WIP Prod for legacy

.drone.yml

@@ -0,0 +1,60 @@
+image: inspirehep/invenio-drone:latest
+script:
+    # Autotools
+    - aclocal
+    - automake -a
+    - autoconf
+    - ./configure
+
+    # Create destination
+    - sudo mkdir -p /opt/invenio
+    - sudo chown drone:drone /opt/invenio
+    - mkdir -p /opt/invenio/lib/python/invenio
+    - sudo ln -s /opt/invenio/lib/python/invenio /usr/local/lib/python2.7/dist-packages/invenio
+
+    # Install
+    - make
+    - make install
+
+    # Config
+    - sed -i 's/www-data/drone/g' ~/invenio-local.conf
+    - mv ~/invenio-local.conf /opt/invenio/etc/invenio-local.conf
+    - /opt/invenio/bin/inveniocfg --update-all
+    - /opt/invenio/bin/inveniocfg --load-bibfield-conf
+
+    # Mails
+    - sudo service postfix start
+
+    # Apache
+    - /opt/invenio/bin/inveniocfg --create-apache-conf
+    - sed -i 's/WSGIDaemonProcess invenio/WSGIDaemonProcess invenio user=drone/g' /opt/invenio/etc/apache/invenio-apache-vhost.conf
+    - sed -i 's/WSGIDaemonProcess invenio/WSGIDaemonProcess invenio user=drone/g' /opt/invenio/etc/apache/invenio-apache-vhost-ssl.conf
+    - sudo ln -fs /opt/invenio/etc/apache/invenio-apache-vhost.conf /etc/apache2/sites-available/invenio.conf
+    - sudo ln -fs /opt/invenio/etc/apache/invenio-apache-vhost-ssl.conf /etc/apache2/sites-available/invenio-ssl.conf
+    - sudo /usr/sbin/a2ensite invenio
+    - sudo /usr/sbin/a2ensite invenio-ssl
+    - touch /opt/invenio/var/log/apache.err
+    - sudo chown www-data:www-data /opt/invenio/var/log/apache.err
+
+    # Redis
+    - sudo service redis-server start
+
+    # Database
+    - sudo mv /var/lib/mysql /dev/shm/mysql
+    - sudo ln -s /dev/shm/mysql /var/lib/mysql
+    - sudo service mysql start
+    - mysql -e "CREATE DATABASE invenio DEFAULT CHARACTER SET utf8 COLLATE utf8_general_ci" -u root
+    - mysql -e "GRANT ALL PRIVILEGES ON invenio.* TO invenio@localhost IDENTIFIED BY 'my123p\$ss'" -u root
+
+    # Load records
+    - /opt/invenio/bin/inveniocfg --create-tables --yes-i-know
+    - /opt/invenio/bin/inveniocfg --create-demo-site --yes-i-know
+    - /opt/invenio/bin/inveniocfg --load-demo-records --yes-i-know
+
+    # Start apache after creating the demo site
+    # to be able to populate startup caches properly
+    - sudo service apache2 start
+
+    # Tests
+    - nosetests -v /opt/invenio/lib/python/invenio/*_unit_tests.py
+    - nosetests -v /opt/invenio/lib/python/invenio/*_regression_tests.py

.travis.yml

@@ -25,7 +25,7 @@ python:
 
 install:
   - sudo apt-get update
-  - git clone https://github.com/tiborsimko/invenio-devscripts /tmp/invenio-devscripts
+  - git clone https://github.com/kaplun/invenio-devscripts /tmp/invenio-devscripts --branch no-pip-upgrade
   - CFG_INVENIO_SRCDIR=$(pwd) /tmp/invenio-devscripts/invenio-kickstart --yes-i-know --yes-i-really-know
 
 script:

Makefile.am

@@ -26,7 +26,7 @@ EXTRA_DIST = UNINSTALL THANKS RELEASE-NOTES configure-tests.py config.nice.in \
 
