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Commit 982c1625 authored by Davide Lagoa's avatar Davide Lagoa
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Dockerfile 0 → 100755
View file @ 982c1625
FROM python:3-onbuild
COPY . /usr/src/app
WORKDIR /workdir
EXPOSE 80
CMD ["python", "/home/workersManager.py"]
code/.idea/TransytLatestVersion.iml 0 → 100644
View file @ 982c1625
<?xml version="1.0" encoding="UTF-8"?>
<module type="PYTHON_MODULE" version="4">
<component name="Flask">
<option name="enabled" value="true" />
</component>
<component name="NewModuleRootManager">
<content url="file://$MODULE_DIR$" />
<orderEntry type="jdk" jdkName="Python 3.6 (untitled1)" jdkType="Python SDK" />
<orderEntry type="sourceFolder" forTests="false" />
</component>
<component name="TemplatesService">
<option name="TEMPLATE_CONFIGURATION" value="Jinja2" />
<option name="TEMPLATE_FOLDERS">
<list>
<option value="$MODULE_DIR$/templates" />
</list>
</option>
</component>
<component name="TestRunnerService">
<option name="PROJECT_TEST_RUNNER" value="Unittests" />
</component>
</module>
\ No newline at end of file
code/.idea/misc.xml 0 → 100644
View file @ 982c1625
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="JavaScriptSettings">
<option name="languageLevel" value="ES6" />
</component>
<component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6 (untitled1)" project-jdk-type="Python SDK" />
</project>
\ No newline at end of file
code/.idea/modules.xml 0 → 100644
View file @ 982c1625
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectModuleManager">
<modules>
<module fileurl="file://$PROJECT_DIR$/.idea/TransytLatestVersion.iml" filepath="$PROJECT_DIR$/.idea/TransytLatestVersion.iml" />
</modules>
</component>
</project>
\ No newline at end of file
code/.idea/workspace.xml 0 → 100644
View file @ 982c1625
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ChangeListManager">
<list default="true" id="b7761742-cf0b-462b-a78e-3cbc6fd32d3b" name="Default Changelist" comment="" />
<option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
<option name="SHOW_DIALOG" value="false" />
<option name="HIGHLIGHT_CONFLICTS" value="true" />
<option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
<option name="LAST_RESOLUTION" value="IGNORE" />
</component>
<component name="FileEditorManager">
<leaf>
<file pinned="false" current-in-tab="false">
<entry file="file://$PROJECT_DIR$/manager.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="356">
<caret line="217" column="11" lean-forward="true" selection-start-line="217" selection-start-column="11" selection-end-line="217" selection-end-column="11" />
</state>
</provider>
</entry>
</file>
<file pinned="false" current-in-tab="false">
<entry file="file://$PROJECT_DIR$/templates/status.html">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="-664" />
</provider>
</entry>
</file>
<file pinned="false" current-in-tab="true">
<entry file="file://$PROJECT_DIR$/templates/download.html">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="456">
<caret line="52" column="6" lean-forward="true" selection-start-line="52" selection-start-column="6" selection-end-line="52" selection-end-column="6" />
<folding>
<element signature="n#style#0;n#body#0;n#html#0;n#!!top" expanded="true" />
</folding>
</state>
</provider>
</entry>
</file>
<file pinned="false" current-in-tab="false">
<entry file="file://$PROJECT_DIR$/static/css/downloadButton.css">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="80">
<caret line="4" column="21" lean-forward="true" selection-start-line="4" selection-start-column="21" selection-end-line="4" selection-end-column="21" />
</state>
</provider>
</entry>
</file>
</leaf>
</component>
<component name="FileTemplateManagerImpl">
<option name="RECENT_TEMPLATES">
<list>
<option value="CSS File" />
</list>
</option>
</component>
<component name="FindInProjectRecents">
<findStrings>
<find>debug</find>
</findStrings>
</component>
<component name="IdeDocumentHistory">
<option name="CHANGED_PATHS">
<list>
<option value="$PROJECT_DIR$/manager.py" />
<option value="$PROJECT_DIR$/static/css/downloadButton.css" />
