Merge pull request #23 from opensciencegrid/master

Catching up with upstream

.github/workflows/validate-code.yml

@@ -23,10 +23,12 @@ jobs:
       - name: Test API
         run: |
           export TOPOLOGY_CONFIG=$PWD/src/config-ci.py
+          export FLASK_DEBUG=1
           py.test ./src/tests/test_api.py
       - name: Test StashCache
         run: |
           export TOPOLOGY_CONFIG=$PWD/src/config-ci.py
+          export FLASK_DEBUG=1
           py.test ./src/tests/test_stashcache.py
       - name: Test cacher
         run: |

Dockerfile

@@ -24,7 +24,7 @@ RUN alternatives --set python3 /usr/bin/python3.9
 WORKDIR /app
 
 # Install application dependencies
-COPY requirements-apache.txt src/ ./
+COPY requirements-apache.txt requirements-rootless.txt ./
 RUN pip3 install --no-cache-dir -r requirements-apache.txt
 
 # Create data directory, and gather SSH keys for git
@@ -38,6 +38,8 @@ RUN echo "45 */6 * * * root /usr/sbin/fetch-crl -q -r 21600 -p 10" >  /etc/cron.
     echo "@reboot      root /usr/sbin/fetch-crl -q          -p 10" >> /etc/cron.d/fetch-crl && \
     echo "0 0 * * *    root /usr/bin/pkill -USR1 httpd"            >  /etc/cron.d/httpd
 
+# Install application
+COPY src/ ./
 
 # Set up Apache configuration
 # Remove default SSL config: default certs don't exist on EL8 so the

Dockerfile.client

@@ -1,6 +1,6 @@
 FROM quay.io/centos/centos:stream8
 
-LABEL maintainer="OSG Software <help@opensciencegrid.org>"
+LABEL maintainer="OSG Software <help@osg-htc.org>"
 LABEL name="OSG 3.5 OSG-Notify client"
 
 RUN yum -y install https://repo.opensciencegrid.org/osg/3.5/osg-3.5-el8-release-latest.rpm \

README.md

@@ -146,4 +146,4 @@ for the VO(s) that you support:
 | LHC VOs                     | [GGUS](https://ggus.eu)                          |
 | Anyone else                 | [Helpdesk](https://support.opensciencegrid.org) |
 
-Or email us at help@opensciencegrid.org.
+Or email us at help@osg-htc.org.

bin/next_downtime_id

@@ -4,6 +4,7 @@ set -o pipefail
 cd "$(dirname "$0")"/..
 
 unset GREP_OPTIONS
-egrep -h '^ *ID: *[0-9]{1,9}\>' topology/*/*/*_downtime.yaml |
+# After 18 digits we might start running into integer overflow issues...
+egrep -h '^ *ID: *[0-9]{1,18}\>' topology/*/*/*_downtime.yaml |
   awk '$2 > max {max = $2}; END {print max + 1}'
 

bin/osg-notify

@@ -5,6 +5,7 @@
 A simple tool for generating notification emails to the OSG
 """
 import os
+import re
 import sys
 import getpass
 import smtplib
@@ -157,7 +158,12 @@ def network_ok(bypass_dns_check):
 
 def replace_smart_quotes_and_dashes(contents):
     # Replace smart quotes and em/en dashes
-    replaced = contents.replace('“','"').replace('”','"').replace("–","-").replace("—","-")
+    regex_sub_map = [(r'[“”]', '"'),
+                     (r'[‘’]', "'"),
+                     (r'[—–]', '-')]
+    replaced = contents
+    for pattern, sub in regex_sub_map:
+        replaced = re.sub(pattern, sub, replaced)
     return replaced
 
 def has_non_printable_ascii_characters(contents):

docker/apache.conf

@@ -5,7 +5,7 @@ LoadModule wsgi_module /usr/local/lib64/python3.9/site-packages/mod_wsgi/server/
 WSGIPythonPath /app
 
 # Run apps in separate processes to stop yaml.CSafeLoader import-time error
-WSGIDaemonProcess topology  home=/app
+WSGIDaemonProcess topology  home=/app processes=5
 WSGIDaemonProcess topomerge home=/app
 
 # vhost for topology, SSL terminated here (for gridsite auth)
@@ -35,6 +35,14 @@ WSGIDaemonProcess topomerge home=/app
 
   WSGIScriptAlias /        /app/topology.wsgi         process-group=topology application-group=topology
 
+  # Enable compression for text files
+  AddOutputFilterByType DEFLATE text/html text/plain text/xml text/css text/javascript application/javascript application/json
+
+  # Enable memory caching
+  CacheSocache shmcb
+  CacheSocacheMaxSize 102400
+  CacheEnable socache /
+
 </VirtualHost>
 
