database queries integration to website

Dockerfile

@@ -3,5 +3,6 @@ RUN mkdir /configs
 COPY ./configs /configs
 COPY ./code /home
 WORKDIR /workdir
+RUN pip install neo4j-driver==1.3.1
 EXPOSE 80
 CMD ["python", "/home/workersManager.py"]

code/manager.py

@@ -10,6 +10,7 @@ import logging
 import re
 import time
 import requests
+from transyt_request import database_retriever_by_id
 
 CONFIGURATIONS = FilesUtilities.read_conf_file('/configs/docker_config.conf')
 
@@ -29,7 +30,6 @@ logger = logging.getLogger(__name__)
 logger.addHandler(handler)
 logger.setLevel(logging.DEBUG)
 
-
 logger.info("Docker configurations: " + str(CONFIGURATIONS))
 
 logger.info('Starting server')
@@ -46,6 +46,7 @@ last_submission_ID = 0
 
 print('SERVER WORKING')
 
+
 @app.after_request
 def after_request(response):
     response.headers["Cache-Control"] = "no-cache, no-store, must-revalidate, public, max-age=0"
@@ -53,6 +54,7 @@ def after_request(response):
     response.headers["Pragma"] = "no-cache"
     return response
 
+
 @app.route("/")
 def index():
     logger.info('Welcome page rendering...')
@@ -93,20 +95,6 @@ def submitMerlinPlugin(taxonomyId):
     return run(files, taxonomyId, True)
 
 
-@app.route("/reaction/<reactionId>", methods=["GET"])
-def getReactionInfo(reactionId):
-
-    pattern = re.compile("^TR\d{6}")
-
-    patternFound = bool(pattern.match(reactionId))
-
-    if patternFound:
-        return jsonify({"Result": "Success",
-                        "Purpose": "Future page for transyt reaction " + reactionId}), 200
-    else:
-        logger.info('Bad request to get reaction. Request done: ' + reactionId)
-        return jsonify({"Result": "Bad request, page does not exist!"}), 400
-
 def run(files, taxonomyId, isRest):
     logger.debug('New submission in progress...')
 
@@ -266,8 +254,9 @@ def display_msg(submissionID, isRest):
 def download(submissionID):
     logger.debug("Request to download submission " + submissionID + " results")
     timestr = time.strftime("%Y%m%d_%H%M%S")
-    return send_file(RESULTS_PATH + submissionID + "/results" + timestr + ".zip", as_attachment=True,
-                     attachment_filename='results.zip')
+    return send_file(RESULTS_PATH + submissionID + "/results.zip", as_attachment=True,
+                     attachment_filename='results' + timestr + '.zip')
+
 
 @app.route("/debug/logs/<level>")
 def logsRetriever(level):
@@ -287,7 +276,7 @@ def logsRetriever(level):
 
     os.makedirs(saveFilesPath)
 
-    #implement service here when running
+    # implement service here when running
 
     if level == 'manager':
         logger.info("Collecting manager logs.")
@@ -340,6 +329,52 @@ def getWorkersLogs(savePath):
             logger.debug("Worker " + host + " not alive!")
 
 
+@app.route('/reactions/<reactionId>')
+def reactions(reactionId):
+    pattern = re.compile("^T[A-Z]\d{7}")
+
+    patternFound = bool(pattern.match(reactionId))
+
+    if patternFound:
+        results_dict = result_parser(reactionId)
+        if results_dict:
+            return render_template("record.html", subId=reactionId, dictt=results_dict), 200
+
+    return render_template("noresutls.html", subId=reactionId), 200
+
+
+@app.template_filter('enumerate_items')
+def enumerate_items(*args, **kwargs):
+    return enumerate(*args, **kwargs)
+
+
+def result_parser(id):
+    databases, tc_systems, reactionID, metaID, reaction, metabolites = database_retriever_by_id(id)
+
+    if not metabolites:
+        return None
+
+    tc_systems2 = {}
+
+    for tc in tc_systems:
+
+        tc_elements = tc.split('@')
+
+        if tc_elements[0] in tc_systems2:
+            tc_systems2[tc_elements[0]].append(tc_elements[1])
+        else:
+            tc_systems2[tc_elements[0]] = [tc_elements[1]]
+
+    res_dict = {'databases': databases,
+                'tc_systems': tc_systems2,
+                'reactionID': reactionID,
+                'metaID': metaID,
+                'reaction': reaction,
+                'metabolites': metabolites}
+
+    return res_dict
+
+
 def countEntriesBelow(l, id):
     id = int(id)
     res = 0

code/neo4jPythonDriver.py

+from neo4j.v1 import GraphDatabase
+
+
+class neo4jPythonDriver:
+
+    ###### CONSTRUCTOR ######
+
+    def __init__(self, uri, user, password):
+
+        self.__uri = uri
+        self.__user = user
+        self.__password = password
+        self.__driver = self.__initDriver()
+
+
+    def __initDriver(self):
+
+        return GraphDatabase.driver(self.__getUri(), auth=(self.__getUser(), self.__getPassword()))
+
+    def initSession(self):
+
+        return self.__driver.session()
+
+
+    def __getUri(self):
+
+        return self.__uri
+
+
+    def __getUser(self):
+
+        return self.__user
+
+
+    def __getPassword(self):
+
+        return self.__password
+
+
+    def __getDriver(self):
+
+        return self.__driver
+
+
+    def __setUri(self, value):
+
+        self.__uri = value
+
+
+    def __setUser(self, value):
+
+        self.__user = value
+
+
+    def __setPassword(self, value):
+
+        self.__password = value
+
+
+    def __setDriver(self, value):
+
+        self.__driver = value
+
+
+
+
+
+
+

