From 3f1b150b91d754275fd3298b8ef6658279a2b5f4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Primo=C5=BE=20Godec?= Date: Thu, 20 Jun 2019 10:20:54 +0200 Subject: [PATCH 1/3] Remove validate_email requirement --- conda_environment.yml | 1 - orangecontrib/text/pubmed.py | 3 --- orangecontrib/text/tests/test_pubmed.py | 7 ------- requirements.txt | 2 +- 4 files changed, 1 insertion(+), 12 deletions(-) diff --git a/conda_environment.yml b/conda_environment.yml index 70feec4d2..45a8b7914 100644 --- a/conda_environment.yml +++ b/conda_environment.yml @@ -16,7 +16,6 @@ dependencies: - recommonmark - pip: - - validate_email - tweepy - simhash - wikipedia diff --git a/orangecontrib/text/pubmed.py b/orangecontrib/text/pubmed.py index f203439a3..e13126637 100644 --- a/orangecontrib/text/pubmed.py +++ b/orangecontrib/text/pubmed.py @@ -6,7 +6,6 @@ import numpy as np from Bio import Entrez from Bio import Medline -from validate_email import validate_email try: from Orange.misc import environ @@ -173,8 +172,6 @@ class Pubmed: MAX_BATCH_SIZE = 1000 def __init__(self, email, progress_callback=None, error_callback=None): - if not validate_email(email): - raise ValueError('{} is not a valid email address.'.format(email)) Entrez.email = email diff --git a/orangecontrib/text/tests/test_pubmed.py b/orangecontrib/text/tests/test_pubmed.py index 8c15da874..fcff48e24 100644 --- a/orangecontrib/text/tests/test_pubmed.py +++ b/orangecontrib/text/tests/test_pubmed.py @@ -78,13 +78,6 @@ def setUp(self): error_callback=error_callback ) - def test_pubmed_object_creation(self): - self.assertRaises( - ValueError, - Pubmed, - 'faulty_email' - ) - def test_mesh_headings_to_class(self): input_headings = [ 'heading1 & heading2/heading3,heading4/*heading5', diff --git a/requirements.txt b/requirements.txt index c6e08c291..23cace81e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,7 @@ scipy nltk>=3.0.5 # TweetTokenizer introduces in 3.0.5 scikit-learn numpy -validate_email +# fixing boto issue in gensim; TODO: remove after while and check if tests passes gensim>=0.12.3 # LDA's show topics unified in 0.12.3 setuptools-git Orange3>=3.4.3 From e269d1444f222c95f26e745c0d4305f5d980f68b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Primo=C5=BE=20Godec?= Date: Thu, 20 Jun 2019 10:44:22 +0200 Subject: [PATCH 2/3] Update widget to save email safely like NYtimes widget --- orangecontrib/text/widgets/owpubmed.py | 151 +++++++++++++++---------- 1 file changed, 91 insertions(+), 60 deletions(-) diff --git a/orangecontrib/text/widgets/owpubmed.py b/orangecontrib/text/widgets/owpubmed.py index a518b0c8b..80c5a837a 100644 --- a/orangecontrib/text/widgets/owpubmed.py +++ b/orangecontrib/text/widgets/owpubmed.py @@ -1,12 +1,14 @@ import os +import re from datetime import date from AnyQt.QtCore import QDate, Qt from AnyQt.QtWidgets import (QApplication, QComboBox, QDateEdit, QTextEdit, - QFrame, QDialog, QCalendarWidget, QVBoxLayout) -from validate_email import validate_email + QFrame, QDialog, QCalendarWidget, QVBoxLayout, + QFormLayout) from Orange.widgets import gui +from Orange.widgets.credentials import CredentialManager from Orange.widgets.settings import Setting from Orange.widgets.widget import OWWidget, Msg from orangecontrib.text.corpus import Corpus @@ -20,11 +22,71 @@ def _i(name, icon_path='icons'): return os.path.join(widget_path, icon_path, name) +EMAIL_REGEX = re.compile(r"[^@]+@[^@]+\.[^@]+") + + +def validate_email(email): + return EMAIL_REGEX.match(email) + + class Output: CORPUS = 'Corpus' class OWPubmed(OWWidget): + class EmailCredentialsDialog(OWWidget): + name = "Pubmed Email" + want_main_area = False + resizing_enabled = False + email_manager = CredentialManager('Email') + email_input = '' + + class Error(OWWidget.Error): + invalid_credentials = Msg('This email is invalid.') + + def __init__(self, parent): + super().