.options.data.concat(a):"prepend"===b?[].concat(a).concat(this.options.data):this.data,"server"!==this.options.sidePagination&&this.initSort()},o.prototype.initSort=function(){var b=this,c=this.options.sortName,d="desc"===this.options.sortOrder?-1:1,e=a.inArray(this.options.sortName,this.header.fields);-1!==e&&this.data.sort(function(f,g){b.header.sortNames[e]&&(c=b.header.sortNames[e]);var i=m(f,c,b.options.escape),j=m(g,c,b.options.escape),k=h(b.header,b.header.sorters[e],[i,j]);return void 0!==k?d*k:((void 0===i||null===i)&&(i=""),(void 0===j||null===j)&&(j=""),a.isNumeric(i)&&a.isNumeric(j)?(i=parseFloat(i),j=parseFloat(j),j>i?-1*d:d):i===j?0:("string"!=typeof i&&(i=i.toString()),-1===i.localeCompare(j)?-1*d:d))})},o.prototype.onSort=function(b){var c="keypress"===b.type?a(b.currentTarget):a(b.currentTarget).parent(),d=this.$header.find("th").eq(c.index());return this.$header.add(this.$header_).find("span.order").remove(),this.options.sortName===c.data("field")?this.options.sortOrder="asc"===this.options.sortOrder?"desc":"asc":(this.options.sortName=c.data("field"),this.options.sortOrder="asc"===c.data("order")?"desc":"asc"),this.trigger("sort",this.options.sortName,this.options.sortOrder),c.add(d).data("order",this.options.sortOrder),this.getCaret(),"server"===this.options.sidePagination?void this.initServer(this.options.silentSort):(this.initSort(),void this.initBody())},o.prototype.initToolbar=function(){var b,d,f=this,g=[],i=0,j=0;this.$toolbar.find(".bars").children().length&&a("body").append(a(this.options.toolbar)),this.$toolbar.html(""),("string"==typeof this.options.toolbar||"object"==typeof this.options.toolbar)&&a(c('
',this.options.toolbarAlign)).appendTo(this.$toolbar).append(a(this.options.toolbar)),g=[c('
',this.options.buttonsAlign,this.options.buttonsAlign)],"string"==typeof this.options.icons&&(this.options.icons=h(null,this.options.icons)),this.options.showPaginationSwitch&&g.push(c('"),this.options.showRefresh&&g.push(c('"),this.options.showToggle&&g.push(c('"),this.options.showColumns&&(g.push(c('
',this.options.formatColumns()),'",'","
")),g.push("
"),(this.showToolbar||g.length>2)&&this.$toolbar.append(g.join("")),this.options.showPaginationSwitch&&this.$toolbar.find('button[name="paginationSwitch"]').off("click").on("click",a.proxy(this.togglePagination,this)),this.options.showRefresh&&this.$toolbar.find('button[name="refresh"]').off("click").on("click",a.proxy(this.refresh,this)),this.options.showToggle&&this.$toolbar.find('button[name="toggle"]').off("click").on("click",function(){f.toggleView()}),this.options.showColumns&&(b=this.$toolbar.find(".keep-open"),j<=this.options.minimumCountColumns&&b.find("input").prop("disabled",!0),b.find("li").off("click").on("click",function(a){a.stopImmediatePropagation()}),b.find("input").off("click").on("click",function(){var b=a(this);f.toggleColumn(e(f.columns,a(this).data("field")),b.prop("checked"),!1),f.trigger("column-switch",a(this).data("field"),b.prop("checked"))})),this.options.search&&(g=[],g.push('
',c('',this.options.formatSearch()),"