 # current MathJax version and packages
 # See also modules/miscutil/lib/htmlutils.py (get_mathjax_header)
-MJV = 2.3
+MJV = 2.5.3
 MATHJAX = http://invenio-software.org/download/mathjax/MathJax-v$(MJV).zip
 
 # current CKeditor version

modules/bibauthorid/lib/bibauthorid.js

@@ -38,7 +38,36 @@ var ticketbox = {
         };
     }(),
 
-    app: { debug: false }
+    app: { debug: true, hasFocus: false },
+
+    sureUpdate: function() {
+        var time = 1000;
+        var growth = 0.1;
+        var app = ticketbox.app;
+
+        var poller = function() {
+
+            var failure = function() {
+                    time += time * growth;
+                    window.setTimeout(poller, time);
+                    app.debug && console.log("[SureUpdate] FAILED: Retrying in " + time/1000 + " seconds.");
+            };
+
+            var success = function() {
+                app.debug && console.log("[SureUpdate] Update succeeded after multiple attempts.");
+            };
+
+            if (app.hasFocus) {
+                app.userops.fetch({"on": 'user', "error": failure, "success": success});
+            }
+        };
+
+        return function(coll, resp, opt) {
+            window.setTimeout(poller, time);
+        };
+
+
+    }
 };
 
 /**
@@ -115,9 +144,17 @@ var ticketbox = {
         params.data = {};
         params.data.jsondata = Server.dataOn({}, options.on);
 
-        // Set success and error callbacks
+        var syncCallback = function(jqXHR, status) {
+            var sureUpdate = ticketbox.sureUpdate();
+            if (method != "read") {
+                app.userops.fetch({"on": 'user', "error": sureUpdate});
+            }
+        };
+
+        // Set AJAX callbacks
         params.success = options.success;
         params.error = options.error;
+        params.complete = syncCallback;
 
         var generateRequest = function(type) {
             var requestTypes  = {
@@ -144,7 +181,7 @@ var ticketbox = {
                 app.debug && console.error("[Operation Model] ERROR: No request type defined.");
                 return {};
             }
-        }
+        };
 
         switch (method) {
             case 'create':
@@ -344,7 +381,7 @@ var ticketbox = {
 
         events: {
             'click .removeOp': 'removeOperation',
-            'click select': 'bibrefSelected'
+            'change select': 'bibrefSelected'
         },
 
         initialize: function(){
@@ -1616,8 +1653,24 @@ jQuery(function($) {
 
     disableLinks($("#person_menu").find("li.disabled"));
 
-    // Stupid polling
-    setInterval(function() { app.userops.fetch({"on": 'user'});}, 15000);
+    // Window focus event binding
+    var updater = (function() {
+        app.hasFocus = true;
+        $(window).focus(function(event) {
+            app.hasFocus = true;
+            var successFocus = function() {
+                app.debug && console.log("[Focus Update] Update succeeded.");
+            };
+
+            var sureUpdate = ticketbox.sureUpdate();
+            app.userops.fetch({"on": 'user', "error": sureUpdate, "success": successFocus});
+            app.debug && console.log("Focus update triggered.");
+        }).blur(function(event) {
+            app.hasFocus = false;
+            app.debug && console.log("Focus lost.");
+        });
+    })();
+
 
 //    // PidSearch test
 //    var searchModel = new PidSearch.SearchModel();
@@ -1627,13 +1680,6 @@ jQuery(function($) {
 //    app.search = searchModel;
 //    app.searchView = searchInterface;
 
-    console.log("Ticketing Loaded.");
-
-    var profilePageRegex = /\/author\/profile\//;
-    var profilePage = profilePageRegex.test(window.location.pathname);
-    if (profilePage) {
-        $("#bai_content").prepend("<div class='well'><h4>Welcome to the improved author profiles!</h4><p>We have revised our author page. Please let us know what you think via <a href='mailto:[email protected]?subject=Revised%20Author%20Profiles'>[email protected]</a></p></div>");
-    }
 
