From: Agnibho Mondal Date: Tue, 8 Dec 2015 19:09:21 +0000 (+0530) Subject: First commit X-Git-Url: https://code.agnibho.com/repo?a=commitdiff_plain;h=49346f79fdffaccfa0a65dc0ba412311aa27a668;p=ddstorm.git First commit --- diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..94a9ed0 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md deleted file mode 100644 index 41e7c81..0000000 --- a/README.md +++ /dev/null @@ -1,2 +0,0 @@ -# ddstorm -A python application for brainstorming medical differential diagnosis diff --git a/README.txt b/README.txt new file mode 100644 index 0000000..f9106e2 --- /dev/null +++ b/README.txt @@ -0,0 +1,38 @@ + DDStorm + ======= + +What is DDStorm? +------------------- + +DDStorm is a python application for brainstorming medical differential +diagnosis. + +DDStorm is still in development phase and not ready for deployment. + +Licensing +--------- + +Copyright (c) 2015 Agnibho Mondal +All rights reserved + +This file is part of DDStorm. + +DDStorm is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +DDStorm is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with DDStorm. If not, see . + +Contacts +-------- + +Agnibho Mondal +mail@agnibho.com +www.agnibho.com diff --git a/__main__.py b/__main__.py new file mode 100644 index 0000000..1b430c2 --- /dev/null +++ b/__main__.py @@ -0,0 +1,141 @@ +#! /usr/bin/python3 + +# DDStorm +# ------- +# Copyright (c) 2015 Agnibho Mondal +# All rights reserved + +# This file is part of DDStorm. + +# DDStorm is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# DDStorm is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with DDStorm. If not, see . + +import sys, time, subprocess +from PyQt4 import QtGui, QtCore +from _symptoms import Symptoms +from _differentials import Differentials +from ddstorm import DDStorm +from conf import Conf +from _extras import * +from const import * + +conf=False + +class Content(QtGui.QWidget): + change=QtCore.pyqtSignal() + def __init__(self): + super(Content, self).__init__() + self.dd=DDStorm(True,conf) + if(not self.dd.compiler.clean): + ret=QtGui.QMessageBox.warning(self, "Compilation Error", "Error was encountered while compiling the Knowledgebase.", "Ignore", "View Log") + if(ret==1): + x_logfile() + self.initUI() + def initUI(self): + global conf + + grid=QtGui.QGridLayout() + self.setLayout(grid) + + self.symp=Symptoms(self.dd.symptoms()) + self.symp.setFrameShape(QtGui.QFrame.StyledPanel) + self.symp.changed.connect(self.update) + + self.diff=Differentials() + self.diff.setFrameShape(QtGui.QFrame.StyledPanel) + + grid.addWidget(self.symp, 0, 0) + grid.addWidget(self.diff, 0, 1) + grid.setColumnStretch(0, 1) + grid.setColumnStretch(1, 1) + QtGui.QApplication.setStyle(QtGui.QStyleFactory.create("Cleanlooks")) + def update(self, data): + self.diff.update(self.dd.dd(data)) + self.change.emit() + +class Window(QtGui.QMainWindow): + def __init__(self): + super(Window, self).__init__() + self.initUI() + def initUI(self): + global conf + self.con=Content() + self.sett=SettingsDialog(conf) + if(conf.get("status_message")=="on"): + self.con.change.connect(self.showStatus) + + menu=self.menuBar() + menuFile=menu.addMenu("&File") + menuFile.addAction("&Save").triggered.connect(self.savefile) + menuFile.addAction("E&xit").triggered.connect(self.close) + menuEdit=menu.addMenu("&Edit") + menuEdit.addAction("&Add").triggered.connect(self.con.symp.addItem) + menuEdit.addAction("&Browse Symptoms").triggered.connect(self.con.symp.browseSymptoms) + rmAction=QtGui.QAction("&Remove", self) + rmAction.setShortcut("Delete") + rmAction.triggered.connect(self.con.symp.remove) + menuEdit.addAction(rmAction) + menuEdit.addAction("&Clear All").triggered.connect(self.con.symp.removeAll) + menuTool=menu.addMenu("&Tools") + menuTool.addAction("&Library").triggered.connect(x_lib) + menuTool.addAction("&Settings").triggered.connect(self.settings) + menuTool.addAction("&View