code/static/css/accordion_results.css

+#aspect-content {
+  margin: 10px 10px 0px 10px;
+  font-family: 'Oxygen';
+}
+
+.tab-element {
+  position: relative;
+  width: 90%;
+  margin: 0 auto 10px;
+  border-radius: 4px;
+  background-color: #ffffff;
+  box-shadow: 3px -1px 5px 3px #bdc3c7;
+  opacity: 1;
+  transition: box-shadow .2s, opacity .4s;
+}
+
+.tab-element:hover {
+    box-shadow: 0 4px 10px 0 rgba(0, 0, 0, .11);
+}
+
+.inner-tab-element {
+  position: relative;
+  width: 100%;
+  border-radius: 4px;
+  background-color: #34495e;
+  box-shadow: 3px -1px 5px 3px #bdc3c7;
+  opacity: 1;
+  transition: box-shadow .2s, opacity .4s;
+}
+
+.inner-tab-element:hover {
+    box-shadow: 0 4px 10px 0 rgba(0, 0, 0, .11);
+}
+
+.outer-input {
+  display: none;
+}
+
+.inner-input {
+  display: none;
+}
+
+.outer-input:checked ~ .outer-label-content + .dropdown-content-outer-wrapper {
+  max-height: 8000px;
+}
+
+.outer-input:checked ~ .outer-label-content:after {
+    transform: rotate(0);
+}
+
+.inner-input:checked ~ .outer-label-content + .dropdown-content-outer-wrapper {
+  max-height: 8000px;
+}
+
+.inner-input:checked ~ .outer-label-content:after {
+    transform: rotate(0);
+}
+
+
+.outer-input:checked ~ .inner-label-content + .dropdown-content-outer-wrapper {
+  max-height: 8000px;
+}
+
+.outer-input:checked ~ .inner-label-content:after {
+    transform: rotate(0);
+}
+
+
+.inner-input:checked ~ .inner-label-content + .dropdown-content-outer-wrapper {
+  max-height: 8000px;
+}
+
+.inner-input:checked ~ .inner-label-content:after {
+    transform: rotate(0);
+}
+
+
+.outer-label {
+  position: absolute;
+  top: 0;
+  left: 0;
+  height: 100%;
+  max-height: 50px;
+  width: 100%;
+  margin: 0;
+  padding: 0;
+  font-size: 0;
+  z-index: 1;
+  cursor: pointer;
+}
+
+.inner-label {
+  position: absolute;
+  top: 0;
+  left: 0;
+  height: 100%;
+  max-height: 50px;
+  width: 100%;
+  margin: 0;
+  padding: 0;
+  font-size: 0;
+  z-index: 1;
+  cursor: pointer;
+}
+
+.outer-label-content {
+  position: relative;
+  display: block;
+  height: 50px;
+  margin: 0;
+  padding: 0;
+  font-size: 0;
+  white-space: nowrap;
+  cursor: pointer;
+}
+
+.outer-label-content:before  {
+    content: '';
+    display: inline-block;
+    vertical-align: middle;
+    height: 100%;
+}
+
+.outer-label-content:after {
+    content: '';
+    display: inline-block;
+    vertical-align: middle;
+    position: absolute;
+    width: 24px;
+    height: 100%;
+    right: 30px;
+    background-image: url('data:image/svg+xml;base64,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');
+    background-repeat: no-repeat;
+    background-position: center;
+    transform: rotate(180deg);
+  }
+
+.outer-label-content + .dropdown-content-outer-wrapper {
+  max-height: 0;
+  overflow: hidden;
+  transition: max-height .3s;
+}
+
+.outer-label-content > div {
+  display: inline-block;
+  vertical-align: middle;
+}
+
+.inner-label-content {
+  position: relative;
+  display: block;
+  height: 50px;
+  margin: 0;
+  padding: 0;
+  font-size: 0;
+  white-space: nowrap;
+  cursor: pointer;
+}
+
+.inner-label-content:before  {
+    content: '';
+    display: inline-block;
+    vertical-align: middle;
+    height: 100%;
+}
+
+.inner-label-content:after {
+    content: '';
+    display: inline-block;
+    vertical-align: middle;
+    position: absolute;
+    width: 24px;
+    height: 100%;
+    right: 30px;
+    background-image: url('data:image/svg+xml;base64,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');
+    background-repeat: no-repeat;
+    background-position: center;
+    transform: rotate(180deg);
+  }
+
+.inner-label-content + .dropdown-content-outer-wrapper {
+  max-height: 0;
+  overflow: hidden;
+  transition: max-height .3s;
+}
+
+.inner-label-content > div {
+  display: inline-block;
+  vertical-align: middle;
+}
+
+.aspect-info {
+  width: 100%;
+  white-space: nowrap;
+  font-size: 0;
+}
+
+.aspect-info:before {
+    content: '';
+    display: inline-block;
+    vertical-align: middle;
+  }
+
+.aspect-name {
+  display: inline-block;
+  width: 33%;
+  max-height: 22px;
+  color: #000000;
+  text-align: left;
+  vertical-align: middle;
+  font-size: 16px;
+  margin: 0 0 0 20px;
+
+}
+
+.aspect-name > p {
+  display: inline-block;
+  font-size: 16px;
+}
+
+.aspect-name > a {
+  display: inline-block;
+}
+
+.dropdown-content-outer-wrapper {
+  background-color: #ecf0f1;
+  font-size: 0;
+  text-align: justify;
+}
+
+.inner-tab-element-wrapper {
+  padding: 10px 10px 10px 10px;
+}
+
+.inner-inner-tab-element-wrapper {
+  padding: 10px 10px 10px 10px;
+  display: flex;
+  flex-wrap: wrap;
+}
+
+.inner-inner-tab-element-wrapper > div {
+  display: inline-block;
+  width: 100%;
+  height: 100%;
+  flex: 0 0 20%
+}
+
+.inner-inner-tab-element-wrapper > div > div {
+  width: 100%;
+  height: 100%;
+  padding: 10px 10px 10px 10px;
+  background-color: #ecf0f1;
+  text-align: left;
+}
+
+.content {
+    position: relative;
+    width: 100%;
+    font-size: 13px;
+    color: #2c3e50;
+}
+
+.external-links-button {
+
+    display: inline-block;
+    background: none;
+    padding: 10px;
+    margin: 10px;
+    cursor:pointer;
+    border: 2px solid #2c3e50;
+    border-radius: 10px;
+
+}
+
+.external-links-button:hover {
+
+    display: inline-block;
+    background: #2c3e50;
+    transition: 0.5s;
+}
+
+.external-links-button >p {
+
+    margin: 0;
+    color: #2c3e50;
+
+}
+
+.external-links-button:hover >p {
+
+    margin: 0;
+    color: #ffffff;
+    transition: 0.5s;
+
+}
+
+.inner-external-links-title {
+
+    padding-bottom: 15px;
+
+}
+
+.inner-external-links-title >a {
+
+    font-size: 16px;
+    color: #2980b9;
+
+}
+
+.inner-external-links-title:hover >a {
+
+    text-decoration: underline;
+    cursor: pointer;
+    color: #95a5a6;
+
+}
+
+.inner-external-links {
+
+    display: inline-block;
+    background: none;
+    padding: 10px;
+    margin: 10px;
+    border: 1px solid #95a5a6;
+    border-radius: 10px;
+    width: 90%;
+
+}
+
+.inner-external-links >div{
+
+    vertical-align: middle;
+    display: flex;
+    flex-wrap: wrap;
+    margin-left: 5%;
+    width: 80%;
+}
+
+.inner-external-links >div >div {
+    flex: 0 0 33%;
+    vertical-align: middle;
+}
+
+.par-inner-external-links {
+
+    vertical-align: middle;
+    margin: 10px;
+    font-size: 14px;
+    color: #95a5a6;
+    display: inline-block;
+
+
+}
+
+
+.external-links-button-close {
+
+    padding:10px 0 10px 50%;
+    margin: 0;
+    cursor: pointer;
+    align-content: center;
+
+}
+