 # Separate vhost for map, no SSL required (terminated in traefik)

mappings/project_institution.yaml

@@ -58,6 +58,7 @@ Rochester: "University of Rochester"
 Rowan: "Rowan University"
 RPI: "Rensselaer Polytechnic Institute"
 SalemState: "Salem State University"
+SBU: "State University of New York at Stony Brook"
 SIUE: "Southern Illinois University Edwardsville"
 SDSU: "San Diego State University"
 SUNYUpstateMed: "SUNY Upstate Medical University"

projects/Arizona_Chan_Steward.yaml

@@ -0,0 +1,6 @@
+Department: Department of Astronomy and Steward Observatory
+Description: Scalable astronomical data analytics for the Department of Astronomy
+  and Steward Observatory at the University of Arizona
+FieldOfScience: Physics
+Organization: University of Arizona
+PIName: Chi-kwan Chan

projects/Caltech_Vallisneri.yaml

@@ -0,0 +1,12 @@
+Description: >
+  The NANOGrav collaboration is a cross-university, cross-discipline collection of astrophysicists, 
+  data analysts, and engineers who are currently working to detect a gravitational wave background 
+  via Pulsar Timing Arrays (PTAs).  Our group's current projects are related to cross-validation and 
+  posterior predictive checking methods for parameter estimation and detection analyses for Bayesian 
+  PTA studies. Another project is related to increasing computational efficiency of PTA analyses by 
+  developing likelihood reweighting methods for PTAs. More information on NANOGrav can be 
+  found here:  http://nanograv.org/
+Department:  California Institute of Technology
+FieldOfScience: Astronomy and Astrophysics
+Organization: California Institute of Technology
+PIName: Michele Vallisneri

projects/Cornell_Sandoz.yaml

@@ -0,0 +1,5 @@
+Description: We study bacterial survival. Particularly, we are interested in cell wall modifications in response to changing environments. https://www.ksandozlab.com/new-page-2
+Department: Population Medicine and Diagnostic Sciences
+FieldOfScience: Biological and Biomedical Sciences
+Organization: Cornell University
+PIName: Kelsi Sandoz

projects/Dartmouth_Chaboyer.yaml

@@ -0,0 +1,9 @@
+Description: >
+  Computational stellar models are widely used in astrophysics and are often consulted to interpret observations of starlight.
+  My research group aims to improve stellar models by incorporating updated physics into the models, creating a database of 
+  stellar models for use by other researchers, and to use these improved stellar models to study a variety of issues related 
+  to galactic archelogy and the formation of galaxies. https://stellar.host.dartmouth.edu
+Department: Physics and Astronomy
+FieldOfScience: Astronomy and Astrophysics
+Organization: Dartmouth College
+PIName: Brian Chaboyer

projects/Duke_Charbonneau.yaml

@@ -0,0 +1,8 @@
+Description: >
+  Periodic microphases universally emerge in systems for which short-range inter-particle attraction is frustrated by long-range repulsion.
+  The morphological richness of these phases makes them desirable material targets, but our relatively coarse understanding of even simple models limits our grasp of their assembly. 
+  The OSG computing resources will enable us to explore more solutions of the equilibrium phase behavior of a family of similar microscopic microphase formers through specialized Monte Carlo simulations.
+Department: Chemistry
+FieldOfScience: Computational Condensed Matter Physics
+Organization: Duke University
+PIName: Patrick Charbonneau

projects/FIU_Hamid.yaml

@@ -0,0 +1,9 @@
+Description:  https://fphlm.cs.fiu.edu/
+Department:  IHRC
+FieldOfScience: Ocean Sciences and Marine Sciences
+Organization: Florida International University
+PIName: Shahid Hamid
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/GATech_Coogan.yaml

@@ -0,0 +1,12 @@
+Description: We are attempting to run a simulation for Georgia Tech's
+  Robotarium on our website when users upload run files. Our simulator is
+  based on https://github.com/robotarium/robotarium_python_simulator ,
+  with edits to certain functions.
+Department: Electrical and Computer Engineering
+FieldOfScience: Electrical, Electronic, and Communications
+Organization: Georgia Institute of Technology
+PIName: Samuel Coogan
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/GSU_ARCTIC.yaml