Log").triggered.connect(x_logfile) + menuHelp=menu.addMenu("&Help") + menuHelp.addAction("&Help").triggered.connect(x_help) + menuHelp.addAction("&About").triggered.connect(self.about) + + self.setCentralWidget(self.con) + self.status=self.statusBar() + self.setGeometry(200, 200, 600, 400) + self.setWindowTitle("D/D Storm") + self.setWindowIcon(QtGui.QIcon("icons/icon.png")) + self.showMaximized() + self.con.symp.new.setFocus() + def showStatus(self): + if(self.con.symp.getList() and self.con.diff.getList()): + self.status.showMessage(str(len(self.con.diff.getList()))+" differential diagnosis for "+str(len(self.con.symp.getList()))+" symptom(s).") + else: + self.status.showMessage("") + def savefile(self): + x_save(self, self.con.symp.getList(), self.con.diff.getList()) + def settings(self): + self.sett.exec_() + def about(self): + QtGui.QMessageBox.about(self, "About", "

DDStorm

\nBrainstorm Medicine") + +def main(): + app=QtGui.QApplication(sys.argv) + + global conf + conf=Conf() + if(conf.get("clean_log")=="yes"): + open(LOG_FILE, "w").close() + if(conf.get("splash_screen")=="yes"): + ss=True + else: + ss=False + if(ss): + splash=QtGui.QSplashScreen(QtGui.QPixmap("icons/splash.png")) + splash.show() + time.sleep(0.1) + app.processEvents() + splash.showMessage("Loading...") + + w=Window() + if(ss): + splash.finish(w) + + sys.exit(app.exec_()) + +if(__name__=="__main__"): + main() diff --git a/_differentials.py b/_differentials.py new file mode 100644 index 0000000..16f86d3 --- /dev/null +++ b/_differentials.py @@ -0,0 +1,47 @@ +# DDStorm +# ------- +# Copyright (c) 2015 Agnibho Mondal +# All rights reserved + +# This file is part of DDStorm. + +# DDStorm is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# DDStorm is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with DDStorm. If not, see . + +from PyQt4 import QtGui + +class Differentials(QtGui.QFrame): + data=[] + def __init__(self): + super(Differentials, self).__init__() + self.initUI() + def initUI(self): + self.label=QtGui.QLabel("Differential Diagnosis") + self.label.setStyleSheet("font-size:18px") + self.listWidget=QtGui.QListWidget(self) + self.listWidget.setStyleSheet("font-size:14px") + self.listWidget.setSelectionMode(0) + box=QtGui.QVBoxLayout() + box.addWidget(self.label) + box.addWidget(self.listWidget) + self.setLayout(box) + + def update(self, data): + self.data=data + self.listWidget.clear() + if(self.data): + for d in self.data: + QtGui.QListWidgetItem(d, self.listWidget) + + def getList(self): + return self.data diff --git a/_extras.py b/_extras.py new file mode 100644 index 0000000..d15e627 --- /dev/null +++ b/_extras.py @@ -0,0 +1,163 @@ +# DDStorm +# ------- +# Copyright (c) 2015 Agnibho Mondal +# All rights reserved + +# This file is part of DDStorm. + +# DDStorm is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# DDStorm is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with DDStorm. If not, see . + +import subprocess, os +from PyQt4 import QtGui, QtCore +from const import * + +def x_settings(): + subprocess.Popen(["xdg-open", CONF_FILE]) + +def x_lib(): + if(os.path.isfile(CONF_FILE)): + with open(CONF_FILE) as conf: + for line in conf: + if(line.startswith("library_path=")): + library_path=line[13:-1] + if(os.path.isdir(library_path)): + subprocess.Popen(["xdg-open", library_path]) + +def x_save(w, symp, diff): + fname=QtGui.QFileDialog.getSaveFileName(w, "Save File", "~", "HTML files('*.html')") + if(not fname.endswith(".html")): + fname=fname+".html" + with open(fname, "w") as f: + print("Differential Diagnosis", file=f) + print("

Differential Diagnosis

", file=f) + print("", file=f) + print("", file=f) + print("
SymptomsDiffrential Diagnosis
    ", file=f) + for s in symp: + print("
  1. "+s+"
    2. ", file=f) + print("
    ", file=f) + for d in diff: + print("
  1. "+d+"
    2. ", file=f) + print("