code/static/css/center.css

@@ -2,7 +2,6 @@
 .center {
   margin: auto;
   width: 60%;
-  border: 3px solid #000066;
   padding: 10px;
     word-wrap: break-word;
     font-family: 'Oxygen';
@@ -22,6 +21,14 @@
         font-size: 20px;
 
 
+}
+
+.center h4 {
+  color: black;
+      font-family: 'Oxygen';
+        font-size: 18px;
+
+
 }
 
 .center p {
@@ -35,3 +42,47 @@
       font-family: 'Oxygen';
 
 }
+
+.center-download {
+  margin: auto;
+  width: 90%;
+  padding: 20px;
+    word-wrap: break-word;
+    font-family: 'Oxygen';
+
+}
+
+.center-download h1 {
+  color: black;
+      font-family: 'Oxygen';
+    font-size: 28px;
+
+}
+
+.center-download h3 {
+  color: black;
+      font-family: 'Oxygen';
+        font-size: 20px;
+
+
+}
+
+.center-download h4 {
+  color: black;
+      font-family: 'Oxygen';
+        font-size: 18px;
+
+
+}
+
+.center-download p {
+  color: black;
+      font-family: 'Oxygen';
+
+}
+
+.center-download li {
+  color: black;
+      font-family: 'Oxygen';
+
+}

code/static/css/footer.css

+.footer{
+    text-align: center;
+    font-family: Oxygen;
+    padding: 40px 10% 40px 10%;
+    display: flex;
+    flex-wrap: wrap;
+    max-width: 100%;
+    height: 150px;
+}
+
+.footer a {
+    max-height: 100%;
+    max-width: 100%;
+}
+
+.footer img {
+    max-height: 80%;
+    max-width: 80%;
+}
+
+.footer table {
+    border: 0;
+    width: 100%;
+    max-width: 100%;
+}
+
+.footer th {
+    border: 0;
+    text-align: center;
+    width: 25%;
+}
\ No newline at end of file