 });
 

modules/bibauthorid/lib/bibauthorid_config.py

@@ -92,8 +92,10 @@
 # Special for ADS: Focus on ASTRONOMY collection
 if GLOBAL_CONFIG and CFG_ADS_SITE:
     LIMIT_TO_COLLECTIONS = ["ASTRONOMY"]
-else:
+elif CFG_INSPIRE_SITE:
     LIMIT_TO_COLLECTIONS = ['HEP']
+else:
+    LIMIT_TO_COLLECTIONS = []
 
 # Exclude documents that are visible in a collection mentioned here:
 EXCLUDE_COLLECTIONS = ["HEPDATA","Data", "HEPNAMES", "INST", "Deleted", "DELETED", "deleted"]
@@ -171,7 +173,7 @@
 # their use explicit.
 DEBUG_CHECKS = False
 
-TORTOISE_FILES_PATH = '/opt/tortoise_cache/'
+TORTOISE_FILES_PATH = '/opt/invenio/var/cache/bibauthorid/tortoise_cache'
 
 # force skip ui arxiv stub page (specific for inspire)
 BIBAUTHORID_UI_SKIP_ARXIV_STUB_PAGE = True

modules/bibauthorid/lib/bibauthorid_dbinterface.py

@@ -954,7 +954,7 @@ def get_author_info_of_confirmed_paper(sig):   ### personid_name_from_signature
                              and flag > -2""",
                              sig )
 
-    assert len(conf_author) < 2, "More that one author hold the same signature: %s" % conf_author
+    assert len(conf_author) < 2, "More than one author hold the same signature: %s" % str(conf_author)
 
     return conf_author
 
@@ -1128,7 +1128,7 @@ def get_authors_by_name_regexp(name_regexp):   ### get_all_personids_by_name
                       (name_regexp,) )
 
 
-def get_authors_by_name(name):   ### find_pids_by_exact_name
+def get_authors_by_name(name, limit_to_recid=False):   ### find_pids_by_exact_name
     '''
     Gets all authors who have records with the specified name.
 
@@ -1138,8 +1138,14 @@ def get_authors_by_name(name):   ### find_pids_by_exact_name
     @return: author identifiers
     @rtype: set set((int),)
     '''
-    return set(_select_from_aidpersonidpapers_where(select=['personid'], name=name))
-
+    if limit_to_recid:
+        pids = run_sql("select personid from aidPERSONIDPAPERS where name=%s and bibrec=%s and flag>-2",
+                       (name, limit_to_recid))
+        return set(pids)
+    else:
+        pids = run_sql("select personid from aidPERSONIDPAPERS where name=%s and flag>-2",
+                       (name,))
+        return set(pids)
 
 def get_paper_to_author_and_status_mapping():   ### get_bibrefrec_to_pid_flag_mapping
     '''
@@ -2696,12 +2702,12 @@ def get_papers_affected_since(since):   ### personid_get_recids_affected_since
     '''
     recs = set(_split_signature_string(sig[0])[2] for sig in run_sql("""select distinct value
                                                                        from aidUSERINPUTLOG
-                                                                       where timestamp > %s""",
+                                                                       where timestamp >= %s""",
                                                                        (since,) ) if ',' in sig[0] and ':' in sig[0])
 
     pids = set(int(pid[0]) for pid in run_sql("""select distinct personid
                                                  from aidUSERINPUTLOG
-                                                 where timestamp > %s""",
+                                                 where timestamp >= %s""",
                                                  (since,) ) if pid[0] > 0)
 
     if pids:
@@ -4124,6 +4130,8 @@ def get_all_valid_papers():   ### get_all_valid_bibrecs
     @return: paper identifiers
     @rtype: list [int,]
     '''
+    if not bconfig.LIMIT_TO_COLLECTIONS:
+        return perform_request_search(p="")
     collection_restriction_pattern = " or ".join(["980__a:\"%s\"" % x for x in bconfig.LIMIT_TO_COLLECTIONS])
 
     return perform_request_search(p="%s" % collection_restriction_pattern, rg=0)

modules/bibauthorid/lib/bibauthorid_general_utils.py

@@ -31,7 +31,6 @@
 except ImportError:
     from xml.etree import ElementTree as ET
 from urllib import urlopen
-from urllib2 import HTTPError
 from collections import deque
 
 import multiprocessing as mp
@@ -48,6 +47,9 @@
 if NEWLINE or FO:
     TERMINATOR = '\n'
 