__init__() + self.parent = parent + self.api = None + + form = QFormLayout() + form.setContentsMargins(5, 5, 5, 5) + self.email_edit = gui.lineEdit( + self, self, 'email_input', controlWidth=400) + form.addRow('Email:', self.email_edit) + self.controlArea.layout().addLayout(form) + self.submit_button = gui.button( + self.controlArea, self, "OK", self.accept) + + self.load_credentials() + + def setVisible(self, visible): + super().setVisible(visible) + self.email_edit.setFocus() + + def load_credentials(self): + self.email_edit.setText(self.email_manager.key) + + def save_credentials(self): + self.email_manager.key = self.email_input + + def check_credentials(self): + if validate_email(self.email_input): + self.save_credentials() + return True + else: + return False + + def accept(self, silent=False): + if not silent: + self.Error.invalid_credentials.clear() + valid = self.check_credentials() + if valid: + self.parent.sync_email(self.email_input) + super().accept() + else: + self.Error.invalid_credentials() + name = 'Pubmed' description = 'Fetch data from Pubmed.' icon = 'icons/Pubmed.svg' @@ -39,7 +101,6 @@ class OWPubmed(OWWidget): MIN_DATE = date(1800, 1, 1) # Settings. - recent_emails = Setting([]) author = Setting('') pub_date_from = Setting('') pub_date_to = Setting('') @@ -54,11 +115,14 @@ class OWPubmed(OWWidget): includes_abstract = Setting(True) includes_url = Setting(True) + email = None + class Warning(OWWidget.Warning): no_query = Msg('Please specify the keywords for this query.') class Error(OWWidget.Error): api_error = Msg('API error: {}.') + email_error = Msg('Email not set. Pleas set it with the email button.') def __init__(self): super().__init__() @@ -66,24 +130,19 @@ def __init__(self): self.output_corpus = None self.pubmed_api = None self.progress = None - self.email_is_valid = False self.record_count = 0 self.download_running = False + # API key + self.email_dlg = self.EmailCredentialsDialog(self) + gui.button(self.controlArea, self, 'Email', + callback=self.email_dlg.exec_, + focusPolicy=Qt.NoFocus) + gui.separator(self.controlArea) + # To hold all the controls. Makes access easier. self.pubmed_controls = [] - h_box = gui.hBox(self.controlArea) - label = gui.label(h_box, self, 'Email:') - label.setMaximumSize(label.sizeHint()) - # Drop-down for recent emails. - self.email_combo = QComboBox(h_box) - self.email_combo.setMinimumWidth(150) - self.email_combo.setEditable(True) - self.email_combo.lineEdit().textChanged.connect(self.sync_email) - h_box.layout().addWidget(self.email_combo) - self.email_combo.activated[int].connect(self.select_email) - # RECORD SEARCH self.search_tabs = gui.tabWidget(self.controlArea) # --- Regular search --- @@ -228,48 +287,29 @@ def __init__(self): self, 'Number of records retrieved: /') - # Load the most recent emails. - self.set_email_list() - # Load the most recent queries. self.set_keyword_list() - # Check the email and enable controls accordingly. - if self.recent_emails: - email = self.recent_emails[0] - self.email_is_valid = validate_email(email) - - self.enable_controls() - - def sync_email(self): - email = self.email_combo.currentText() - self.email_is_valid = validate_email(email) - self.enable_controls() - - def enable_controls(self): - # Enable/disable controls accordingly. - for control in self.pubmed_controls: - control.setEnabled(self.email_is_valid) - if self.pubmed_api is None or self.pubmed_api.search_record_count == 0: - self.retrieve_records_button.setEnabled(False) - if not self.email_is_valid: - self.email_combo.setFocus() + def sync_email(self, email): + self.Error.email_error.clear() + self.email = email def run_search(self): self.Error.clear() self.Warning.clear() + + # check if email exists + if self.email is None: + self.Error.email_error() + return + self.run_search_button.setEnabled(False) self.retrieve_records_button.setEnabled(False) - # Add the email to history. - email = self.email_combo.currentText() - if email not in self.recent_emails: - self.recent_emails.insert(0, email) - # Check if the PubMed object is present. if self.pubmed_api is None: self.pubmed_api = Pubmed( - email=email, + email=self.email, progress_callback=self.api_progress_callback, error_callback=self.api_error_callback, ) @@ -309,6 +349,13 @@ def run_search(self): self.enable_controls() self.update_search_info() + def enable_controls(self): + # Enable/disable controls