code/static/css/submit.css

-
-.search_bar {
-  display: -ms-flexbox;
-  display: flex;
-  -ms-flex-pack: center;
-      justify-content: center;
-  -ms-flex-align: center;
-      align-items: center;
-  font-family: 'Oxygen';
-  max-width: 450px;
-}
-
-.search_bar form {
-  width: 100%;
-  max-width: 450px;
-  margin-bottom: 0;
-}
-
-.search_bar form .inner-form {
-  background: #fff;
-  display: -ms-flexbox;
-  display: flex;
-  width: 100%;
-  -ms-flex-pack: justify;
-      justify-content: space-between;
-  -ms-flex-align: center;
-      align-items: center;
-  box-shadow: 20px 8px 20px 8px rgba(0, 0, 0, 0.15);
-}
-
-.search_bar form .inner-form .input-field {
-  height: 60px;
-}
-
-.search_bar form .inner-form .input-field input {
-  height: 100%;
-  background: transparent;
-  border: 0;
-  display: block;
-  width: 100%;
-  padding: 10px 10px;
-  font-size: 16px;
-  color: #555;
-}
-
-.search_bar form .inner-form .input-field input[type=file] {
-  display: none;
-}
-
-.search_bar form .inner-form .input-field input[type=submit] {
-  display: none;
-}
-
-.search_bar form .inner-form .input-field input.placeholder {
-  color: #888;
-  font-size: 16px;
-}
-
-.search_bar form .inner-form .input-field input:-moz-placeholder {
-  color: #888;
-  font-size: 16px;
-}
-
-.search_bar form .inner-form .input-field input::-webkit-input-placeholder {
-  color: #888;
-  font-size: 16px;
-}
-
-.search_bar form .inner-form .input-field input:hover, .search_bar form .inner-form .input-field input:focus {
-  box-shadow: none;
-  outline: 0;
-  border-color: #fff;
-}
-
-
-.search_bar form .inner-form .input-field.first-wrap {
-  -ms-flex-positive: 1;
-      flex-grow: 1;
-}
-
-.search_bar form .inner-form .input-field.second-wrap {
-  -ms-flex-positive: 1;
-  flex-grow: 1;
-}
-
-.search_bar form .inner-form .input-field.second-wrap.custom-file-upload {
-  padding: 18px;
-  color: gray;
-  background-color: #ffffff;
-  cursor: pointer;
-  font-weight: lighter;
-  font-size: 18px;
-}
-
-.search_bar form .inner-form .input-field.third-wrap {
-  -ms-flex-positive: 1;
-  flex-grow: 1;
-}
-
-.search_bar form .inner-form .input-field.third-wrap.custom-file-upload {
-  padding: 18px;
-  color: gray;
-  background-color: #ffffff;
-  cursor: pointer;
-  font-weight: lighter;
-  font-size: 18px;
-}
-
-.search_bar form .inner-form .input-field.fourth-wrap {
-  -ms-flex-positive: 1;
-  flex-grow: 1;
-}
-
-.search_bar form .inner-form .input-field.fourth-wrap.custom-file-upload {
-  padding: 14px;
-  background-color: #27ae60;
-  color: #ffffff;
-  font-weight: bold;
-  font-size: 22px;
-  cursor: pointer;
+
+.submit-form {
+  display: -ms-flexbox;
+  display: flex;
+  -ms-flex-pack: center;
+      justify-content: center;
+  -ms-flex-align: center;
+      align-items: center;
+  font-family: 'Oxygen';
+  max-width: 450px;
+}
+
+.submit-form form {
+  width: 100%;
+  max-width: 450px;
+  margin-bottom: 0;
+}
+
+.submit-form form .inner-form {
+  background: #fff;
+  display: -ms-flexbox;
+  display: flex;
+  width: 100%;
+  -ms-flex-pack: justify;
+      justify-content: space-between;
+  -ms-flex-align: center;
+      align-items: center;
+  box-shadow: 20px 8px 20px 8px rgba(0, 0, 0, 0.15);
+}
+
+.submit-form .inner-form {
+  background: #fff;
+  display: -ms-flexbox;
+  display: flex;
+  width: 100%;
+  -ms-flex-pack: justify;
+      justify-content: space-between;
+  -ms-flex-align: center;
+      align-items: center;
+  box-shadow: 20px 8px 20px 8px rgba(0, 0, 0, 0.15);
+}
+
+.submit-form form .inner-form .input-field {
+  height: 60px;
+}
+
+.submit-form form .inner-form .input-field input {
+  height: 100%;
+  background: transparent;
+  border: 0;
+  display: block;
+  width: 100%;
+  padding: 10px 10px;
+  font-size: 16px;
+  color: #555;
+}
+
+.submit-form .inner-form .input-field button {
+  height: 100%;
+  background: transparent;
+  border: 0;
+  display: block;
+  width: 100%;
+  padding: 10px 10px;
+  font-size: 16px;
+  color: #555;
+}
+
+.submit-form .inner-form .input-field button[type=button] {
+  display: none;
+}
+
+.submit-form form .inner-form .input-field input[type=file] {
+  display: none;
+}
+
+.submit-form form .inner-form .input-field input[type=submit] {
+  display: none;
+}
+
+.submit-form form .inner-form .input-field input.placeholder {
+  color: #888;
+  font-size: 16px;
+}
+
+.submit-form form .inner-form .input-field input:-moz-placeholder {
+  color: #888;
+  font-size: 16px;
+}
+
+.submit-form form .inner-form .input-field input::-webkit-input-placeholder {
+  color: #888;
+  font-size: 16px;
+}
+
+.submit-form form .inner-form .input-field input:hover, .submit-form form .inner-form .input-field input:focus {
+  box-shadow: none;
+  outline: 0;
+  border-color: #fff;
+}
+
+.submit-form .inner-form .input-field button:hover, .submit-form .inner-form .input-field button:focus {
+  box-shadow: none;
+  outline: 0;
+  border-color: #fff;
+}
+
+
+.submit-form form .inner-form .input-field.first-wrap {
+  -ms-flex-positive: 1;
+      flex-grow: 1;
+}
+
+.submit-form form .inner-form .input-field.second-wrap {
+  -ms-flex-positive: 1;
+  flex-grow: 1;
+}
+
+.submit-form form .inner-form .input-field.second-wrap.custom-file-upload {
+  padding: 18px;
+  color: gray;
+  background-color: #ffffff;
+  cursor: pointer;
+  font-weight: lighter;
+  font-size: 18px;
+}
+
+.submit-form form .inner-form .input-field.third-wrap {
+  -ms-flex-positive: 1;
+  flex-grow: 1;
+}
+
+.submit-form form .inner-form .input-field.third-wrap.custom-file-upload {
+  padding: 18px;
+  color: gray;
+  background-color: #ffffff;
+  cursor: pointer;
+  font-weight: lighter;
+  font-size: 18px;
+}
+
+.submit-form form .inner-form .input-field.fourth-wrap {
+  -ms-flex-positive: 1;
+  flex-grow: 1;
+}
+
+.submit-form form .inner-form .input-field.fourth-wrap.custom-file-upload {
+  padding: 14px;
+  background-color: #27ae60;
+  color: #ffffff;
+  font-weight: bold;
+  font-size: 22px;
+  cursor: pointer;
+}
+
+.submit-form .inner-form .input-field.fourth-wrap {
+  -ms-flex-positive: 1;
+  flex-grow: 1;
+}
+
+.submit-form .inner-form .input-field.fourth-wrap.custom-button {
+  padding: 14px;
+  background-color: #27ae60;
+  color: #ffffff;
+  font-weight: bold;
+  font-size: 22px;
+  cursor: pointer;
+}
+
+.submit-form .inner-form .input-field.fourth-wrap.custom-button {
+  padding: 14px;
+  background-color: #27ae60;
+  color: #ffffff;
+  font-weight: bold;
+  font-size: 22px;
+  cursor: pointer;
 }
\ No newline at end of file