", file=f) + +def x_help(): + if(os.path.isfile(HELP_FILE)): + subprocess.Popen(["xdg-open", HELP_FILE]) + else: + subprocess.Popen(["xdg-open", "http://www.agnibho.com"]) + +def x_logfile(): + subprocess.Popen(["xdg-open", LOG_FILE]) + +class SettingsDialog(QtGui.QDialog): + def __init__(self, conf): + super(SettingsDialog, self).__init__() + self.setWindowTitle("Settings") + self.conf=conf + self.initUI() + def initUI(self): + self.lpLabel=QtGui.QLabel("Libary Path:") + self.lpEdit=QtGui.QLineEdit(self.conf.get("library_path")) + self.lpBrowse=QtGui.QPushButton("Browse") + self.lpBrowse.clicked.connect(self.lpUpdate) + self.mpLabel=QtGui.QLabel("Module Path:") + self.mpEdit=QtGui.QLineEdit(self.conf.get("module_path")) + self.mpBrowse=QtGui.QPushButton("Browse") + self.mpBrowse.clicked.connect(self.mpUpdate) + self.splash=QtGui.QCheckBox("Show Splash Screen") + if(self.conf.get("splash_screen")=="yes"): + self.splash.setChecked(True) + self.clean=QtGui.QCheckBox("Clean Log on Exit") + if(self.conf.get("clean_log")=="yes"): + self.clean.setChecked(True) + self.status=QtGui.QCheckBox("Show Status Message") + if(self.conf.get("status_message")=="on"): + self.status.setChecked(True) + self.ok=QtGui.QPushButton("Ok") + self.ok.clicked.connect(self.save) + self.cancel=QtGui.QPushButton("Cancel") + self.cancel.clicked.connect(self.close) + self.default=QtGui.QPushButton("Default") + self.default.clicked.connect(self.reset) + + ctrl=QtGui.QHBoxLayout() + ctrl.addWidget(self.ok) + ctrl.addWidget(self.cancel) + ctrl.addWidget(self.default) + layout=QtGui.QGridLayout(self) + layout.addWidget(self.lpLabel, 0, 0) + layout.addWidget(self.lpEdit, 0, 1) + layout.addWidget(self.lpBrowse, 0, 2) + layout.addWidget(self.mpLabel, 1, 0) + layout.addWidget(self.mpEdit, 1, 1) + layout.addWidget(self.mpBrowse, 1, 2) + layout.addWidget(self.splash, 2, 0) + layout.addWidget(self.clean, 3, 0) + layout.addWidget(self.status, 4, 0) + layout.addLayout(ctrl, 5, 1) + + self.cancel.setFocus() + + def lpUpdate(self): + self.lpEdit.setText(self.getFolder()) + def cpUpdate(self): + self.cpEdit.setText(self.getFolder()) + def mpUpdate(self): + self.mpEdit.setText(self.getFolder()) + + def getFolder(self): + dn=QtGui.QFileDialog.getExistingDirectory() + if(dn.startswith(QtCore.QDir.currentPath())): + dn="."+dn[len(QtCore.QDir.currentPath()):]+"/" + else: + dn=dn+"/" + return dn + + def save(self): + self.conf.set("library_path", self.lpEdit.text()) + self.conf.set("class_path", self.cpEdit.text()) + self.conf.set("module_path", self.mpEdit.text()) + if(self.splash.isChecked()): + self.conf.set("splash_screen", "yes") + else: + self.conf.set("splash_screen", "no") + if(self.clean.isChecked()): + self.conf.set("clean_log", "yes") + else: + self.conf.set("clean_log", "no") + if(self.status.isChecked()): + self.conf.set("status_message", "on") + else: + self.conf.set("status_message", "off") + QtGui.QMessageBox.information(self, "Restart required", "Some settings takes effect only after restarting DDStorm") + self.close() + self.conf.write() + + def reset(self): + self.conf.default() + self.lpEdit.setText(self.conf.get("library_path")) + self.cpEdit.setText(self.conf.get("class_path")) + self.mpEdit.setText(self.conf.get("module_path")) + if(self.conf.get("splash_screen")=="yes"): + self.splash.setChecked(True) + else: + self.splash.setChecked(False) + if(self.conf.get("clean_log")=="yes"): + self.clean.setChecked(True) + else: + self.clean.setChecked(False) + if(self.conf.get("status_message")=="on"): + self.status.setChecked(True) + else: + self.status.setChecked(False) diff --git a/_symptoms.py b/_symptoms.py new file mode 100644 index 0000000..2d7d8d6 --- /dev/null +++ b/_symptoms.py @@ -0,0 +1,139 @@ +# DDStorm +# ------- +# Copyright (c) 2015 Agnibho Mondal +# All rights reserved + +# This file is part of DDStorm. + +# DDStorm is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# DDStorm is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with DDStorm. If not, see . + +from PyQt4 import QtGui, QtCore + +class Symptoms(QtGui.QFrame): + sympList=[] + changed=QtCore.pyqtSignal(list) + def __init__(self, auto): + super(Symptoms, self).