<option value="$PROJECT_DIR$/templates/download.html" />
</list>
</option>
</component>
<component name="ProjectFrameBounds" extendedState="7">
<option name="x" value="2" />
<option name="y" value="-918" />
<option name="width" value="1378" />
<option name="height" value="735" />
</component>
<component name="ProjectView">
<navigator proportions="" version="1">
<foldersAlwaysOnTop value="true" />
</navigator>
<panes>
<pane id="ProjectPane">
<subPane>
<expand>
<path>
<item name="TransytLatestVersion" type="b2602c69:ProjectViewProjectNode" />
<item name="TransytLatestVersion" type="462c0819:PsiDirectoryNode" />
</path>
<path>
<item name="TransytLatestVersion" type="b2602c69:ProjectViewProjectNode" />
<item name="TransytLatestVersion" type="462c0819:PsiDirectoryNode" />
<item name="static" type="462c0819:PsiDirectoryNode" />
</path>
<path>
<item name="TransytLatestVersion" type="b2602c69:ProjectViewProjectNode" />
<item name="TransytLatestVersion" type="462c0819:PsiDirectoryNode" />
<item name="static" type="462c0819:PsiDirectoryNode" />
<item name="css" type="462c0819:PsiDirectoryNode" />
</path>
<path>
<item name="TransytLatestVersion" type="b2602c69:ProjectViewProjectNode" />
<item name="TransytLatestVersion" type="462c0819:PsiDirectoryNode" />
<item name="templates" type="462c0819:PsiDirectoryNode" />
</path>
</expand>
<select />
</subPane>
</pane>
<pane id="Scope" />
</panes>
</component>
<component name="PropertiesComponent">
<property name="WebServerToolWindowFactoryState" value="false" />
<property name="last_opened_file_path" value="$PROJECT_DIR$/templates" />
<property name="list.type.of.created.stylesheet" value="CSS" />
<property name="nodejs_interpreter_path.stuck_in_default_project" value="undefined stuck path" />
<property name="nodejs_npm_path_reset_for_default_project" value="true" />
<property name="settings.editor.selected.configurable" value="com.jetbrains.python.configuration.PyActiveSdkModuleConfigurable" />
</component>
<component name="RecentsManager">
<key name="CopyFile.RECENT_KEYS">
<recent name="C:\Users\Diogo\Desktop\TransytLatestVersion\templates" />
</key>
</component>
<component name="RunDashboard">
<option name="ruleStates">
<list>
<RuleState>
<option name="name" value="ConfigurationTypeDashboardGroupingRule" />
</RuleState>
<RuleState>
<option name="name" value="StatusDashboardGroupingRule" />
</RuleState>
</list>
</option>
</component>
<component name="RunManager" selected="Flask server.Flask (manager.py)">
<configuration name="Flask (manager.py)" type="Python.FlaskServer" temporary="true" nameIsGenerated="true">
<module name="TransytLatestVersion" />
<option name="target" value="$PROJECT_DIR$/manager.py" />
<option name="targetType" value="PATH" />
<option name="INTERPRETER_OPTIONS" value="" />
<option name="PARENT_ENVS" value="true" />
<option name="SDK_HOME" value="" />
<option name="WORKING_DIRECTORY" value="" />
<option name="IS_MODULE_SDK" value="true" />
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
<option name="launchJavascriptDebuger" value="false" />
<method v="2" />
</configuration>
<configuration name="TransytLatestVersion" type="Python.FlaskServer">
<module name="TransytLatestVersion" />
<option name="target" value="$PROJECT_DIR$/manager.py" />
<option name="targetType" value="PATH" />
<option name="INTERPRETER_OPTIONS" value="" />
<option name="PARENT_ENVS" value="true" />
<option name="SDK_HOME" value="" />
<option name="WORKING_DIRECTORY" value="" />
<option name="IS_MODULE_SDK" value="false" />
<option name="ADD_CONTENT_ROOTS" value="true" />
<option name="ADD_SOURCE_ROOTS" value="true" />
<EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
<option name="launchJavascriptDebuger" value="false" />
<method v="2" />
</configuration>
<recent_temporary>
<list>
<item itemvalue="Flask server.Flask (manager.py)" />
</list>
</recent_temporary>
</component>
<component name="SvnConfiguration">
<configuration />
</component>
<component name="TaskManager">
<task active="true" id="Default" summary="Default task">
<changelist id="b7761742-cf0b-462b-a78e-3cbc6fd32d3b" name="Default Changelist" comment="" />