+import socket
+from urllib2 import URLError
+
 import os
 PID = os.getpid
 
@@ -247,8 +249,14 @@ def is_arxiv_id_or_doi(identifier):
 def get_title_of_doi(doi):
     try:
         xml = get_marcxml_for_doi(doi)
-    except CrossrefError:
+    except (CrossrefError, socket.timeout):
         return doi
+    except URLError, e:
+    # For python 2.6 socket.timeout cannot be caught directly    
+        if hasattr(e, "reason") and isinstance(e.reason, socket.timeout):
+            return doi
+        else:  # We make sure we don't cut out other URLErrors.
+            raise
 
     root = ET.fromstring(xml)
 
@@ -302,7 +310,14 @@ def get_title_from_arxiv_xml(tree, tags):
         xml = fxml.read()
         fxml.close()
         root = ET.fromstring(xml)
-    except HTTPError:
+    except URLError, e:
+    # For python 2.6 socket.timeout cannot be caught directly
+        if hasattr(e, "reason") and isinstance(e.reason, socket.timeout):
+            return arxiv_pubid
+        else:  # We make sure we don't cut out other URLErrors.
+            raise
+    except socket.timeout:
+        # Python 2.7
         return arxiv_pubid
 
     title = get_title_from_arxiv_xml(root, deque(['GetRecord', 'record', 'metadata', 'dc', 'title']))

modules/bibauthorid/lib/bibauthorid_templates.py

@@ -2813,7 +2813,7 @@ def tmpl_update_hep_name(self, full_name, display_name, email,
                         <TD><span class="span_float_left"><TEXTAREA NAME=Abstract ROWS=3 COLS=30></textarea><FONT SIZE=2>(not displayed)</FONT></span></TD></TR>
                         <tr><TD> <span class="span_float_right"><font size="1">SPAM Robots have been sending us submissions via this form, in order to prevent this we ask that you confirm that you are a real person by answering this question, which should be
                         easy for you, and hard for a SPAM robot. Cutting down on the extraneous submissions we get means that we can handle real requests faster.</font></span></td><td><span class="span_float_left">
-                        <script type="text/javascript" src="http://www.slac.stanford.edu/spires/hepnames/spbeat.js">
+                        <script type="text/javascript" src="https://www.slac.stanford.edu/spires/hepnames/spbeat.js">
                         </SCRIPT><br /><STRONG> How many people in image</STRONG>  <SELECT NAME=beatspam ID=beatspam> <OPTION VALUE=""> </OPTION>
                         <option value="1"> one person</option>
                         <option value="2"> two people</option><option value="3"> three people</option>

modules/bibauthorid/lib/bibauthorid_webauthorprofileinterface.py

@@ -29,6 +29,7 @@
 from invenio.bibauthorid_webapi import get_papers_by_person_id #emitting #pylint: disable-msg=W0611
 from invenio.bibauthorid_dbinterface import get_names_of_author #emitting #pylint: disable-msg=W0611
 from invenio.bibauthorid_dbinterface import get_existing_authors #emitting #pylint: disable-msg=W0611
+from invenio.bibauthorid_dbinterface import get_authors_by_name #emitting #pylint: disable-msg=W0611
 from invenio.bibauthorid_frontinterface import get_confirmed_papers_of_author #emitting #pylint: disable-msg=W0611
 from invenio.bibauthorid_dbinterface import get_title_of_paper #emitting #pylint: disable-msg=W0611
 from invenio.bibauthorid_dbinterface import get_orcid_id_of_author #emitting #pylint: disable-msg=W0611