"),this.$toolbar.append(g.join("")),d=this.$toolbar.find(".search input"),d.off("keyup drop").on("keyup drop",function(a){f.options.searchOnEnterKey&&13!==a.keyCode||(clearTimeout(i),i=setTimeout(function(){f.onSearch(a)},f.options.searchTimeOut))}),n()&&d.off("mouseup").on("mouseup",function(a){clearTimeout(i),i=setTimeout(function(){f.onSearch(a)},f.options.searchTimeOut)}))},o.prototype.onSearch=function(b){var c=a.trim(a(b.currentTarget).val());this.options.trimOnSearch&&a(b.currentTarget).val()!==c&&a(b.currentTarget).val(c),c!==this.searchText&&(this.searchText=c,this.options.searchText=c,this.options.pageNumber=1,this.initSearch(),this.updatePagination(),this.trigger("search",c))},o.prototype.initSearch=function(){var b=this;if("server"!==this.options.sidePagination){var c=this.searchText&&this.searchText.toLowerCase(),d=a.isEmptyObject(this.filterColumns)?null:this.filterColumns;this.data=d?a.grep(this.options.data,function(b){for(var c in d)if(a.isArray(d[c])){if(-1===a.inArray(b[c],d[c]))return!1}else if(b[c]!==d[c])return!1;return!0}):this.options.data,this.data=c?a.grep(this.data,function(d,f){for(var g in d){g=a.isNumeric(g)?parseInt(g,10):g;var i=d[g],j=b.columns[e(b.columns,g)],k=a.inArray(g,b.header.fields);j&&j.searchFormatter&&(i=h(j,b.header.formatters[k],[i,d,f],i));var l=a.inArray(g,b.header.fields);if(-1!==l&&b.header.searchables[l]&&("string"==typeof i||"number"==typeof i))if(b.options.strictSearch){if((i+"").toLowerCase()===c)return!0}else if(-1!==(i+"").toLowerCase().indexOf(c))return!0}return!1}):this.data}},o.prototype.initPagination=function(){if(!this.options.pagination)return void this.$pagination.hide();this.$pagination.show();var b,d,e,f,g,h,i,j,k,l=this,m=[],n=!1,o=this.getData();if("server"!==this.options.sidePagination&&(this.options.totalRows=o.length),this.totalPages=0,this.options.totalRows){if(this.options.pageSize===this.options.formatAllRows())this.options.pageSize=this.options.totalRows,n=!0;else if(this.options.pageSize===this.options.totalRows){var p="string"==typeof this.options.pageList?this.options.pageList.replace("[","").replace("]","").replace(/ /g,"").toLowerCase().split(","):this.options.pageList;a.inArray(this.options.formatAllRows().toLowerCase(),p)>-1&&(n=!0)}this.totalPages=~~((this.options.totalRows-1)/this.options.pageSize)+1,this.options.totalPages=this.totalPages}if(this.totalPages>0&&this.options.pageNumber>this.totalPages&&(this.options.pageNumber=this.totalPages),this.pageFrom=(this.options.pageNumber-1)*this.options.pageSize+1,this.pageTo=this.options.pageNumber*this.options.pageSize,this.pageTo>this.options.totalRows&&(this.pageTo=this.options.totalRows),m.push('
','',this.options.onlyInfoPagination?this.options.formatDetailPagination(this.options.totalRows):this.options.formatShowingRows(this.pageFrom,this.pageTo,this.options.totalRows),""),!this.options.onlyInfoPagination){m.push('');var q=[c('',"top"===this.options.paginationVAlign||"both"===this.options.paginationVAlign?"dropdown":"dropup"),'",'"),m.push(this.options.formatRecordsPerPage(q.join(""))),m.push(""),m.push("