code/static/js/to_show.js

+function showSubmit(event) {
+    document.getElementById( 'to-retrieve' ).style.display = 'none';
+    document.getElementById( 'to-submit' ).style.display = 'inline-block';
+}
+
+function showRetrieve(event) {
+    document.getElementById( 'to-submit' ).style.display = 'none';
+    document.getElementById( 'to-retrieve' ).style.display = 'inline-block';
+}
+
+function showExternal(event) {
+    document.getElementById( 'external-links' ).style.display = 'inline-block';
+    document.getElementById( 'external-links' ).style.padding = '25px';
+    document.getElementById( 'external-links' ).style.textAlign = 'left';
+    document.getElementById( 'external-links' ).style.width = '100%';
+    document.getElementById( 'external-links' ).style.boxShadow = '20px 8px 20px 8px rgba(0, 0, 0, 0.15)';
+}
+
+function closeExternal(event) {
+    document.getElementById( 'external-links' ).style.display = 'none';
+}
+
+function toggleTCsystems() {
+    if(document.getElementById('external-links').style.display == "none") { // if is menuBox displayed, hide it
+        document.getElementById('aspect-content').style.display = "none";
+        document.getElementById('external-links').style.display = "block";
+    }
+
+    else {
+        document.getElementById('external-links').style.display = "none";
+    }
+}
+
+function toggleMetabolites() {
+    if(document.getElementById('aspect-content').style.display == "none") { // if is menuBox displayed, hide it
+        document.getElementById('external-links').style.display = "none";
+        document.getElementById('aspect-content').style.width = "100%";
+        document.getElementById('aspect-content').style.display = "inline-block";
+
+    }
+
+    else {
+        document.getElementById('aspect-content').style.display = "none";
+    }
+}
+
+function toggleMenu2(id) {
+    if(document.getElementById(id).style.display == "none") { // if is menuBox displayed, hide it
+        document.getElementById(id).style.display = "block";
+        document.getElementById(id).style.padding = '10px';
+        document.getElementById(id).style.textAlign = 'left';
+        document.getElementById(id).style.width = '100%';
+    }
+
+    else {
+        document.getElementById(id).style.display = "none";
+    }
+}
\ No newline at end of file

code/templates/download.html

-<!DOCTYPE html>
-<html lang="en">
-<head>
-	<meta charset="UTF-8">
-    <title>TranSyT</title>
-    <link rel="stylesheet" href="{{ url_for('static', filename='css/center.css') }}">
-    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
-    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap-theme.min.css">
-    <link href="//fonts.googleapis.com/css?family=Oxygen&subset=latin,latin-ext" rel="stylesheet" type="text/css">
-    <link rel="stylesheet" href="{{ url_for('static', filename='css/downloadButton.css') }}">
-
-<body style="background: #fefcfe">
-
-<div class="center" align="center" style="border: 0">
-        <h1><b>TranSyT </b></h1>
-    <br>
-    <br>
-    <img src="{{ url_for('static', filename = 'images/transportProtein.gif') }}" alt="Transport Protein">
-    <br>
-    <br>
-    <h3><b>The process is now concluded</b></h3>
-    <br>
-    <p>The result of submission {{subId}} is available for download</p>
-    <br>
-    <p>If you are having trouble downloading the results, please clean the cache of your browser and try again</p>
-    <p>If the problems persists, please try again with a different browser</p>
-    <br>
-    <a href="{{url_for('download', submissionID = subId)}}">
-    <button class="downloadBtn">Download</button>
-    </a>
-    <br>
-    <br>
-    <br>
-    <a href="{{url_for('index')}}"><b>Click here to perform another submission</b></a>
-<br>
-<br>
-<br>
-<br>
-<br>
-</div>
-<div style="text-align: center; color: black; font-family: Oxygen">
-    <a href="{{url_for('index')}}"><b>TranSyT 2019</b></a>
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-    <a href="https://www.eng.uminho.pt/en" target="_blank"> <img border="0" alt="School of Engineering" src="{{ url_for('static', filename = 'images/EENG.jpg') }}" width="90" height="60"></a>
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-    <a href="https://www.ceb.uminho.pt/" target="_blank"> <img border="0" alt="Centre of Biological Engineering" src="{{ url_for('static', filename = 'images/ceb1.png') }}" width="130" height="105"></a>
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-    <a href="https://www.elixir-portugal.org/" target="_blank"> <img border="0" alt="BioData" src="{{ url_for('static', filename = 'images/biodata_elixir.png') }}" width="235" height="30"></a>
-<br>
-    <br>
-</div>
-</body>
-</html>
+<!DOCTYPE html>
+<html lang="en">
+<head>
+	<meta charset="UTF-8">
+    <title>TranSyT</title>
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/center.css') }}">
+    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
+    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap-theme.min.css">
+    <link href="//fonts.googleapis.com/css?family=Oxygen&subset=latin,latin-ext" rel="stylesheet" type="text/css">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/downloadButton.css') }}">
+
+<body style="background: #fefcfe">
+
+<div class="center" align="center" style="border: 0">
+    <h1><b>TranSyT </b></h1>
+    <br>
+    <br>
+    <img src="{{ url_for('static', filename = 'images/transportProtein.gif') }}" alt="Transport Protein">
+    <br>
+    <br>
+    <h3><b>The process is now concluded</b></h3>
+    <br>
+    <p>The result of submission {{subId}} is available for download</p>
+    <br>
+    <p>If you are having trouble downloading the results, please clean the cache of your browser and try again</p>
+    <p>If the problems persists, please try again with a different browser</p>
+    <br>
+    <a href="{{url_for('download', submissionID = subId)}}">
+    <button class="downloadBtn">Download</button>
+    </a>
+    <br>
+    <br>
+    <br>
+    <a href="{{url_for('index')}}"><b>Click here to perform another submission</b></a>
+<br>
+<br>
+<br>
+<br>
+<br>
+</div>
+<div style="text-align: center; color: black; font-family: Oxygen">
+    <a href="{{url_for('index')}}"><b>TranSyT 2019</b></a>
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+    <a href="https://www.eng.uminho.pt/en" target="_blank"> <img border="0" alt="School of Engineering" src="{{ url_for('static', filename = 'images/EENG.jpg') }}" width="90" height="60"></a>
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+    <a href="https://www.ceb.uminho.pt/" target="_blank"> <img border="0" alt="Centre of Biological Engineering" src="{{ url_for('static', filename = 'images/ceb1.png') }}" width="130" height="105"></a>
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+    <a href="https://www.elixir-portugal.org/" target="_blank"> <img border="0" alt="BioData" src="{{ url_for('static', filename = 'images/biodata_elixir.png') }}" width="235" height="30"></a>
+<br>
+    <br>
+</div>
+</body>
+</html>