__init__() + self.auto=auto + self.initUI() + + def initUI(self): + self.label=QtGui.QLabel("Symptoms") + self.label.setStyleSheet("font-size:18px") + + self.listWidget=QtGui.QListWidget(self) + self.listWidget.setStyleSheet("font-size:14px") + self.listWidget.setSelectionMode(4) + + self.rm=QtGui.QPushButton("Remove") + self.rm.clicked.connect(self.remove) + + self.cl=QtGui.QPushButton("Clear All") + self.cl.clicked.connect(self.removeAll) + + self.browse=QtGui.QPushButton("Browse Symptoms") + self.browse.clicked.connect(self.browseSymptoms) + + self.add=QtGui.QPushButton("Add") + self.add.clicked.connect(self.addItem) + + self.new=QtGui.QLineEdit(self) + self.new.returnPressed.connect(self.addItem) + self.completer=QtGui.QCompleter(self.auto) + self.completer.setCaseSensitivity(0) + self.completer.setCompletionMode(2) + self.new.setCompleter(self.completer) + + self.browser=SymptomBrowser(self.auto) + self.browser.added.connect(self.addItem) + + hboxt=QtGui.QHBoxLayout() + hboxt.addWidget(self.new) + hboxt.addWidget(self.add) + hboxb=QtGui.QHBoxLayout() + hboxb.addWidget(self.rm) + hboxb.addWidget(self.cl) + hboxb.addWidget(self.browse) + vbox=QtGui.QVBoxLayout() + vbox.addWidget(self.label) + vbox.addLayout(hboxt) + vbox.addWidget(self.listWidget) + vbox.addLayout(hboxb) + self.setLayout(vbox) + + def addItem(self, text=""): + if(not text): + text=self.new.text() + if(len(text)>0): + if(text in self.sympList): + QtGui.QMessageBox.information(self, "Duplicate Symptom", "'"+text+"' has already been added to the symptom list.") + elif(text in self.auto): + QtGui.QListWidgetItem(text, self.listWidget) + self.sympList.append(text) + self.new.clear() + self.changed.emit(list(self.sympList)) + else: + QtGui.QMessageBox.warning(self, "Symptom Unvailable", "'"+text+"' is not available in the current Library.") + + def remove(self, all=False): + if(len(self.listWidget.selectedItems())>0): + for item in self.listWidget.selectedItems(): + self.sympList.remove(item.text()) + self.listWidget.takeItem(self.listWidget.row(item)) + self.changed.emit(list(self.sympList)) + + def removeAll(self): + self.listWidget.clear() + del self.sympList[:] + self.changed.emit(list(self.sympList)) + + def browseSymptoms(self): + self.browser.exec_() + + def getList(self): + return self.sympList + +class SymptomBrowser(QtGui.QDialog): + added=QtCore.pyqtSignal(str) + def __init__(self, items): + super(SymptomBrowser, self).__init__() + self.setWindowTitle("Choose Symptom") + self.items=items + self.initUI() + + def initUI(self): + self.search=QtGui.QLineEdit() + self.search.textChanged.connect(self.refresh) + self.listItems=QtGui.QListWidget() + self.listItems.activated.connect(self.sendUp) + + layout=QtGui.QVBoxLayout(self) + layout.addWidget(self.search) + layout.addWidget(self.listItems) + + self.listItems.addItems(self.items) + self.search.setFocus() + + def refresh(self): + term=self.search.text() + buff=[] + for i in self.items: + if(term.lower() in i.lower()): + buff.append(i) + self.listItems.clear() + self.listItems.addItems(buff) + + def sendUp(self): + self.added.emit(self.listItems.currentItem().text()) + self.close() diff --git a/alias.py b/alias.py new file mode 100644 index 0000000..d4e013e --- /dev/null +++ b/alias.py @@ -0,0 +1,70 @@ +#! /usr/bin/python3 + +# DDStorm +# ------- +# Copyright (c) 2015 Agnibho Mondal +# All rights reserved + +# This file is part of DDStorm. + +# DDStorm is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# DDStorm is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with DDStorm. If not, see . + +import sys, os +from fnmatch import fnmatch +from conf import Conf +from const import * + +class Alias: + def __init__(self, conf=False): + self.data={} + if(conf): + self.conf=conf + else: + self.conf=Conf() + self.compile() + + def compile(self): + for path, subdirs, files in os.walk(self.conf.get("alias_path")): + for name in files: + if(fnmatch(name, "*.txt")): + with open(self.conf.get("alias_path")+name, "r") as f: + for line in f: + line=line.rstrip().split("#")[0] + if(len(line)==0): + pass + else: + terms=[] + for i in line.split(";"): + if(i.strip()): + terms.append(i.strip()) + if(len(terms)==2): + self.data[terms[-1]]=terms[0] + elif(len(terms)>2): + t=terms.pop(0) + for i in terms: + self.data[i]=t + + def get(self, term): + if(term in self.data): + return self.data[term] + else: + return term + +def main(): + a=Alias() + if(len(sys.argv)>1): + print(a.get(sys.argv[1])) + +if(__name__=="__main__"): + main() diff --git a/compile.py b/compile.py new file mode 100644 index 0000000..a94e730 --- /dev/null +++ b/compile.py @@ -0,0 +1,122 @@ +#! /usr/bin/python3 + +# DDStorm +# ------- +# Copyright (c) 2015 Agnibho Mondal +# All rights reserved + +# This file is part of DDStorm. + +# DDStorm is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# DDStorm is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with DDStorm. If not, see . + +import os, logging, re +from operator import itemgetter +from fnmatch import fnmatch +from conf import Conf +from const import * +from alias import Alias +logging.basicConfig(filename=LOG_FILE) + +class Compile: + def __init__(self, conf=False): + self.source=set() + self.custom=set() + if(conf): + self.conf=conf + else: + self.conf=Conf() + self.alias=Alias(conf) + self.clean=True + for path, subdirs, files in os.walk(self.conf.get("library_path")): + for name in files: + if(fnmatch(name, "*.txt")): + self.source.add(os.path.join(path, name)) + for path, subdirs, files in os.walk(self.conf.get("custom_path")): + for name in files: + if(fnmatch(name, "*.txt")): + self.custom.add(os.path.join(path, name)) + if(not os.path.isdir(self.conf.get("module_path"))): + os.makedirs(self.conf.get("module_path")) + for f in os.listdir(self.conf.get("module_path")): + if(fnmatch(f, "*.module")): + os.unlink(self.conf.get("module_path")+f) + self.priorityRegex=re.compile("(?<=\.)\d+$") + for src in self._sortPriority(self.source): + self._makeModule(src) + for src in self._sortPriority(self.custom): + self._makeModule(src) + + def _sortPriority(self, files): + ls=[] + for addr in files: + name=os.path.splitext(os.path.basename(addr))[0].lower().replace("_"," ").replace("-", " ") + m=re.search(self.priorityRegex, name) + if(m): + ls.append((name.replace("."+m.group(), ""), int(m.group()), addr)) + else: + ls.append((name, 100, addr)) + ls.sort(reverse=True) + if(ls): + return(list(zip(*ls))[2]) + else: + return ls + + def _makeModule(self, src): + module=os.path.splitext(os.path.basename(src))[0].lower().replace("_"," ").replace("-", " ") + m=re.search(self.priorityRegex, module) + if(m): + module=module.replace("."+m.group(), "") + modFile=self.conf.get("module_path")+module+".module" + modFlag=False + with open(src, "r") as sf, open(modFile, "a") as tf: + for line in sf: + line=line.strip().split("#")[0] + if(len(line)==0): + pass + elif(line.startswith("!")): + pass + elif(line.startswith("#")): + pass + elif(line.startswith("+")): + modFlag=True + elif(line.startswith("-")): + modFlag=True + elif(line.replace(" ","").replace("-","").replace("_","").replace("'","").isalnum()): + print(self.alias.get(line).capitalize(), file=tf) + else: + self.clean=False + logging.warning("Syntax error in file '"+src+"': "+line) + if(modFlag): + modFlag=False + with open(src, "r") as f: + for line in f: + line=line.strip().split("#")[0] + if(line[1:].replace(" ","").replace("-","").replace("_","").replace("'","").isalnum()): + if(line.startswith("+")): + with open(modFile, "r") as fn: + text=fn.read() + with open(modFile, "w") as fn: + print(self.alias.get(line[1:]).capitalize()+"\n"+text, file=fn) + elif(line.startswith("-")): + with open(modFile, "r") as fn: + text=fn.read() + text=text.replace(self.alias.get(line[1:]).capitalize()+"\n", "") + with open(modFile, "w") as fn: + print(text, file=fn) + +def