@@ -0,0 +1,5 @@
+Department: Advanced Research Computing Technology and Innovation Core
+Description: https://arctic.gsu.edu/
+FieldOfScience: Research Computing
+Organization: Georgia State University
+PIName: Suranga Edirisinghe

projects/HCC_staff.yaml

@@ -0,0 +1,5 @@
+Description: Cyberinfrastructure Research
+Department: Holland Computing Center
+FieldOfScience: Computer Science
+Organization: University of Nebraska-Lincoln
+PIName: Adam Caprez

projects/IIT_Li.yaml

@@ -0,0 +1,7 @@
+Description: >
+  Develop Lagrangian particle methods for moving interface problems in fluid mechanics and materials science;
+  Develop Physical Informed Neural network (PINN) for Green function-based methods.
+Department:  Applied Mathematics
+FieldOfScience: Materials Science
+Organization: Illinois Institute of Technology
+PIName:  Shuwang Li

projects/Internet2_MS-CC.yaml

@@ -0,0 +1,9 @@
+Description: The Minority Serving - Cyberinfrastructure Consortium envisions a transformational partnership to promote advanced cyberinfrastructure capabilities on HBCU, HSI, TCU, and MSI campuses, with data; research computing; teaching; curriculum development and implementation; collaboration; and capacity-building connections among institutions.  
+Department: MS-CC 
+FieldOfScience: Computer and Information Sciences 
+Organization: Internet2
+PIName: Ana Hunsinger
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/LSU_Cox.yaml

@@ -0,0 +1,7 @@
+Description: >
+  Using machine learning techniques that discover solutions with anatomically and temporally structured sparsity,
+  we aim to test representational predictions from cognitive psychology using whole-brain neuroimaging datasets. 
+Department: Department of Psychology
+FieldOfScience: Behavioral Science
+Organization: Louisiana State University
+PIName: Christopher Cox 

projects/NCSU_2023_Hall

@@ -0,0 +1,9 @@
+Description: Studies of square shaped colloidal particles with internal magnetic dipoles. Objective is to discover the phase behavior of colloids under the presence and absence of a magnetic field. Other research on colloids and soft materials under direction of PI can be found at: https://carolkhall.wordpress.ncsu.edu/research/selected-projects/
+Department: Chemical and Biomolecular Engineering
+FieldOfScience: Chemical Engineering
+Organization: North Carolina State University
+PIName: Carol Hall
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/NIAID_TBPortals.yaml

@@ -0,0 +1,10 @@
+Department: Office of Cyber Infrastructure and Computational Biology
+Description: Training AI models and CT image processing and analysis using these AI
+  models.  The collaboration is part of our TB Portals program https://tbportals.niaid.nih.gov/
+FieldOfScience: Biological and Biomedical Sciences
+Organization: National Institute of Allergy and Infectious Diseases
+PIName: Darrell Hurt
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/NOAA_Fisch.yaml

@@ -0,0 +1,8 @@
+Description: > 
+  My research aims to improve population models of fisheries resources so as to better facilitate seafood sustainability
+  and our understanding of marine and freshwater populations. This involves the development of highly-parameterized
+  non linear models requiring numerical solutions and numerical integration.  
+Department: National Marine Fisheries Service
+FieldOfScience: Natural Resources and Conservation
+Organization: National Oceanic and Atmospheric Administration
+PIName: Nicholas Fisch

projects/Rochester_Franchini.yaml

@@ -0,0 +1,8 @@
+Description: >
+   The primary objective of this research project is to evaluate the efficacy and feasibility of an AI-powered 
+   pre-diagnostic tool for gastrointestinal diseases. Specifically, the project aims to assess the accuracy of 
+   the AI-powered technology in analyzing abdominal sounds and visual data recorded by the user's mobile phone.
+Department: University of Rochester Medical Centre
+FieldOfScience: Biological and Biomedical Sciences
+Organization: University of Rochester
+PIName: Anthony Franchini

projects/SBU_Jia.yaml

@@ -0,0 +1,8 @@
+Description: https://www.stonybrook.edu/commcms/chemistry/faculty/_faculty-profiles/jia-jiangyong
+  Simulation of relativistic heavy ion collisions of atomic nuclei, such
+  as Gold, Lead, Xeon, Oxygen, proton etc using relativistic hydrodynamic
+  code and transport simulation codes.
+Department: Physics
+FieldOfScience: Physics
+Organization: State University of New York at Stony Brook
+PIName: Jiangyong Jia

projects/UCSD_Du.yaml

@@ -0,0 +1,11 @@
+Department: Physics
+Description: Our research group focuses on developing quantum sensing and imaging
+  techniques to study various properties (spin, charge, and heat, etc) of quantum
+  materials in the nanometer scale. In addition, we design and engineer hybrid quantum
+  devices to achieve efficient qubit control for quantum information applications.
+  Our research tools are versatile, including optical measurement based on nitrogen
+  vacancy center in diamond, transport and microwave spectroscopy as well as scanning
+  probe magnetometry.
+FieldOfScience: Physics
+Organization: University of California, San Diego
+PIName: Chunhui Du

projects/UCSD_Guiang.yaml

@@ -0,0 +1,9 @@
+Description: Improve performance of data downsampling tools for future LHC runs
+Department: Physics
+FieldOfScience: Physics
+Organization: University of California, San Diego
+PIName: Jonathan Guiang
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/UConn_Alpay.yaml