code/templates/noresutls.html

+<!DOCTYPE html>
+<html lang="en">
+<head>
+	<meta charset="UTF-8">
+	<title>TranSyT</title>
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/center.css') }}">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/submit.css') }}">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/footer.css') }}">
+    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
+    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap-theme.min.css">
+    <link href="//fonts.googleapis.com/css?family=Oxygen&subset=latin,latin-ext" rel="stylesheet" type="text/css">
+</head>
+
+<body>
+
+<div class="center" align="center" style="border: 0">
+    <br>
+    <br>
+    <h1><b>TranSyT</b></h1>
+    <br>
+    <br>
+    <img src="{{ url_for('static', filename = 'images/transportProtein.gif') }}" alt="Biocoiso" height="325px">
+    <br>
+    <br>
+    <h1>The page that you were looking for doesn't exist</h1>
+    <br>
+    <br>
+    <h4>There are no results for your query: {{ subId }} </h4>
+    <br>
+    <br>
+    <a href="{{url_for('index')}}"><b>Click here to get back to the home page</b></a>
+    <br>
+    <br>
+
+
+<script src="../static/js/show_filename.js"></script>
+<script src="../static/js/to_show.js"></script>
+</div>
+
+<div class="footer">
+
+    <table>
+        <tr>
+            <th><a href="{{url_for('index')}}">TranSyT 2019</a> <br>
+                by <a href="https://www.ceb.uminho.pt/People/Profile/davidelagoa" target="_blank">Davide Lagoa</a> and
+                <a href="https://www.ceb.uminho.pt/People/Profile/odias" target="_blank">Oscar Dias</a>
+            </th>
+            <th><a href="https://www.eng.uminho.pt/en" target="_blank"> <img border="0" alt="School of Engineering" src="{{ url_for('static', filename = 'images/EENG.jpg') }}"></a></th>
+            <th><a href="https://www.ceb.uminho.pt/" target="_blank"> <img border="0" alt="Centre of Biological Engineering" src="{{ url_for('static', filename = 'images/ceb1.png') }}"></a></th>
+            <th><a href="https://www.elixir-portugal.org/" target="_blank"> <img border="0" alt="BioData" src="{{ url_for('static', filename = 'images/biodata_elixir.png') }}"></a></th>
+        </tr>
+    </table>
+
+</div>
+
+</body>
+
+</html>