main(): + c=Compile() + +if(__name__=="__main__"): + main() diff --git a/conf.py b/conf.py new file mode 100644 index 0000000..fb00ae4 --- /dev/null +++ b/conf.py @@ -0,0 +1,100 @@ +#! /usr/bin/python3 + +# DDStorm +# ------- +# Copyright (c) 2015 Agnibho Mondal +# All rights reserved + +# This file is part of DDStorm. + +# DDStorm is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# DDStorm is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with DDStorm. If not, see . + +import os, logging +from const import * +logging.basicConfig(filename=LOG_FILE) + +class Conf: + conf={} + def __init__(self, filename=CONF_FILE): + self.filename=filename + self.default() + self.read() + + def default(self): + self.conf["library_path"]="./library/" + self.conf["custom_path"]="./custom/" + self.conf["index_path"]="./index/" + self.conf["alias_path"]="./alias/" + self.conf["module_path"]="./modules/" + self.conf["splash_screen"]="yes" + self.conf["clean_log"]="no" + self.conf["status_message"]="on" + + def read(self): + if(os.path.isfile(self.filename)): + with open(self.filename) as f: + for line in f: + line="".join(line.split()) + if(line.startswith("#")): + pass + elif(line.startswith("library_path=")): + self.conf["library_path"]=line[13:] + if(os.path.isdir(self.conf["library_path"])): + if(not self.conf["library_path"].endswith("/")): + self.conf["library_path"]+="/" + elif(line.startswith("custom_path=")): + self.conf["custom_path"]=line[12:] + if(os.path.isdir(self.conf["custom_path"])): + if(not self.conf["custom_path"].endswith("/")): + self.conf["custom_path"]+="/" + elif(line.startswith("index_path=")): + self.conf["index_path"]=line[11:] + if(os.path.isdir(self.conf["index_path"])): + if(not self.conf["index_path"].endswith("/")): + self.conf["index_path"]+="/" + elif(line.startswith("alias_path=")): + self.conf["alias_path"]=line[11:] + if(os.path.isdir(self.conf["alias_path"])): + if(not self.conf["alias_path"].endswith("/")): + self.conf["alias_path"]+="/" + elif(line.startswith("module_path=")): + self.conf["module_path"]=line[12:] + if(os.path.isdir(self.conf["module_path"])): + if(not self.conf["module_path"].endswith("/")): + self.conf["module_path"]+="/" + elif(line.startswith("splash_screen=")): + self.conf["splash_screen"]=line[14:] + elif(line.startswith("clean_log=")): + self.conf["clean_log"]=line[10:] + elif(line.startswith("status_message=")): + self.conf["status_message"]=line[15:] + else: + logging.warning("Unrecognized configuration: "+line) + + def get(self, key=False): + if(key): + return self.conf[key] + else: + return self.conf + def set(self, key, value): + self.conf[key]=value + + def write(self): + with open(CONF_FILE, "w") as f: + for k in self.conf: + print(k+"="+self.conf[k], file=f) + +if(__name__=="__main__"): + c=Conf(CONF_FILE) + print(c.get()) diff --git a/const.py b/const.py new file mode 100644 index 0000000..97f2448 --- /dev/null +++ b/const.py @@ -0,0 +1,30 @@ +#! /usr/bin/python3 + +# DDStorm +# ------- +# Copyright (c) 2015 Agnibho Mondal +# All rights reserved + +# This file is part of DDStorm. + +# DDStorm is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# DDStorm is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with DDStorm. If not, see . + +CONF_FILE="./ddstorm.conf" +LOG_FILE="./ddstorm.log" +HELP_FILE="./help.html" + +if(__name__=="__main__"): + print("CONF_FILE="+CONF_FILE) + print("LOG_FILE="+LOG_FILE) + print("HELP_FILE="+HELP_FILE) diff --git a/ddstorm.conf b/ddstorm.conf new file mode 100644 index 0000000..12d4ab9 --- /dev/null +++ b/ddstorm.conf @@ -0,0 +1,8 @@ +splash_screen=no +custom_path=./custom/ +clean_log=yes +library_path=./library/ +index_path=./index/ +alias_path=./alias/ +module_path=./modules/ +status_message=on diff --git a/ddstorm.log b/ddstorm.log new file mode 100644 index 0000000..e69de29 diff --git a/ddstorm.py b/ddstorm.py new file mode 100644 index 0000000..0acf7b2 --- /dev/null +++ b/ddstorm.py @@ -0,0 +1,95 @@ +#! /usr/bin/python3 + +# DDStorm +# ------- +# Copyright (c) 2015 Agnibho Mondal +# All rights reserved + +# This file is part of DDStorm. + +# DDStorm is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# DDStorm is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with DDStorm. If not, see . + +import sys, os +from compile import Compile +from conf import Conf +from index import Index + +class DDStorm: + conf=False + def __init__(self, comp=False, conf=False): + if(conf): + self.conf=conf + else: + self.conf=Conf() + if(comp): + self.compiler=Compile(conf) + self.index=Index(conf) + + def dd(self, symptoms): + if(not symptoms): + return + diff1=self._getDiff(symptoms.pop(0)) + for s in symptoms: + diff2=self._getDiff(s) + temp=[] + if(len(diff1)>len(diff2)): + diff2+=[""]*(len(diff1)-len(diff2)) + elif(len(diff2)>len(diff1)): + diff1+=[""]*(len(diff2)-len(diff1)) + for (s1, s2) in zip(diff1, diff2): + if((s1 not in temp) and (len(s1)>0)): + if(s1 in diff2): + temp.append(s1) + else: + us=self.index.upstream(s1) + for i in us: + if(i in diff2): + temp.append(i) + if((s2 not in temp) and (len(s2)>0)): + if(s2 in diff1): + temp.append(s2) + else: + us=self.index.upstream(s2) + for i in us: + if(i in diff1): + temp.append(i) + diff1=list(temp) + return diff1 + + def _getDiff(self, symptom): + diff=[] + symptom=symptom.lower().replace("_"," ").replace("-", " ") + if(os.path.isfile(self.conf.get("module_path")+symptom+".module")): + with open(self.conf.get("module_path")+symptom+".module", "r") as mf: + for line in mf: + diff.append(line.strip()) + return diff + + def symptoms(self): + symp=[] + for n in os.listdir(self.conf.get("module_path")): + symp.append(os.path.splitext(os.path.basename(n))[0].capitalize()) + return symp + +def main(): + s=DDStorm() + if(len(sys.argv)>1): + for d in s.dd(sys.argv[1:]): + print(d) + else: + for s in s.symptoms(): + print(s) + +if(__name__=="__main__"): + main() diff --git a/help.html b/help.html new file mode 100644 index 0000000..512929a --- /dev/null +++ b/help.html @@ -0,0 +1,34 @@ + + + + + + DDStorm + + +

DDStorm

+

This software is meant to help with brainstorming Medical Differential Diagnosis.

+

This is an alpha version.

+ + + diff --git a/icons/icon.png b/icons/icon.png new file mode 100644 index 0000000..7b7a29f Binary files /dev/null and b/icons/icon.png differ diff --git a/icons/splash.png b/icons/splash.png new file mode 100644 index 0000000..10e2d09 Binary files /dev/null and b/icons/splash.png differ diff --git a/index.py b/index.py new file mode 100644 index 0000000..f1da749 --- /dev/null +++ b/index.py @@ -0,0 +1,89 @@ +#! /usr/bin/python3 + +# DDStorm +# ------- +# Copyright (c) 2015 Agnibho Mondal +# All rights reserved + +# This file is part of DDStorm. + +# DDStorm is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# DDStorm is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with DDStorm. If not, see . + +import sys, os +from fnmatch import fnmatch +from conf import Conf +from const import * + +class Index: + def __init__(self, conf=False): + if(conf): + self.conf=conf + else: + self.conf=Conf() + self.data={} + self.compile() + + def compile(self): + for path, subdirs, files in os.walk(self.conf.get("index_path")): + for name in files: + if(fnmatch(name, "*.txt")): + with open(self.conf.get("index_path")+name, "r") as f: + buff=[] + buff.append([]) + buff.append([]) + for line in f: + line=line.rstrip().split("#")[0] + if(len(line)==0): + pass + else: + ws=len(line)-len(line.lstrip()) + line=line.lstrip().capitalize() + if(ws==0): + del buff[0][:] + buff[0].append(line.lstrip()) + del buff[1][:] + buff[1].append(0) + elif(ws>buff[1][-1]): + buff[0].append(line.lstrip()) + buff[1].append(ws) + self.data[buff[0][-1]]=list(reversed(buff[0])) + elif(ws==buff[1][-1]): + buff[0][-1]=line.lstrip() + buff[1][-1]=ws + self.data[buff[0][-1]]=list(reversed(buff[0])) + elif(ws=ws): + buff[0].pop() + buff[1].pop() + else: + buff[0].append(line.lstrip()) + buff[1].append(ws) + break + self.data[buff[0][-1]]=list(reversed(buff[0])) + + def upstream(self, name): + if(len(name)>0): + if name in self.data: + return self.data[name] + else: + return [] + +def main(): + i=Index() + if(len(sys.argv)>1): + print(i.upstream(sys.argv[1])) + +if(__name__=="__main__"): + main() diff --git a/index/abdomen.txt b/index/abdomen.txt new file mode 100644 index 0000000..2636dc0 --- /dev/null +++ b/index/abdomen.txt @@ -0,0 +1,15 @@ +Peritonitis + Acute peritonitis + Tuberculous peritonitis + Bacterial peritonitis + Streptococcal peritonitis + Gonococcal peritonitis + Pneumococcal peritonitis +Peptic ulcer + Gastric ulcer + Duodenal ulcer +Rupture of spleen + Spontneous rupture of spleen + Traumatic rupture of spleen +Degeneration of fibroid + Red degeneration of fibroid diff --git a/library/Abdominal pain, acute, generalized.txt b/library/Abdominal pain, acute, generalized.txt new file mode 100644 index 0000000..4e984a0 --- /dev/null +++ b/library/Abdominal pain, acute, generalized.txt @@ -0,0 +1,15 @@ +Acute peritonitis +Tuberculous peritonitis +Intestinal obstruction +Lead colic +Gastric crises +Functional abdominal pain + +#General medical diseases- +Malaria +Porphyria +Diabetic ketosis +Blood dyscrasias +Henoch's purpura +Sickle cell anaemia +Hypercalcaemia diff --git a/library/Abdominal pain, acute, localized.txt b/library/Abdominal pain, acute, localized.txt new file mode 100644 index 0000000..e2d3bb2 --- /dev/null +++ b/library/Abdominal pain, acute, localized.txt @@ -0,0 +1,70 @@ +#Gastroduodenal +Perforated peptic ulcer +Perforated gastric carcinoma +Acute gastritis +Irritant poisons + +#Intestinal +Small bowel obstruction +Regional ileitis +Intussusception +Sigmoid volvulus +Acute colonic diverticulitis +Large bowel obstruction +Strangulated hernia +Acute mesenteric occlusion + +#Appendix +Acute appendicitis + +#Pancreas +Acute pancreatitis +Recurrent pancreatitis +Pancreatic trauma + +#Gallbladder and bile ducts +Gallstone +CBD stone +Acute cholecystitis +Acute cholangitis + +#Liver +Liver trauma +Acute hepatitis +Liver malignancy + +#Spleen +Splenic trauma +Spontaneous rupture of spleen +Splenic infarction + +#Urinary tract +Renal calculus +Ureteric calculus +Vesical calculus +Renal trauma +Pyelonephritis +Pyonephrosis + +#Female genitalia +Salpingitis +Pyosalpinx +Ectopic pregnancy +Torsion of fibroid +Degenaration of fibroid +Twisted ovarian cyst +Ruptured ovarian cyst + +#Aorta +Ruptured abdominal aortic aneurysm +Dissecting abdominal aortic aneurysm + +#CNS +Herpes zoster + +#Cardiac +Myocardial infarction +Acute pericarditis + +#Pleura +Acute diaphragmatic pleurisy diff --git a/library/Abdominal pulsation.txt b/library/Abdominal pulsation.txt new file mode 100644 index 0000000..a84c958 --- /dev/null +++ b/library/Abdominal pulsation.txt @@ -0,0 +1,4 @@ +Prominent aorta +Abdominal aortic aneurysm +Abdominal mass #transmission of aortic pulsations +Pulsatile liver diff --git a/library/Abdominal rigidity.txt b/library/Abdominal rigidity.txt new file mode 100644 index 0000000..0db5ef9 --- /dev/null +++ b/library/Abdominal rigidity.txt @@ -0,0 +1,41 @@ +#Gastroduodenal +Perforated peptic ulcer + +#Gallbladder +Acute cholecystitis +Rupture of gallbladder + +#Pancreas +Acute pancreatitis + +#Small intestine +Strangulated hernia +Intestinal perforation +Mesenteric thrombosis +Mesenteric embolism +Meckel's diverticulitis +Acute ileitis + +#Large intestine +Appendicitis +Volvulitis +Perforated diverticulitis + +#Peritoneum +Infective peritonitis + +#Female genital organs +Twisted ovarian cyst +Ruptured ectopic pregnancy +Acute salpingitis +Torsion of fibroid +Degeneration of fibroid +Perforation of uterus +Perforation of vagina + +#Spleen & liver +Rupture of spleen +Rupture of liver + +#Aorta +Ruptured abdominal aortic aneurysm diff --git a/start b/start new file mode 100755 index 0000000..36400a6 --- /dev/null +++ b/start @@ -0,0 +1,2 @@ +#! /bin/bash +python3 __main__.py