",'")}this.$pagination.html(m.join("")),this.options.onlyInfoPagination||(f=this.$pagination.find(".page-list a"),g=this.$pagination.find(".page-first"),h=this.$pagination.find(".page-pre"),i=this.$pagination.find(".page-next"),j=this.$pagination.find(".page-last"),k=this.$pagination.find(".page-number"),this.options.smartDisplay&&(this.totalPages<=1&&this.$pagination.find("div.pagination").hide(),(r.length<2||this.options.totalRows<=r[0])&&this.$pagination.find("span.page-list").hide(),this.$pagination[this.getData().length?"show":"hide"]()),n&&(this.options.pageSize=this.options.formatAllRows()),f.off("click").on("click",a.proxy(this.onPageListChange,this)),g.off("click").on("click",a.proxy(this.onPageFirst,this)),h.off("click").on("click",a.proxy(this.onPagePre,this)),i.off("click").on("click",a.proxy(this.onPageNext,this)),j.off("click").on("click",a.proxy(this.onPageLast,this)),k.off("click").on("click",a.proxy(this.onPageNumber,this)))},o.prototype.updatePagination=function(b){b&&a(b.currentTarget).hasClass("disabled")||(this.options.maintainSelected||this.resetRows(),this.initPagination(),"server"===this.options.sidePagination?this.initServer():this.initBody(),this.trigger("page-change",this.options.pageNumber,this.options.pageSize))},o.prototype.onPageListChange=function(b){var c=a(b.currentTarget);c.parent().addClass("active").siblings().removeClass("active"),this.options.pageSize=c.text().toUpperCase()===this.options.formatAllRows().toUpperCase()?this.options.formatAllRows():+c.text(),this.$toolbar.find(".page-size").text(this.options.pageSize),this.updatePagination(b)},o.prototype.onPageFirst=function(a){this.options.pageNumber=1,this.updatePagination(a)},o.prototype.onPagePre=function(a){this.options.pageNumber-1==0?this.options.pageNumber=this.options.totalPages:this.options.pageNumber--,this.updatePagination(a)},o.prototype.onPageNext=function(a){this.options.pageNumber+1>this.options.totalPages?this.options.pageNumber=1:this.options.pageNumber++,this.updatePagination(a)},o.prototype.onPageLast=function(a){this.options.pageNumber=this.totalPages,this.updatePagination(a)},o.prototype.onPageNumber=function(b){this.options.pageNumber!==+a(b.currentTarget).text()&&(this.options.pageNumber=+a(b.currentTarget).text(),this.updatePagination(b))},o.prototype.initBody=function(b){var f=this,g=[],i=this.getData();this.trigger("pre-body",i),this.$body=this.$el.find(">tbody"),this.$body.length||(this.$body=a("").appendTo(this.$el)),this.options.pagination&&"server"!==this.options.sidePagination||(this.pageFrom=1,this.pageTo=i.length);for(var k=this.pageFrom-1;k"),this.options.cardView&&g.push(c('',this.header.fields.length)),!this.options.cardView&&this.options.detailView&&g.push("",'',c('',this.options.iconsPrefix,this.options.icons.detailOpen),"",""),a.each(this.header.fields,function(b,i){var j="",l=m(n,i,f.options.escape),q="",r={},s="",t=f.header.classes[b],u="",v="",w="",x=f.columns[e(f.columns,i)];if(x.visible){if(o=c('style="%s"',p.concat(f.header.styles[b]).join("; ")),l=h(x,f.header.formatters[b],[l,n,k],l),n["_"+i+"_id"]&&(s=c(' id="%s"',n["_"+i+"_id"])),n["_"+i+"_class"]&&(t=c(' class="%s"',n["_"+i+"_class"])),n["_"+i+"_rowspan"]&&(v=c(' rowspan="%s"',n["_"+i+"_rowspan"])),n["_"+i+"_title"]&&(w=c(' title="%s"',n["_"+i+"_title"])),r=h(f.header,f.header.cellStyles[b],[l,n,k],r),r.classes&&(t=c(' class="%s"',r.classes)),r.css){var y=[];for(var z in r.css)y.push(z+": "+r.css[z]);o=c('style="%s"',y.concat(f.header.styles[b]).join("; "))}n["_"+i+"_data"]&&!a.isEmptyObject(n["_"+i+"_data"])&&a.each(n["_"+i+"_data"],function(a,b){"index"!==a&&(u+=c(' data-%s="%s"',a,b))}),x.checkbox||x.radio?(q=x.checkbox?"checkbox":q,q=x.radio?"radio":q,j=[c(f.options.cardView?'
':'',x["class"]||""),"",f.header.formatters[b]&&"string"==typeof l?l:"",f.options.cardView?"