<created>1570451179714</created>
<option name="number" value="Default" />
<option name="presentableId" value="Default" />
<updated>1570451179714</updated>
<workItem from="1570451195629" duration="3284000" />
</task>
<servers />
</component>
<component name="TimeTrackingManager">
<option name="totallyTimeSpent" value="3284000" />
</component>
<component name="ToolWindowManager">
<frame x="-90" y="-908" width="1456" height="876" extended-state="6" />
<editor active="true" />
<layout>
<window_info id="Favorites" order="0" side_tool="true" />
<window_info active="true" content_ui="combo" id="Project" order="1" visible="true" weight="0.13610315" />
<window_info id="Structure" order="2" side_tool="true" weight="0.25" />
<window_info anchor="bottom" id="Database Changes" order="0" />
<window_info anchor="bottom" id="Terminal" order="1" />
<window_info anchor="bottom" id="Event Log" order="2" side_tool="true" />
<window_info anchor="bottom" id="Version Control" order="3" />
<window_info anchor="bottom" id="Python Console" order="4" />
<window_info anchor="bottom" id="Docker" order="5" show_stripe_button="false" />
<window_info anchor="bottom" id="Message" order="6" />
<window_info anchor="bottom" id="Find" order="7" />
<window_info anchor="bottom" id="Run" order="8" visible="true" weight="0.32974428" />
<window_info anchor="bottom" id="Debug" order="9" weight="0.4" />
<window_info anchor="bottom" id="Cvs" order="10" weight="0.25" />
<window_info anchor="bottom" id="Inspection" order="11" weight="0.4" />
<window_info anchor="bottom" id="TODO" order="12" />
<window_info anchor="right" id="Database" order="0" />
<window_info anchor="right" id="Commander" internal_type="SLIDING" order="1" type="SLIDING" weight="0.4" />
<window_info anchor="right" id="SciView" order="2" />
<window_info anchor="right" id="Ant Build" order="3" weight="0.25" />
<window_info anchor="right" content_ui="combo" id="Hierarchy" order="4" weight="0.25" />
</layout>
<layout-to-restore>
<window_info id="Favorites" order="0" side_tool="true" />
<window_info content_ui="combo" id="Project" order="1" visible="true" weight="0.13610315" />
<window_info id="Structure" order="2" side_tool="true" weight="0.25" />
<window_info anchor="bottom" id="Database Changes" order="0" />
<window_info anchor="bottom" id="Terminal" order="1" />
<window_info anchor="bottom" id="Event Log" order="2" side_tool="true" />
<window_info anchor="bottom" id="Version Control" order="3" />
<window_info anchor="bottom" id="Python Console" order="4" />
<window_info anchor="bottom" id="Docker" order="5" show_stripe_button="false" />
<window_info anchor="bottom" id="Message" order="6" />
<window_info anchor="bottom" id="Find" order="7" />
<window_info active="true" anchor="bottom" id="Run" order="8" visible="true" weight="0.32974428" />
<window_info anchor="bottom" id="Debug" order="9" weight="0.4" />
<window_info anchor="bottom" id="Cvs" order="10" weight="0.25" />
<window_info anchor="bottom" id="Inspection" order="11" weight="0.4" />
<window_info anchor="bottom" id="TODO" order="12" />
<window_info anchor="right" id="Database" order="0" />
<window_info anchor="right" id="Commander" internal_type="SLIDING" order="1" type="SLIDING" weight="0.4" />
<window_info anchor="right" id="SciView" order="2" />
<window_info anchor="right" id="Ant Build" order="3" weight="0.25" />
<window_info anchor="right" content_ui="combo" id="Hierarchy" order="4" weight="0.25" />
</layout-to-restore>
</component>
<component name="TypeScriptGeneratedFilesManager">
<option name="version" value="1" />
</component>
<component name="com.intellij.coverage.CoverageDataManagerImpl">
<SUITE FILE_PATH="coverage/TransytLatestVersion$Flask__manager_py_.coverage" NAME="Flask (manager.py) Coverage Results" MODIFIED="1570452950979" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="" />
</component>
<component name="editorHistoryManager">
<entry file="file://$PROJECT_DIR$/manager.py">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="356">
<caret line="217" column="11" lean-forward="true" selection-start-line="217" selection-start-column="11" selection-end-line="217" selection-end-column="11" />