accordingly. + self.run_search_button.setEnabled(True) + enabled = self.pubmed_api is not None and \ + not self.pubmed_api.search_record_count == 0 + self.retrieve_records_button.setEnabled(enabled) + def retrieve_records(self): self.Warning.clear() self.Error.clear() @@ -318,13 +365,11 @@ def retrieve_records(self): if self.download_running: self.download_running = False - self.run_search_button.setEnabled(True) self.retrieve_records_button.setText('Retrieve records') self.pubmed_api.stop_retrieving() return self.download_running = True - self.run_search_button.setEnabled(False) self.output_corpus = None # Clear the old records. # Change the button label. @@ -401,20 +446,6 @@ def update_retrieval_info(self): self.retrieval_info_label.sizeHint() ) - def select_email(self, n): - if n < len(self.recent_emails): - email = self.recent_emails[n] - del self.recent_emails[n] - self.recent_emails.insert(0, email) - - if len(self.recent_emails) > 0: - self.set_email_list() - - def set_email_list(self): - self.email_combo.clear() - for email in self.recent_emails: - self.email_combo.addItem(email) - def select_keywords(self, n): if n < len(self.recent_keywords): keywords = self.recent_keywords[n] From fd0c256328de3d24dd2201bfc369c66b65a6c3d8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Primo=C5=BE=20Godec?= Date: Thu, 20 Jun 2019 10:48:32 +0200 Subject: [PATCH 3/3] Code cleanup --- orangecontrib/text/widgets/owpubmed.py | 39 +++++++++++++------------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/orangecontrib/text/widgets/owpubmed.py b/orangecontrib/text/widgets/owpubmed.py index 80c5a837a..14f8ec78e 100644 --- a/orangecontrib/text/widgets/owpubmed.py +++ b/orangecontrib/text/widgets/owpubmed.py @@ -242,18 +242,18 @@ def __init__(self): # RECORD RETRIEVAL # Text includes box. - text_includes_box = gui.widgetBox(self.controlArea, - 'Text includes', addSpace=True) - self.authors_checkbox = gui.checkBox(text_includes_box, self, - 'includes_authors', 'Authors') - self.title_checkbox = gui.checkBox(text_includes_box, self, - 'includes_title', 'Article title') - self.mesh_checkbox = gui.checkBox(text_includes_box, self, - 'includes_mesh', 'Mesh headings') - self.abstract_checkbox = gui.checkBox(text_includes_box, self, - 'includes_abstract', 'Abstract') - self.url_checkbox = gui.checkBox(text_includes_box, self, - 'includes_url', 'URL') + text_includes_box = gui.widgetBox( + self.controlArea, 'Text includes', addSpace=True) + self.authors_checkbox = gui.checkBox( + text_includes_box, self, 'includes_authors', 'Authors') + self.title_checkbox = gui.checkBox( + text_includes_box, self, 'includes_title', 'Article title') + self.mesh_checkbox = gui.checkBox( + text_includes_box, self, 'includes_mesh', 'Mesh headings') + self.abstract_checkbox = gui.checkBox( + text_includes_box, self, 'includes_abstract', 'Abstract') + self.url_checkbox = gui.checkBox( + text_includes_box, self, 'includes_url', 'URL') self.pubmed_controls.append(self.authors_checkbox) self.pubmed_controls.append(self.title_checkbox) self.pubmed_controls.append(self.mesh_checkbox) @@ -485,18 +485,18 @@ def send_report(self): ('Query', terms if terms else None), ('Authors', authors if authors else None), ('Date', 'from {} to {}'.format(self.pub_date_from, - self.pub_date_to)), - ('Number of records retrieved', '{}/{}'.format(len( - self.output_corpus) if self.output_corpus else 0, - max_records_count)) + self.pub_date_to)), + ('Number of records retrieved', '{}/{}'.format( + len(self.output_corpus) if self.output_corpus else 0, + max_records_count)) )) else: query = self.advanced_query_input.toPlainText() self.report_items(( ('Query', query if query else None), - ('Number of records retrieved', '{}/{}'.format(len( - self.output_corpus) if self.output_corpus else 0, - max_records_count)) + ('Number of records retrieved', '{}/{}'.format( + len(self.output_corpus) if self.output_corpus else 0, + max_records_count)) )) @@ -529,6 +529,7 @@ def __init__(self, parent, windowTitle='Date picker'): def set_date(self, date): self.picked_date = date.toString('yyyy/MM/dd') + if __name__ == '__main__': app = QApplication([]) widget = OWPubmed()