":""].join(""),n[f.header.stateField]=l===!0||l&&l.checked):(l="undefined"==typeof l||null===l?f.options.undefinedText:l,j=f.options.cardView?['
',f.options.showHeader?c('%s',o,d(f.columns,"field","title",i)):"",c('%s',l),"
"].join(""):[c("",s,t,o,u,v,w),l,""].join(""),f.options.cardView&&f.options.smartDisplay&&""===l&&(j='
')),g.push(j)}}),this.options.cardView&&g.push(""),g.push("")}g.length||g.push('',c('%s',this.$header.find("th").length,this.options.formatNoMatches()),""),this.$body.html(g.join("")),b||this.scrollTo(0),this.$body.find("> tr[data-index] > td").off("click dblclick").on("click dblclick",function(b){var d=a(this),g=d.parent(),h=f.data[g.data("index")],i=d[0].cellIndex,j=f.header.fields[f.options.detailView&&!f.options.cardView?i-1:i],k=f.columns[e(f.columns,j)],l=m(h,j,f.options.escape);if(!d.find(".detail-icon").length&&(f.trigger("click"===b.type?"click-cell":"dbl-click-cell",j,l,h,d),f.trigger("click"===b.type?"click-row":"dbl-click-row",h,g),"click"===b.type&&f.options.clickToSelect&&k.clickToSelect)){var n=g.find(c('[name="%s"]',f.options.selectItemName));n.length&&n[0].click()}}),this.$body.find("> tr[data-index] > td > .detail-icon").off("click").on("click",function(){var b=a(this),d=b.parent().parent(),e=d.data("index"),g=i[e];if(d.next().is("tr.detail-view"))b.find("i").attr("class",c("%s %s",f.options.iconsPrefix,f.options.icons.detailOpen)),d.next().remove(),f.trigger("collapse-row",e,g);else{b.find("i").attr("class",c("%s %s",f.options.iconsPrefix,f.options.icons.detailClose)),d.after(c('',d.find("td").length));var j=d.next().find("td"),k=h(f.options,f.options.detailFormatter,[e,g,j],"");1===j.length&&j.append(k),f.trigger("expand-row",e,g,j)}f.resetView()}),this.$selectItem=this.$body.find(c('[name="%s"]',this.options.selectItemName)),this.$selectItem.off("click").on("click",function(b){b.stopImmediatePropagation();var c=a(this),d=c.prop("checked"),e=f.data[c.data("index")];f.options.maintainSelected&&a(this).is(":radio")&&a.each(f.options.data,function(a,b){b[f.header.stateField]=!1}),e[f.header.stateField]=d,f.options.singleSelect&&(f.$selectItem.not(this).each(function(){f.data[a(this).data("index")][f.header.stateField]=!1}),f.$selectItem.filter(":checked").not(this).prop("checked",!1)),f.updateSelected(),f.trigger(d?"check":"uncheck",e,c)}),a.each(this.header.events,function(b,c){if(c){"string"==typeof c&&(c=h(null,c));var d=f.header.fields[b],e=a.inArray(d,f.getVisibleFields());f.options.detailView&&!f.options.cardView&&(e+=1);for(var g in c)f.$body.find(">tr:not(.no-records-found)").each(function(){var b=a(this),h=b.find(f.options.cardView?".card-view":"td").eq(e),i=g.indexOf(" "),j=g.substring(0,i),k=g.substring(i+1),l=c[g];h.find(k).off(j).on(j,function(a){var c=b.data("index"),e=f.data[c],g=e[d];l.apply(this,[a,g,e,c])})})}}),this.updateSelected(),this.resetView(),this.trigger("post-body")},o.prototype.initServer=function(b,c){var d,e=this,f={},g={ +searchText:this.searchText,sortName:this.options.sortName,sortOrder:this.options.sortOrder};this.options.pagination&&(g.pageSize=this.options.pageSize===this.options.formatAllRows()?this.options.totalRows:this.options.pageSize,g.pageNumber=this.options.pageNumber),(this.options.url||this.options.ajax)&&("limit"===this.options.queryParamsType&&(g={search:g.searchText,sort:g.sortName,order:g.sortOrder},this.options.pagination&&(g.limit=this.options.pageSize===this.options.formatAllRows()?this.options.totalRows:this.options.pageSize,g.offset=this.options.pageSize===this.options.formatAllRows()?0:this.options.pageSize*(this.options.pageNumber-1))),a.isEmptyObject(this.filterColumnsPartial)||(g.filter=JSON.stringify(this.filterColumnsPartial,null)),f=h(this.options,this.options.queryParams,[g],f),a.extend(f,c||{}),f!==!1&&(b||this.