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/templates/home.html">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="-240" />
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/static/css/downloadButton.css">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="80">
<caret line="4" column="21" lean-forward="true" selection-start-line="4" selection-start-column="21" selection-end-line="4" selection-end-column="21" />
</state>
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/templates/status.html">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="-664" />
</provider>
</entry>
<entry file="file://$PROJECT_DIR$/templates/download.html">
<provider selected="true" editor-type-id="text-editor">
<state relative-caret-position="456">
<caret line="52" column="6" lean-forward="true" selection-start-line="52" selection-start-column="6" selection-end-line="52" selection-end-column="6" />
<folding>
<element signature="n#style#0;n#body#0;n#html#0;n#!!top" expanded="true" />
</folding>
</state>
</provider>
</entry>
</component>
</project>
\ No newline at end of file
code/docker_config.conf 0 → 100644
View file @ 982c1625
#docker workers configuration
#1 - name of the workers
name = transyt_worker_
#2 - number of workers
limit = 3
#3 - workers port
port = 80
code/manager.py 0 → 100644
View file @ 982c1625
# -*- coding: utf-8 -*-
from flask import Flask, render_template, request, send_file, jsonify
import os
import socket
import shutil
import logging
logPath = '/usr/src/app/logs/'
if not os.path.exists(logPath):
os.makedirs(logPath)
logPath = logPath + 'manager.log'
logging.basicConfig(filename=logPath, level=logging.DEBUG, format='%(asctime)s: %(levelname)s: >>>%(message)s')
logging.info('Starting server')
# subprocess.Popen(["python", "/home/workersManager.py"])
app = Flask(__name__)
hostname = socket.gethostname()
SUBMISSIONS_LIMIT = 100
SUBMISSIONS_PATH = '/workdir/submissions_pool/'
PROCESSING_PATH = '/workdir/processing_pool/'
RESULTS_PATH = '/workdir/results_pool/'
last_submission_ID = 0
print('SERVER WORKING')
@app.route("/")
def index():
logging.info('Welcome page rendering...')
return render_template("home.html")
@app.route("/submit", methods=["POST"])
def submit():
logging.info('HTML submission')
files = request.files.getlist("file")
taxonomyId = request.form["text"]
validInput = verifyInput(taxonomyId)
if not validInput:
return jsonify({"Genome": "Input genome must be in .faa or .fasta format",
"Model": "Model must be in .xml format or a list of metabolites in .txt format (one metabolite per line)",
"Taxonomy ID": "Input must only contain digits"}), 406
logging.info("Taxonomy identifier: " + taxonomyId)
return run(files, taxonomyId, False)
@app.route("/submitMerlinPlugin/<taxonomyId>", methods=["POST"])
def submitMerlinPlugin(taxonomyId):
logging.info('Merlin plugin submission')
files = request.files.getlist("file")
logging.info("files in submission " + str(files))
validInput = verifyInput(taxonomyId)
if not validInput:
return jsonify({"Genome": "Input genome must be in .faa or .fasta format",
"Model": "Model must be in .xml format or a list of metabolites in .txt format (one metabolite per line)",
"Taxonomy ID": "Input must only contain digits"}), 406
return run(files, taxonomyId, True)
def run(files, taxonomyId, isRest):
logging.debug('New submission in progress...')
total = len(os.listdir(SUBMISSIONS_PATH))
if total > SUBMISSIONS_LIMIT:
logging.error('Server capacity overload! Returning error 503 to client!')
return jsonify({"result": "Server overload",
"message": "The server cannot handle the submission due to capacity overload. Please try again later!"}), 503
global last_submission_ID
last_submission_ID += 1
if not request.files.getlist("file")[0].filename:
return jsonify({"result": "rejected",
"message": "fewer files than needed submitted! Submission rejected!", }), 400
submission_path = SUBMISSIONS_PATH + str(last_submission_ID)
if os.path.exists(submission_path):
shutil.rmtree(submission_path, ignore_errors=True)
os.makedirs(submission_path)
logging.debug("Submission " + str(last_submission_ID) + " folder created!")