code/templates/record.html

+<!DOCTYPE html>
+<html lang="en">
+<head>
+	<meta charset="UTF-8">
+    <title>TranSyT</title>
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/center.css') }}">
+    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
+    <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap-theme.min.css">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/header.css') }}">
+    <link href="//fonts.googleapis.com/css?family=Oxygen&subset=latin,latin-ext" rel="stylesheet" type="text/css">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/nav.css') }}">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/downloadButton.css') }}">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/accordion_results.css') }}">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/footer.css') }}">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/center.css') }}">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/submit.css') }}">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/footer.css') }}">
+
+<body style="background: #fefcfe">
+
+<div class="center-download" align="center">
+    <h1><b>TranSyT</b></h1>
+    <br>
+    <br>
+    <div style="width: 100%; text-align: left; border: 2px solid #2c3e50; border-radius: 10px; padding: 25px">
+        <h4>
+            TranSyT identifier:
+        </h4>
+        <br>
+        <p>{{subId}}</p>
+
+        <br>
+        <br>
+
+        <h4>
+            Meta identifier:
+        </h4>
+        <br>
+        <p>{{ dictt['metaID'] }}</p>
+
+        <br>
+        <br>
+
+        <h4>
+            Reaction:
+        </h4>
+        <br>
+        <p>
+        {% if ' $<<>>$' in dictt['reaction'] %}
+            {{ dictt['reaction'].split('$<<>>$')[0] }}
+            <a target="_blank" style="padding-left: 5px; padding-right: 5px"><img border="0" src="{{ url_for('static', filename = 'images/reversible_arrow.png') }}" width="28" height="28"></a>
+            {{ dictt['reaction'].split('$<<>>$')[1] }}
+        {% else %}
+            {{ dictt['reaction'].split('$>>$')[0] }}
+            <a target="_blank" style="padding-left: 5px; padding-right: 5px"><img border="0" src="{{ url_for('static', filename = 'images/right_arrow.png') }}" width="28" height="28"></a>
+            {{ dictt['reaction'].split('$>>$')[1] }}
+        {% endif %}
+        </p>
+
+        <br>
+        <br>
+        <div style="display: flex; flex-wrap: wrap; width: 50%">
+            <div style="flex: 0 0 33%">
+                <label class="external-links-button">
+                    <button style="display: none" onclick="toggleTCsystems()" type="button"></button>
+                    <p>TC systems</p>
+                </label>
+            </div>
+            <div style="flex: 0 0 33%">
+                <label class="external-links-button">
+                    <button style="display: none" onclick="toggleMetabolites()" type="button"></button>
+                    <p>Metabolites</p>
+                </label>
+            </div>
+        </div>
+        <br>
+        <br>
+        <div id="external-links" style="display: none">
+            {% for i , system in dictt['tc_systems'] | enumerate_items %}
+                <div class="inner-external-links">
+                    <div class="inner-external-links-title">
+                        <a target="_blank" href="http://www.tcdb.org/search/result.php?tc={{system}}"><b>{{system}}</b></a>
+                    </div>
+
+                    {% for system2 in dictt['tc_systems'][system] %}
+
+                        <div>
+                            <div>
+                                <p class="par-inner-external-links">{{ system2 }}</p>
+                            </div>
+                            <div>
+                                <a target="_blank"
+                                href="http://www.tcdb.org/search/result.php?acc={{system2}}&tc={{system}}">
+                                    <img border="0" src="{{ url_for('static', filename = 'images/tcdb_logo.png') }}"
+                                         width="170" height="38">
+                                </a>
+                            </div>
+                            <div>
+                                <a target="_blank" href="https://www.uniprot.org/uniprot/{{system2}}">
+                                    <img border="0" src="{{ url_for('static', filename = 'images/uniprot_logo2.png') }}"
+                                         width="56" height="32">
+                                </a>
+                            </div>
+                        </div>
+                    {% endfor %}
+                </div>
+
+            {% endfor %}
+            <br>
+            <label class="external-links-button-close">
+                <button style="display: none" onclick="closeExternal()" type="button"></button>
+                <img border="0" src="{{ url_for('static', filename = 'images/close_icon.png') }}" width="32" height="32">
+            </label>
+        </div>
+        <div id="aspect-content" style="display: none">
+        {% for db, val in dictt['databases'].items() %}
+        {% if val %}
+        <div class="tab-element ">
+            <input id="{{ db }}" type="checkbox" class="outer-input" name="aspect">
+            <label for="{{ db }}" class="outer-label"></label>
+            <div class="outer-label-content">
+                <div class="aspect-info">
+                    <div class="aspect-name"> {{ db }}
+                    </div>
+                    <div class="aspect-name">
+                    </div>
+                    <div class="aspect-name">
+                    </div>
+                </div>
+            </div>
+
+            <div class="dropdown-content-outer-wrapper">
+                {% for role in ['Reactants', 'Products'] %}
+                <div class="inner-tab-element-wrapper">
+                    <div class="inner-tab-element ">
+                        <input id="{{ db+role }}" type="checkbox" class="inner-input" name="aspect">
+                        <label for="{{ db+role }}" class="inner-label"></label>
+                        <div class="inner-label-content">
+                            <div class="aspect-info">
+                                <div class="aspect-name" style="color: #ffffff"> {{role}}
+                                </div>
+                            </div>
+                        </div>
+
+                        <div class="dropdown-content-outer-wrapper">
+                            <div class="inner-inner-tab-element-wrapper" style="padding: 10px 10px 0px 10px">
+                                <div>
+                                    <div style="padding: 10px 10px 0px 10px">
+                                        <div class="content" style="height: 20px">
+                                            <span><b>Identifier</b></span>
+                                            <br>
+                                        </div>
+                                    </div>
+                                </div>
+                                <div>
+                                    <div style="padding: 10px 10px 0px 10px">
+                                        <div class="content" style="height: 20px">
+                                            <span><b>Name</b></span>
+                                            <br>
+                                        </div>
+                                    </div>
+                                </div>
+                                <div>
+                                    <div style="padding: 10px 10px 0px 10px">
+                                        <div class="content" style="height: 20px">
+                                            <span><b>Stoichiometry</b></span>
+                                            <br>
+                                        </div>
+                                    </div>
+                                </div>
+                                <div>
+                                    <div style="padding: 10px 10px 0px 10px">
+                                        <div class="content" style="height: 20px">
+                                            <span><b>Aliases</b></span>
+                                            <br>
+                                        </div>
+                                    </div>
+                                </div>
+                                <div>
+                                    <div style="padding: 10px 10px 0px 10px">
+                                        <div class="content" style="height: 20px">
+                                            <span><b>Formula</b></span>
+                                            <br>
+                                        </div>
+                                    </div>
+                                </div>
+                            </div>
+                        {% for cpd in dictt['metabolites'][db + '_' + role.lower()[:-1]] %}
+                            <div class="inner-inner-tab-element-wrapper">
+                                <div>
+                                    <div>
+                                        <div class="content">
+                                            {% if db == 'MetaCyc' %}
+                                                <span><a href="https://metacyc.org/compound?orgid=META&id={{ cpd[5:] }}" target="_blank">{{ cpd }}</a></span>
+                                            {% elif db == 'KEGG' %}
+                                                <span><a href="https://identifiers.org/kegg.compound:{{ cpd }}" target="_blank">{{ cpd }}</a></span>
+                                            {% elif db == 'ModelSEED' %}
+                                                <span><a href="https://identifiers.org/seed.compound:{{ cpd }}" target="_blank">{{ cpd }}</a></span>
+                                            {% else %}
+                                                <span><a href="https://identifiers.org/bigg.metabolite:{{ cpd }}" target="_blank">{{ cpd }}</a></span>
+                                            {% endif %}
+                                        </div>
+                                    </div>
+                                </div>
+                                <div>
+                                    <div>
+                                        <div class="content">
+                                            <span>{{ dictt['metabolites'][db + '_' + role.lower()[:-1]][cpd]['name'] }}</span>
+                                        </div>
+                                    </div>
+                                </div>
+                                <div>
+                                    <div>
+                                        <div class="content">
+                                            <span>{{ dictt['metabolites'][db + '_' + role.lower()[:-1]][cpd]['stoichiometry'] }}</span>
+                                        </div>
+                                    </div>
+                                </div>
+                                <div>
+                                    <div>
+                                        <div class="content">
+                                            {% for alias in dictt['metabolites'][db + '_' + role.lower()[:-1]][cpd]['aliases'] %}
+                                                <span>{{ alias }}<br></span>
+                                            {% endfor %}
+                                        </div>
+                                    </div>
+                                </div>
+                                <div>
+                                    <div>
+                                        <div class="content">
+                                            <span>{{ dictt['metabolites'][db + '_' + role.lower()[:-1]][cpd]['formula'] }}</span>
+                                        </div>
+                                    </div>
+                                </div>
+                            </div>
+                        {% endfor %}
+                        </div>
+                    </div>
+                </div>
+                {% endfor %}
+            </div>
+        </div>
+        {% else %}
+        {% endif %}
+    {% endfor %}
+    </div>
+    </div>
+    <br>
+    <br>
+    <a href="{{url_for('index')}}"><b>Click here to get back to the home page</b></a>
+<br>
+<br>
+<br>
+</div>
+
+<script src="../static/js/to_show.js"></script>
+
+<div class="footer">
+
+    <table>
+        <tr>
+            <th><a href="{{url_for('index')}}">TranSyT 2019</a> <br>
+                by <a href="https://www.ceb.uminho.pt/People/Profile/davidelagoa" target="_blank">Davide Lagoa</a> and
+                <a href="https://www.ceb.uminho.pt/People/Profile/odias" target="_blank">Oscar Dias</a>
+            </th>
+            <th><a href="https://www.eng.uminho.pt/en" target="_blank"> <img border="0" alt="School of Engineering" src="{{ url_for('static', filename = 'images/EENG.jpg') }}"></a></th>
+            <th><a href="https://www.ceb.uminho.pt/" target="_blank"> <img border="0" alt="Centre of Biological Engineering" src="{{ url_for('static', filename = 'images/ceb1.png') }}"></a></th>
+            <th><a href="https://www.elixir-portugal.org/" target="_blank"> <img border="0" alt="BioData" src="{{ url_for('static', filename = 'images/biodata_elixir.png') }}"></a></th>
+        </tr>
+    </table>
+
+</div>
+
+</body>
+</html>