@@ -0,0 +1,9 @@
+Description: >
+  Our team of scientists uses computational and theoretical methodologies to understand and address
+  fundamental problems in materials science and engineering. Collectively, we have a broad spectrum of research interests 
+  with myriad applications. We use our understanding to design advanced materials that impact the way we live, 
+  including functional materials, smart materials, aerospace, nanostructured materials and materials for energy efficiency. https://alpay.ims.uconn.edu/
+Department: Materials Science and Engineering
+FieldOfScience: Materials Science
+Organization: University of Connecticut
+PIName: Pamir Alpay

projects/UF_Strother.yaml

@@ -0,0 +1,10 @@
+Description: >
+  The Strother Lab focuses on questions at the interface between physiology and physics. 
+  Our lab is especially interested in understanding processes at multiple levels of organization, 
+  from the properties of individual cells up to the responses of the whole animal. 
+  Current projects in the lab examine a range of topics, including the effects of stress on animal behavior,
+  nervous control of the cardiovascular system, and sensory physiology. See also www.strotherlab.org.
+Department: Whitney Laboratory for Marine Bioscience
+FieldOfScience: Neuroscience, biomechanics, microscopy
+Organization: University of Florida
+PIName: James Strother

projects/UMassLowell_Delhommelle.yaml

@@ -0,0 +1,10 @@
+Description: Unraveling Crystallization and Phase Transition Processes
+  through Topology, Rare-Event Simulations, and Machine Learning 
+Department: Chemistry
+FieldOfScience: Physical Chemistry
+Organization: University of Massachusetts Lowell
+PIName: Jerome Delhommelle
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/UMontana_Roy.yaml

@@ -0,0 +1,15 @@
+Description: >
+  1) Virtual screening - Computational or virtual screening of molecules can accelerate drug development programs.
+  We have developed a virtual screening method to screen billions of molecules for hit generation against specific protein targets. 
+  We want to develop the method further and also want to use the method to develop hits against specific proteins, 
+  such as the one announced in this competition. https://cache-challenge.org/ 2) Entropy from surface properties - 
+  Calculating entropy is tricky, as, in principle, it requires sampling vast phase space to count all available microstates. 
+  We are developing a method for calculating the entropy of small molecules from their surface properties. 
+  Such a method will benefit computational chemistry, especially the virtual screening community. https://www.biorxiv.org/content/10.1101/2021.05.26.445640v1.abstract 
+  3) Transferability of polygenic risk scores (PRS) - PRS is a useful tool to estimate one's health condition propensity from their genetic makeup. 
+  Historically, most of the PRS models were built from European ancestry samples. We are working on a network model to identify the best way 
+  to transfer a PRS model from the population it was developed for to another population not included in the study.
+Department: Department of Biomedical and Pharmaceutical Sciences
+FieldOfScience: Biological and Biomedical Sciences
+Organization: University of Montana
+PIName:  Amitava Roy

projects/UWMadison_Curtin.yaml

@@ -0,0 +1,5 @@
+Department: Psychology
+Description: 'https://arc.psych.wisc.edu/'
+FieldOfScience: Social, Behavioral & Economic Sciences
+Organization: University of Wisconsin-Madison
+PIName: John Curtin

projects/UWMadison_Gitter.yaml

@@ -0,0 +1,5 @@
+Department: Biostatistics and Medical Informatics
+Description: 'https://www.biostat.wisc.edu/~gitter/'
+FieldOfScience: Medical (NIH)
+Organization: University of Wisconsin-Madison
+PIName: Anthony Gitter

projects/UWMadison_Livny.yaml

@@ -0,0 +1,5 @@
+Department: Computer Sciences
+Description: http://chtc.cs.wisc.edu/
+FieldOfScience: Computer & Information Science & Engineering
+Organization: University of Wisconsin-Madison
+PIName: Miron Livny

projects/UWMadison_Pool.yaml

@@ -0,0 +1,5 @@
+Department: Genetics
+Description: http://www.genetics.wisc.edu/user/338
+FieldOfScience: Biological Sciences
+Organization: University of Wisconsin-Madison
+PIName: John Pool

projects/WichitaState_Hwang.yaml

@@ -0,0 +1,9 @@
+Description: Analysis of porous media using pore-scale simulations of additively manufactured wicks with X-ray computed tomography.
+Department: Department of Mechanical Engineering
+FieldOfScience: Mechanical Engineering
+Organization: Wichita State University
+PIName: Gisuk Hwang
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/ePIC.yaml

@@ -0,0 +1,8 @@
+Department: Physics
+Description: the ePIC collaboration based out of the EIC
+FieldOfScience: Nuclear Physics
+Organization: Brookhaven National Laboratory
+PIName: John Lajoie
+Sponsor:
+  VirtualOrganization:
+    Name: EIC