inputCheck = []
for file in files:
formats = {".faa":"genome.faa", ".fasta":"genome.faa", ".xml":"model.xml"}
fileName = file.filename
inFormats = False
for key in formats:
if fileName.endswith(key):
fileName = formats[key]
inFormats = True
inputCheck.append(formats[key])
if not inFormats and "genome.faa" in inputCheck and fileName.endswith(".txt"):
logging.info("ESTOU A ENTRAR AQUI")
fileName = "metabolites.txt"
inputCheck.append("metabolites.txt")
destination = "/".join([submission_path, fileName])
logging.debug('Saving file ' + fileName + ' at ' + destination)
file.save(destination)
validInput = ["genome.faa","model.xml"]
validInput2 = ["genome.faa","metabolites.txt"]
validInputs = [validInput, validInput2]
logging.info("taxID -> " + taxonomyId)
logging.info("inputCheck -> " + str(inputCheck))
if inputCheck in validInputs:
with open("/".join([submission_path,"taxID.txt"]), "w") as taxFile:
taxFile.write(taxonomyId) # write TaxonomyID file
else:
return jsonify({"Genome":"Input genome must be in .faa or .fasta format", "Model":"Model must be in .xml format or a list of metabolites in .txt format (one metabolite per line)", "Taxonomy ID":"Input must only contain digits"}), 415
with open(submission_path + "/submissionComplete", "w") as f:
f.write("Submission of files complete: ")
if len(os.listdir(submission_path)) < 4:
shutil.rmtree(submission_path)
return jsonify({"result": "rejected",
"message": "fewer files than needed submitted! Submission rejected!", }), 400
if isRest:
return jsonify({"result": "submitted",
"message": "submission accepted. Waiting in queue with " + str(total + 1) + " submissions!",
"queue": total,
"submissionID": str(last_submission_ID)}), 201
#return render_template("status.html", subId = str(last_submission_ID))
return display_msg(str(last_submission_ID), isRest)
@app.route('/status/<submissionID>/<isRest>')
def display_msg(submissionID, isRest):
if isRest == 'False':
isRest = False
elif isRest == 'True':
isRest = True
logging.info("isRest request: " + str(isRest) + " > type: " + str(type(isRest)))
logging.debug("Request to check submission " + submissionID + " status")
folders = os.listdir(SUBMISSIONS_PATH)
logging.info("submissions " + str(folders))
if submissionID in folders:
total = len(folders)
inQueue = countEntriesBelow(folders, submissionID)
if isRest:
return jsonify({"result": "queued",
"message": "Waiting in queue with " + str(total + 1) + " submissions!",
"queue": str(inQueue)}), 201
subStatus = {"result": "queued",
"message": "Waiting in queue",
"queue": "There are " + str(inQueue) + " submissions ahead of yours"}
return render_template("status.html", subId=submissionID, status=subStatus)
folders = os.listdir(PROCESSING_PATH)
logging.info("processing " + str(folders))
if submissionID in folders: # up and running response
logging.debug("Submission " + submissionID + "still running")
if isRest:
return jsonify({"result": "processing", "message": "accepted but process still running, please wait."}), 202
subStatus = {"result": "processing", "message": "accepted but process still running, please wait."}
return render_template("status.html", subId=submissionID, status=0), 202
folders = os.listdir(RESULTS_PATH)
logging.info("results " + str(folders))
if submissionID in folders:
logging.debug("Submission " + submissionID + " results complete")
if isRest:
return jsonify(
{"result": "success", "message": "the process is now complete. Download the results at ./downloads"}), 200
#return download(submissionID)
return render_template("download.html", subId = submissionID), 200
return jsonify({"result": "Server error",
"message": "Something went wrong while processing the request, please try again", }), 500
@app.route("/download/<submissionID>")
def download(submissionID):
logging.debug("Request to download submission " + submissionID + " results")
return send_file(RESULTS_PATH + submissionID + "/results.zip", as_attachment=True,
attachment_filename='results.zip')
def countEntriesBelow(l, id):
id = int(id)
res = 0
for d in l:
if int(d) == id:
return res
elif int(d) < id:
res += 1
return res
def verifyInput(userInput):
userInput = str(userInput)
validTaxID = False
if userInput:
validTaxID = True
digits = "0123456789"
for character in userInput:
if character not in digits:
validTaxID = False
return validTaxID
logging.info('Server running!')