$tableLoading.show(),d=a.extend({},h(null,this.options.ajaxOptions),{type:this.options.method,url:this.options.url,data:"application/json"===this.options.contentType&&"post"===this.options.method?JSON.stringify(f):f,cache:this.options.cache,contentType:this.options.contentType,dataType:this.options.dataType,success:function(a){a=h(e.options,e.options.responseHandler,[a],a),e.load(a),e.trigger("load-success",a),b||e.$tableLoading.hide()},error:function(a){e.trigger("load-error",a.status,a),b||e.$tableLoading.hide()}}),this.options.ajax?h(this,this.options.ajax,[d],null):a.ajax(d)))},o.prototype.initSearchText=function(){if(this.options.search&&""!==this.options.searchText){var a=this.$toolbar.find(".search input");a.val(this.options.searchText),this.onSearch({currentTarget:a})}},o.prototype.getCaret=function(){var b=this;a.each(this.$header.find("th"),function(c,d){a(d).find(".sortable").removeClass("desc asc").addClass(a(d).data("field")===b.options.sortName?b.options.sortOrder:"both")})},o.prototype.updateSelected=function(){var b=this.$selectItem.filter(":enabled").length&&this.$selectItem.filter(":enabled").length===this.$selectItem.filter(":enabled").filter(":checked").length;this.$selectAll.add(this.$selectAll_).prop("checked",b),this.$selectItem.each(function(){a(this).closest("tr")[a(this).prop("checked")?"addClass":"removeClass"]("selected")})},o.prototype.updateRows=function(){var b=this;this.$selectItem.each(function(){b.data[a(this).data("index")][b.header.stateField]=a(this).prop("checked")})},o.prototype.resetRows=function(){var b=this;a.each(this.data,function(a,c){b.$selectAll.prop("checked",!1),b.$selectItem.prop("checked",!1),b.header.stateField&&(c[b.header.stateField]=!1)})},o.prototype.trigger=function(b){var c=Array.prototype.slice.call(arguments,1);b+=".bs.table",this.options[o.EVENTS[b]].apply(this.options,c),this.$el.trigger(a.Event(b),c),this.options.onAll(b,c),this.$el.trigger(a.Event("all.bs.table"),[b,c])},o.prototype.resetHeader=function(){clearTimeout(this.timeoutId_),this.timeoutId_=setTimeout(a.proxy(this.fitHeader,this),this.$el.is(":hidden")?100:0)},o.prototype.fitHeader=function(){var b,d,e,f,h=this;if(h.$el.is(":hidden"))return void(h.timeoutId_=setTimeout(a.proxy(h.fitHeader,h),100));if(b=this.$tableBody.get(0),d=b.scrollWidth>b.clientWidth&&b.scrollHeight>b.clientHeight+this.$header.outerHeight()?g():0,this.$el.css("margin-top",-this.$header.outerHeight()),e=a(":focus"),e.length>0){var i=e.parents("th");if(i.length>0){var j=i.attr("data-field");if(void 0!==j){var k=this.$header.find("[data-field='"+j+"']");k.length>0&&k.find(":input").addClass("focus-temp")}}}this.$header_=this.$header.clone(!0,!0),this.$selectAll_=this.$header_.find('[name="btSelectAll"]'),this.$tableHeader.css({"margin-right":d}).find("table").css("width",this.$el.outerWidth()).html("").attr("class",this.$el.attr("class")).append(this.$header_),f=a(".focus-temp:visible:eq(0)"),f.length>0&&(f.focus(),this.$header.find(".focus-temp").removeClass("focus-temp")),this.$header.find("th[data-field]").each(function(){h.$header_.find(c('th[data-field="%s"]',a(this).data("field"))).data(a(this).data())});var l=this.getVisibleFields();this.$body.find(">tr:first-child:not(.no-records-found) > *").each(function(b){var d=a(this),e=b;h.options.detailView&&!h.options.cardView&&(0===b&&h.$header_.find("th.detail").find(".fht-cell").width(d.innerWidth()),e=b-1),h.$header_.find(c('th[data-field="%s"]',l[e])).find(".fht-cell").width(d.innerWidth())}),this.$tableBody.off("scroll").on("scroll",function(){h.$tableHeader.scrollLeft(a(this).scrollLeft()),h.options.showFooter&&!h.options.cardView&&h.$tableFooter.scrollLeft(a(this).scrollLeft())}),h.trigger("post-header")},o.prototype.resetFooter=function(){var b=this,d=b.getData(),e=[];this.options.showFooter&&!this.options.cardView&&(!this.options.cardView&&this.options.detailView&&e.push('
 
