Merge pull request #2 from togoannotator/elasticsearch

fowarding to recent

bin/make_correct_data_tmplate.py

@@ -0,0 +1,91 @@
+import requests
+import json
+import argparse
+import hashlib
+import re
+import regex
+
+class CorrectDataTemplate(object):
+    def __init__(self, query, dictionary):
+        #query = "Hog protein"
+        self.dictionary = dictionary
+        self.queue = []
+        self.query_types = ["term_after", "term_before", "mlt_after", "mlt_before"]
+        self.both_ends_space = re.compile("^\s*|\s*$")
+        self.both_ends_double_quote = re.compile("^\"\s*|\s*\"$")    
+        self.double_quote_pattern = re.compile("^\s*|\s*$")
+        self.symbols = re.compile("[\-/,:\+\(\)]")
+        self.spaces = re.compile("\s+")
+        self.putative_spaces = re.compile("^putative\s+", re.IGNORECASE)
+        self.probable_spaces = re.compile("^probable\s+", re.IGNORECASE)
+        self.possible_spaces = re.compile("^possible\s+", re.IGNORECASE)
+
+        #b4name置換用定義
+        self.putative_symbols = re.compile("^putative[\-/,:\+\(\)]", re.IGNORECASE)
+        self.probable_symbols = re.compile("^probable[\-/,:\+\(\)]", re.IGNORECASE)
+        self.possible_symbols = re.compile("^possible[\-/,:\+\(\)]", re.IGNORECASE)
+
+        self.diacritics = regex.compile(r"\p{M}")
+        self.prime = regex.compile(r"\b\w+[\s-]prime\b")
+        self.greek = regex.compile(r"\b(?:\p{Greek}|Alpha|Beta|Gamma|Delta|Epsilon|Zeta|Eta|Theta|Iota|Kappa|Lambda|Mu|Nu|Xi|Omicron|Pi|Rho|Sigma|Tau|Upsilon|Phi|Chi|Psi|Omega)\b") # マッチしなければ加点
+
+        url = "https://togoannotator.dbcls.jp/gene?query=" + query + "&dictionary=" + dictionary + "&limit=10"
+
+        headers = {"content-type": "application/json"}
+        r = requests.get(url, headers=headers)
+        data = r.json()
+        #print(json.dumps(data, indent=4))
+        self.output(data)
+
+    def convert_full(self, text):
+        text = re.sub(self.both_ends_space, "", text)
+        text = re.sub(self.both_ends_double_quote, "", text)
+        text = re.sub(self.putative_spaces, "", text)
+        text = re.sub(self.probable_spaces, "", text)
+        text = re.sub(self.possible_spaces, "", text)
+        text = text.lower()
+        text = re.sub(self.symbols, " ", text)
+        text = re.sub(self.spaces, " ", text)
+        text = re.sub(self.both_ends_space, "", text)
+        return text        
+
+    def concat_md5(self, text1, text2, query_type):
+        if query_type.endswith("_before"):
+            return "{0}{1}{2}".format(hashlib.md5(text1.encode()).hexdigest(), hashlib.md5(text2.encode()).hexdigest(),
+                                      query_type)
+        else:
+            return "{0}{1}".format(hashlib.md5(text1.encode()).hexdigest(), query_type)
+
+    def name2term_after_id(self, text):
+        converted_name = self.convert_full(text)
+        return self.concat_md5(converted_name, "", "term_after")
+
+    def output2(self,data):
+         #検索キーワード    辞書    結果1   結果1_ID    結果1_検索順位  結果2   結果2_ID    結果2_検索順位, ...
+         #j = json.loads(data)
+         #print(json.dumps(data, indent=4))
+         hits = len(data['result_array'])
+         o = [ data['query'], self.dictionary, data['match'], str(hits)]
+         for item in data['result_array']:
+             o.append(item)
+             o.append(self.concat_md5(item,"", "term_after"))
+             o.append("")
+
+         #print("\t".join(data['result_array']))
+         print("\t".join(o))
+
+    def output(self,data):
+        hits = len(data['result_array'])
+        o = [ data['query'], self.dictionary, data['match'], str(hits)]
+        for item in data['result_array']:
+            #print("\t".join(o + [item, self.concat_md5(item,"", "term_after"),""]))
+            print("\t".join(o + [item, self.name2term_after_id(item),""]))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-q", type=str)
+    parser.add_argument("-d", type=str)
+    args = parser.parse_args()
+
+    CorrectDataTemplate(args.q, args.d)