code/transyt_request.py

+from neo4jPythonDriver import neo4jPythonDriver
+
+def database_retriever_by_id(id):
+    url = 'bolt://palsson.di.uminho.pt:7688'
+    user = 'neo4j'
+    password = 'password'
+
+    driver = neo4jPythonDriver(url, user, password)
+    session = driver.initSession()
+
+    query = "MATCH (r:Reaction)<-[:has_reaction]-(tc:TC_Number)<-[:has_tc]-(ua:Uniprot_Accession) WHERE r.ReactionID = \'" + id + "\' " \
+            "MATCH (r)-[rm]-(y) WHERE EXISTS((y)-[:has_name|:has_molecular_formula]-()) MATCH (y)-[]->(z) RETURN tc.TC_Number, ua, r, rm, y, z"
+
+    result = session.run(query)
+    session.close()
+
+    LABELS = ['MetaCyc', 'KEGG', 'ModelSEED', 'BiGG']
+
+    databases = {}
+
+    for label in LABELS:
+        databases[label] = False
+
+    metabolites = {}
+
+    tc_systems = []
+    reactionID = None
+    metaID = None
+    reaction = None
+
+    output = {}
+
+    for r in result:
+        entry = r[0] + '@' + r[1]['Accession_Number']
+
+        if entry not in tc_systems:
+            tc_systems.append(entry)
+
+        reactionID = r[2]['ReactionID']
+        metaID = r[2]['MetaID']
+        reaction = r[2]['Reaction']
+
+        relationshipType = r[3].type
+
+        metaboliteLabel = list(r[4].labels)[0]
+
+        alias = None
+        formula = None
+
+        if 'Molecular_formula' in list(r[5].labels)[0]:
+            formula = r[5]['Molecular_Formula']
+        elif 'Metabolite_Name' in list(r[5].labels)[0]:
+            alias = r[5]['Name']
+
+        for label in databases.keys():
+            if label in metaboliteLabel:
+                databases[label] = True
+                key = None
+
+                if 'reactant' in relationshipType:
+                    key = label + '_' + 'reactant'
+                elif 'product' in relationshipType:
+                    key = label + '_' + 'product'
+
+                if key is not None:
+
+                    metabolite = {}
+
+                    metaboliteId = r[4]['MetaboliteID']
+
+                    metabolite['name'] = r[4]['Name']
+                    #metabolite['id'] = r[4]['MetaboliteID']
+                    metabolite['stoichiometry'] = r[3]['Stoichiometry']
+                    metabolite['aliases'] = []
+                    metabolite['formula'] = None
+
+
+                    if key not in metabolites:
+                        metabolites[key] = {}
+
+                    #print("coiso" + str(metabolites[key]))
+
+                    #for m in metabolites[key]:
+                    #    print(m)
+
+                    if metaboliteId not in metabolites[key].keys():
+                        metabolites[key][metaboliteId] = metabolite
+
+                    if alias is not None and alias not in metabolites[key][metaboliteId]['aliases']:
+                        metabolites[key][metaboliteId]['aliases'].append(alias)
+
+                    if formula is not None and metabolites[key][metaboliteId]['formula'] is None:
+                        metabolites[key][metaboliteId]['formula'] = formula
+
+    return databases, tc_systems, reactionID, metaID, reaction, metabolites
+
+    # id = 'TR3000069'        #small case
+    # #id = 'TR0000067'       #extreme case
+
+# print()
+# print("########################")
+# print()
+# print(databases)
+# print(tc_systems)
+# print(reactionID)
+# print(metaID)
+# print(reaction)
+# print(metabolites)
+# for key in metabolites:
+#     print(key + "   " + str(metabolites[key]))

requirements.txt

 Flask
 flask-restful
 requests
+neo4j-driver==1.3.1
\ No newline at end of file