if __name__ == "__main__":
app.run(host="0.0.0.0", port=80, threaded=True, debug=True)
code/static/css/center.css 0 → 100644
View file @ 982c1625
.center {
margin: auto;
width: 60%;
border: 3px solid #000066;
padding: 10px;
word-wrap: break-word;
font-family: 'Oxygen';
}
.center h1 {
color: black;
font-family: 'Oxygen';
font-size: 28px;
}
.center h3 {
color: black;
font-family: 'Oxygen';
font-size: 20px;
}
.center p {
color: black;
font-family: 'Oxygen';
}
.center li {
color: black;
font-family: 'Oxygen';
}
code/static/css/downloadButton.css 0 → 100644
View file @ 982c1625
.downloadBtn {
background-color: DodgerBlue;
border: none;
color: white;
padding: 12px 30px;
cursor: pointer;
font-size: 18px;
}
/* Darker background on mouse-over */
.downloadBtn:hover {
background-color: RoyalBlue;
}
\ No newline at end of file
code/static/css/submit.css 0 → 100644
View file @ 982c1625
.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;
}
\ No newline at end of file
code/templates/download.html 0 → 100644
View file @ 982c1625
<!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') }}">
<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/home.html 0 → 100644
View file @ 982c1625
<!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="//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 style="background: #fefcfe">
<div class="center" align="center" style="border: 0">
<br>
<br>
<h1><b>Welcome to TranSyT </b></h1>
<br>
<br>
<img src="{{ url_for('static', filename = 'images/transportProtein.gif') }}" alt="Transport Protein">
<br>
<br>
<h1>Transport Systems Tracker</h1>
<br>
<br>
<p align="justify">The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes, based on the annotations of the Transporter Classification Database (TCDB).
In addition, this tool also generates the respective transport reactions while providing the respective Gene-Protein-Reaction associations.</p>
<p align="justify">TranSyT can receive as input the organism NCBI taxonomy identifier, its genome sequence in a fasta file format and its constraint-based metabolic model in the SBML file format or a metabolites list in text file format.</p>
<br>
<br>
<div class="search_bar">
<form id="upload-form" action="{{url_for('submit')}}" method="POST" enctype="multipart/form-data">
<h3>Submit NCBI Taxonomy number</h3>
<br>
<div class="inner-form">
<div class="input-field first-wrap">
<input placeholder="Example: 83333 for Escherichia coli" name="text"/>
</div>
</div>
<br>
<br>
<h3>Upload genome file in <b>fasta</b> format</h3>
<br>
<div class="inner-form">
<div class="input-field third-wrap">
<label class="input-field third-wrap custom-file-upload">
<input type="file" name="file" multiple />
Upload Genome
</label>
</div>
</div>
<br>
<br>
<h3>Upload a model file in <b>xml</b> format or a metabolites list in <b>txt</b> format </h3>
<br>
<div class="inner-form">
<div class="input-field third-wrap">
<label class="input-field third-wrap custom-file-upload">
<input type="file" name="file" multiple/>
Upload Model or Metabolites
</label>
</div>
</div>
<br>
<br>
<br>
<br>
<div class="inner-form" style="background-color: #27ae60; max-width: 30%">
<div class="input-field fourth-wrap">
<label class="input-field fourth-wrap custom-file-upload">
<input type="submit" name="send" />
Submit
</label>
</div>
</div>
</form>
</div>
</div>
<br>
<br>
<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/status.html 0 → 100644
View file @ 982c1625
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="refresh" content="5;url={{url_for('display_msg', submissionID = subId, isRest = False)}}">
<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') }}">
<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>Status report</b></h3>
<p>Submission ID: {{subId}}</p> <br>
{% if status["queue"] %}
<h3>{{status["queue"]}}</h3>
{% endif %}
{% if status["message"] %}
<h3>{{status["message"]}}</h3>
{% endif %}
<h3>This page refreshes automatically, 5 seconds at a time. Please wait for your download to be ready!</h3>
</div>
<br>
<br>
<br>
<br>
<br>
<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/upload2.html 0 → 100644
View file @ 982c1625
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Upload</title>
</head>
<body>
<h1>TranSyT's NEW Files Uploader</h1>
<p>The submissions will only be valid if the following files are submitted:</p>
<p>Genome as 'genome.faa'</p>
<p>Taxonomy identifier (write the number inside a simple txt file) as taxID.txt</p>