'),a.each(this.columns,function(a,f){var g="",i="",j=c(' class="%s"',f["class"]);f.visible&&(!b.options.cardView||f.cardVisible)&&(g=c("text-align: %s; ",f.falign?f.falign:f.align),i=c("vertical-align: %s; ",f.valign),e.push(""),e.push('
'),e.push(h(f,f.footerFormatter,[d]," ")||" "),e.push("
"),e.push('
'),e.push(""),e.push(""))}),this.$tableFooter.find("tr").html(e.join("")),clearTimeout(this.timeoutFooter_),this.timeoutFooter_=setTimeout(a.proxy(this.fitFooter,this),this.$el.is(":hidden")?100:0))},o.prototype.fitFooter=function(){var b,c,d;return clearTimeout(this.timeoutFooter_),this.$el.is(":hidden")?void(this.timeoutFooter_=setTimeout(a.proxy(this.fitFooter,this),100)):(c=this.$el.css("width"),d=c>this.$tableBody.width()?g():0,this.$tableFooter.css({"margin-right":d}).find("table").css("width",c).attr("class",this.$el.attr("class")),b=this.$tableFooter.find("td"),void this.$body.find(">tr:first-child:not(.no-records-found) > *").each(function(c){var d=a(this);b.eq(c).find(".fht-cell").width(d.innerWidth())}))},o.prototype.toggleColumn=function(a,b,d){if(-1!==a&&(this.columns[a].visible=b,this.initHeader(),this.initSearch(),this.initPagination(),this.initBody(),this.options.showColumns)){var e=this.$toolbar.find(".keep-open input").prop("disabled",!1);d&&e.filter(c('[value="%s"]',a)).prop("checked",b),e.filter(":checked").length<=this.options.minimumCountColumns&&e.filter(":checked").prop("disabled",!0)}},o.prototype.toggleRow=function(a,b,d){-1!==a&&this.$body.find("undefined"!=typeof a?c('tr[data-index="%s"]',a):c('tr[data-uniqueid="%s"]',b))[d?"show":"hide"]()},o.prototype.getVisibleFields=function(){var b=this,c=[];return a.each(this.header.fields,function(a,d){var f=b.columns[e(b.columns,d)];f.visible&&c.push(d)}),c},o.prototype.resetView=function(a){var b=0;if(a&&a.height&&(this.options.height=a.height),this.$selectAll.prop("checked",this.$selectItem.length>0&&this.$selectItem.length===this.$selectItem.filter(":checked").length),this.options.height){var c=k(this.$toolbar),d=k(this.$pagination),e=this.options.height-c-d;this.$tableContainer.css("height",e+"px")}return this.options.cardView?(this.$el.css("margin-top","0"),void this.$tableContainer.css("padding-bottom","0")):(this.options.showHeader&&this.options.height?(this.$tableHeader.show(),this.resetHeader(),b+=this.$header.outerHeight()):(this.$tableHeader.hide(),this.trigger("post-header")),this.options.showFooter&&(this.resetFooter(),this.options.height&&(b+=this.$tableFooter.outerHeight()+1)),this.getCaret(),this.$tableContainer.css("padding-bottom",b+"px"),void this.trigger("reset-view"))},o.prototype.getData=function(b){return!this.searchText&&a.isEmptyObject(this.filterColumns)&&a.isEmptyObject(this.filterColumnsPartial)?b?this.options.data.slice(this.pageFrom-1,this.pageTo):this.options.data:b?this.data.slice(this.pageFrom-1,this.pageTo):this.data},o.prototype.load=function(b){var c=!1;"server"===this.options.sidePagination?(this.options.totalRows=b.total,c=b.fixedScroll,b=b[this.options.dataField]):a.isArray(b)||(c=b.fixedScroll,b=b.data),this.initData(b),this.initSearch(),this.initPagination(),this.initBody(c)},o.prototype.append=function(a){this.initData(a,"append"),this.initSearch(),this.initPagination(),this.initSort(),this.initBody(!0)},o.prototype.prepend=function(a){this.initData(a,"prepend"),this.initSearch(),this.initPagination(),this.initSort(),this.initBody(!0)},o.prototype.remove=function(b){var c,d,e=this.options.data.length;if(b.hasOwnProperty("field")&&b.hasOwnProperty("values")){for(c=e-1;c>=0;c--)d=this.options.data[c],d.hasOwnProperty(b.field)&&-1!==a.inArray(d[b.field],b.values)&&this.options.data.splice(c,1);e!==this.options.data.length&&(this.initSearch(),this.initPagination(),this.initSort(),this.initBody(!0))}},o.prototype.removeAll=function(){this.options.data.length>0&&(this.options.data.splice(0,this.options.data.length),this.initSearch(),this.initPagination(),this.initBody(!0))},o.prototype.getRowByUniqueId=function(a){var b,c,d,e=this.options.uniqueId,f=this.options.data.length,g=null;for(b=f-1;b>=0;b--){if(c=this.options.data[b],c.hasOwnProperty(e))d=c[e];else{if(!c._data.hasOwnProperty(e))continue;d=c._data[e]}if("string"==typeof d?a=a.toString():"number"==typeof d&&(Number(d)===d&&d%1===0?a=parseInt(a):d===Number(d)&&0!