diff options
Diffstat (limited to 'app')
| -rw-r--r-- | app/run_docking.py | 82 | ||||
| -rw-r--r-- | app/run_local.py | 82 | ||||
| -rw-r--r-- | app/views.py | 3 |
3 files changed, 2 insertions, 165 deletions
diff --git a/app/run_docking.py b/app/run_docking.py deleted file mode 100644 index 1b86d92..0000000 --- a/app/run_docking.py +++ /dev/null @@ -1,82 +0,0 @@ -import mysql.connector as con - -mycon = con.connect(host="sql12.freesqldatabase.com",user="sql12352288",password="7X35JENbK3",port=3306,database="sql12352288") -mycursor = mycon.cursor() - -sql_select_Query = "select * from curie where done=0 LIMIT 1" -mycursor.execute(sql_select_Query) - -records = mycursor.fetchall() - -def email(zipArchive): - import smtplib - from email.mime.multipart import MIMEMultipart - from email.mime.text import MIMEText - from email.mime.base import MIMEBase - from email import encoders - - fromaddr = "navanchauhan@gmail.com" - toaddr = toEmail - - msg = MIMEMultipart() - msg['From'] = fromaddr - msg['To'] = toaddr - msg['Subject'] = "Curie Web Results for Job ID " + str(jobID) - body = "Attached Zip contains the docked files, PLIP report and PyMOL Visualisations. If the ZIP file does not contain these files, please report this issue by replying to this email. Job was submitted on {} with the description {}".format(date, description) - - msg.attach(MIMEText(body, 'plain')) - filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip" - p = MIMEBase('application', 'octet-stream') - with open((str(zipArchive) + ".zip"), "rb") as attachment: - p.set_payload((attachment).read()) - encoders.encode_base64(p) - p.add_header('Content-Disposition', "attachment; filename= %s" % filename) - msg.attach(p) - - s = smtplib.SMTP('smtp.gmail.com', 587) - s.starttls() - s.login(fromaddr, 'ircd mday avbc tice') - - text = msg.as_string() - - s.sendmail(fromaddr, toaddr, text) - s.quit() - - -print(records[0]) -r = records[0] -jobID = r[0] -toEmail = r[1] -target = r[2] -ligand = r[3] -config = r[4] -date = r[5] -description = r[6] - -import os -cd = os.getcwd() -f = os.path.join(cd,"static/uploads") -t = os.path.join(f,"receptor",target) -r = os.path.join(f,"ligands",ligand) -c = os.path.join(f,"configs",config) -print(f) -import tempfile -from shutil import copy -from shutil import make_archive - -with tempfile.TemporaryDirectory() as directory: - print('The created temporary directory is %s' % directory) - os.chdir(directory) - copy(t,os.getcwd()) - copy(r,os.getcwd()) - copy(c, os.getcwd()) - os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c %s -dpi" % (target,ligand,config)) - #copy("report.pdf",f) - z = "Curie_Web_Result_"+str(jobID) - zi = os.path.join(f,z) - make_archive(zi, 'zip', directory) - #copy(("Curie_Web_Result_"+str(jobID)),f) - email(zi) - #print((str(zi) + ".zip")) - mycursor.execute("UPDATE curie set done=1 where id={}".format(jobID)) - mycon.commit()
\ No newline at end of file diff --git a/app/run_local.py b/app/run_local.py deleted file mode 100644 index 4b902d2..0000000 --- a/app/run_local.py +++ /dev/null @@ -1,82 +0,0 @@ -import mysql.connector as con - -mycon = con.connect(host="sql12.freesqldatabase.com",user="sql12352288",password="7X35JENbK3",port=3306,database="sql12352288") -mycursor = mycon.cursor() - -sql_select_Query = "select * from curie where done=0 LIMIT 1" -mycursor.execute(sql_select_Query) - -records = mycursor.fetchall() - -def email(zipArchive): - import smtplib - from email.mime.multipart import MIMEMultipart - from email.mime.text import MIMEText - from email.mime.base import MIMEBase - from email import encoders - - fromaddr = "navanchauhan@gmail.com" - toaddr = toEmail - - msg = MIMEMultipart() - msg['From'] = fromaddr - msg['To'] = toaddr - msg['Subject'] = "Curie Web Results for Job ID " + str(jobID) - body = "Attached Zip contains the docked files, PLIP report and PyMOL Visualisations. If the ZIP file does not contain these files, please report this issue by replying to this email. Job was submitted on {} with the description {}".format(date, description) - - msg.attach(MIMEText(body, 'plain')) - filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip" - p = MIMEBase('application', 'octet-stream') - with open((str(zipArchive) + ".zip"), "rb") as attachment: - p.set_payload((attachment).read()) - encoders.encode_base64(p) - p.add_header('Content-Disposition', "attachment; filename= %s" % filename) - msg.attach(p) - - s = smtplib.SMTP('smtp.gmail.com', 587) - s.starttls() - s.login(fromaddr, 'ircd mday avbc tice') - - text = msg.as_string() - - s.sendmail(fromaddr, toaddr, text) - s.quit() - - -print(records[0]) -r = records[0] -jobID = r[0] -toEmail = r[1] -target = r[2] -ligand = r[3] -config = r[4] -date = r[5] -description = r[6] - -import os -cd = os.getcwd() -f = os.path.join(cd,"static/uploads") -t = os.path.join(f,"receptor",target) -r = os.path.join(f,"ligands",ligand) -c = os.path.join(f,"configs",config) -print(f) -import tempfile -from shutil import copy -from shutil import make_archive - -with tempfile.TemporaryDirectory() as directory: - print('The created temporary directory is %s' % directory) - os.chdir(directory) - copy(t,os.getcwd()) - copy(r,os.getcwd()) - copy(c, os.getcwd()) - os.system("main_local.sh -r %s -l %s -c %s -dpi" % (target,ligand,config)) - #copy("report.pdf",f) - z = "Curie_Web_Result_"+str(jobID) - zi = os.path.join(f,z) - make_archive(zi, 'zip', directory) - #copy(("Curie_Web_Result_"+str(jobID)),f) - email(zi) - #print((str(zi) + ".zip")) - mycursor.execute("UPDATE curie set done=1 where id={}".format(jobID)) - mycon.commit() diff --git a/app/views.py b/app/views.py index 65dd4a9..86a01fd 100644 --- a/app/views.py +++ b/app/views.py @@ -222,7 +222,8 @@ def dock_upload(): mycon.commit() print("Description",description) - + cwd = os.path.join(os.getcwd(),"app") + subprocess.Popen(['python3', 'dock-docker.py'],cwd=cwd) return render_template('display_result.html', filename="OwO", description=description,job=jobID) flash_errors(form) |