<p>Model as 'model.xml'!!</p>
<p></p>
<p>Please submit the files with the names above!</p>
<form id="upload-form" action="{{url_for('submit')}}" method="POST" enctype="multipart/form-data">
<input type="file" name="file" multiple>
<input type="submit" name="send">
</form>
</body>
</html>
code/workersManager.py 0 → 100644
View file @ 982c1625
import logging
import time
import os
import requests
import shutil
import subprocess
RESULTS_LIMIT = 30
SUBMISSIONS_PATH = '/workdir/submissions_pool/'
PROCESSING_PATH = '/workdir/processing_pool/'
RESULTS_PATH = '/workdir/results_pool/'
CONFIGURATION_FILE = '/home/docker_config.conf'
if os.path.exists(SUBMISSIONS_PATH):
shutil.rmtree(SUBMISSIONS_PATH, ignore_errors=True)
if os.path.exists(PROCESSING_PATH):
shutil.rmtree(PROCESSING_PATH, ignore_errors=True)
if os.path.exists(RESULTS_PATH):
shutil.rmtree(RESULTS_PATH, ignore_errors=True)
os.makedirs(SUBMISSIONS_PATH)
os.makedirs(PROCESSING_PATH)
os.makedirs(RESULTS_PATH)
logPath = '/usr/src/app/logs/'
if not os.path.exists(logPath):
os.makedirs(logPath)
logPath = logPath + 'managerWorkers.log'
logging.basicConfig(filename=logPath, level=logging.DEBUG, format='%(asctime)s: %(levelname)s: >>>%(message)s')
def run():
mapping = initializeWorkers()
while True: # infinite loop
submissionID = None
workerID = None
try:
submissions = os.listdir(SUBMISSIONS_PATH)
# logging.info("Submissions len = " + str(len(submissions)))
if len(submissions) > 0:
submissionID = getNextInQueue(submissions)
logging.info("Next in queue = " + submissionID)
workerID = findAvailableWorker(mapping)
logging.info("Available workerID = " + str(workerID))
if workerID is not None:
mapping[workerID] = submissionID
port = configs.get('port')
processingPath = PROCESSING_PATH + submissionID
shutil.move(SUBMISSIONS_PATH + submissionID, processingPath)
processingPath = processingPath.replace('/', '$')
logging.info("Sending request to start to " + str(workerID))
logging.info(
"http://" + workerID + ":" + port + "/start/" + processingPath + "/" + RESULTS_PATH.replace('/',
'$') + submissionID)
requests.get("http://" + workerID + ":" + port + "/start/" + processingPath + "/" + RESULTS_PATH.replace('/',
'$') + submissionID) # request worker docker to run
results = os.listdir(RESULTS_PATH)
processes = os.listdir(PROCESSING_PATH)
for key in mapping.keys(): # reset workers that finished
if mapping[key] in results:
subResult = os.listdir(RESULTS_PATH + mapping[key])
if 'processComplete' in subResult or mapping[key] not in processes:
mapping[key] = None
cleanResultsDirectory()
except:
path = SUBMISSIONS_PATH + str(submissionID)
logging.error('An error occurred while processing submission ' + str(submissionID) + '!')
if os.path.exists(path):
shutil.rmtree(path)
time.sleep(5)
def getNextInQueue(l):
integerList = [int(i) for i in l]
while len(integerList) > 0:
nextSub = min(integerList)
if len(os.listdir(SUBMISSIONS_PATH + str(nextSub))) > 3:
return str(nextSub)
integerList.remove(nextSub)
return None
def initializeWorkers():
dic = {}
workersLimit = int(configs.get('limit'))
for i in range(1, workersLimit + 1):
key = configs['name'] + str(i)
logging.info('new worker instantiated -> ' + key)
dic[key] = None
logging.info(str(workersLimit) + " workers initialized")
return dic
def findAvailableWorker(mapping):
logging.info('Workers status: ' + str(mapping))
print(mapping)
for key in mapping.keys():
if mapping[key] is None:
return key
return None
def cleanResultsDirectory():
results = os.listdir(RESULTS_PATH)
while len(results) > RESULTS_LIMIT:
directoryID = getNextInQueue(results)
logging.info('Deleting directory ' + directoryID + ' from results!')
shutil.rmtree(RESULTS_PATH + directoryID, ignore_errors=True)
if os.path.exists(PROCESSING_PATH):
shutil.rmtree(PROCESSING_PATH + directoryID, ignore_errors=True)
results.remove(directoryID)
def read_conf_file():
res = {}
with open(CONFIGURATION_FILE) as file:
lines = file.readlines()
for line in lines:
if '=' in line:
l = line.replace(" ", "").replace("\n", "")
l_str = l.split('=')
res[l_str[0]] = l_str[1]
logging.info('Configurations: ' + str(res))
return res
configs = read_conf_file()
logging.info("Docker configurations: " + str(configs))
if __name__ == '__main__':
logging.info("Starting server!")
subprocess.Popen(["python", "/home/manager.py"])
logging.info("Starting service!")
run()
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