==d&&(a=parseFloat(a))),d===a){g=c;break}}return g},o.prototype.removeByUniqueId=function(a){var b=this.options.data.length,c=this.getRowByUniqueId(a);c&&this.options.data.splice(this.options.data.indexOf(c),1),b!==this.options.data.length&&(this.initSearch(),this.initPagination(),this.initBody(!0))},o.prototype.updateByUniqueId=function(b){var c;b.hasOwnProperty("id")&&b.hasOwnProperty("row")&&(c=a.inArray(this.getRowByUniqueId(b.id),this.options.data),-1!==c&&(a.extend(this.data[c],b.row),this.initSort(),this.initBody(!0)))},o.prototype.insertRow=function(a){a.hasOwnProperty("index")&&a.hasOwnProperty("row")&&(this.data.splice(a.index,0,a.row),this.initSearch(),this.initPagination(),this.initSort(),this.initBody(!0))},o.prototype.updateRow=function(b){b.hasOwnProperty("index")&&b.hasOwnProperty("row")&&(a.extend(this.data[b.index],b.row),this.initSort(),this.initBody(!0))},o.prototype.showRow=function(a){(a.hasOwnProperty("index")||a.hasOwnProperty("uniqueId"))&&this.toggleRow(a.index,a.uniqueId,!0)},o.prototype.hideRow=function(a){(a.hasOwnProperty("index")||a.hasOwnProperty("uniqueId"))&&this.toggleRow(a.index,a.uniqueId,!1)},o.prototype.getRowsHidden=function(b){var c=a(this.$body[0]).children().filter(":hidden"),d=0;if(b)for(;dtr");if(this.options.detailView&&!this.options.cardView&&(g+=1),e=j.eq(f).find(">td").eq(g),!(0>f||0>g||f>=this.data.length)){for(c=f;f+h>c;c++)for(d=g;g+i>d;d++)j.eq(c).find(">td").eq(d).hide();e.attr("rowspan",h).attr("colspan",i).show()}},o.prototype.updateCell=function(a){a.hasOwnProperty("index")&&a.hasOwnProperty("field")&&a.hasOwnProperty("value")&&(this.data[a.index][a.field]=a.value,a.reinit!==!1&&(this.initSort(),this.initBody(!0)))},o.prototype.getOptions=function(){return this.options},o.prototype.getSelections=function(){var b=this;return a.grep(this.data,function(a){return a[b.header.stateField]})},o.prototype.getAllSelections=function(){var b=this;return a.grep(this.options.data,function(a){return a[b.header.stateField]})},o.prototype.checkAll=function(){this.checkAll_(!0)},o.prototype.uncheckAll=function(){this.checkAll_(!1)},o.prototype.checkInvert=function(){var 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$elem.wrap('').parent().prepend($('').html(buttonWord)); + }) + + // After we have found all of the file inputs let's apply a listener for tracking the mouse movement. + // This is important because the in order to give the illusion that this is a button in FF we actually need to move the button from the file input under the cursor. Ugh. + .promise().done(function () { + + // As the cursor moves over our new Bootstrap button we need to adjust the position of the invisible file input Browse button to be under the cursor. + // This gives us the pointer cursor that FF denies us + $('.file-input-wrapper').mousemove(function (cursor) { + + var input, wrapper, + wrapperX, wrapperY, + inputWidth, inputHeight, + cursorX, cursorY; + + // This wrapper element (the button surround this file input) + wrapper = $(this); + // The invisible file input element + input = wrapper.find("input"); + // The left-most position of the wrapper + wrapperX = wrapper.offset().left; + // The top-most position of the wrapper + wrapperY = wrapper.offset().top; + // The with of the browsers input field + inputWidth = input.width(); + // The height of the browsers input field + inputHeight = input.height(); + //The position of the cursor in the wrapper + cursorX = cursor.pageX; + cursorY = cursor.pageY; + + //The positions we are to move the 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