WIP: Regolith Grant Report Builder

regolith/builder.py

@@ -15,6 +15,7 @@
 from regolith.builders.coabuilder import RecentCollaboratorsBuilder
 from regolith.builders.beamplanbuilder import BeamPlanBuilder
 from regolith.builders.activitylogbuilder import ActivitylogBuilder
+from regolith.builders.grantreportbuilder import GrantReportBuilder
 
 
 BUILDERS = {
@@ -34,6 +35,7 @@
     "resume": ResumeBuilder,
     "review-man": ManRevBuilder,
     "review-prop": PropRevBuilder,
+    "grantreport": GrantReportBuilder
 }
 
 

regolith/builders/grantreportbuilder.py

@@ -0,0 +1,131 @@
+"""Builder for Proposal Reviews."""
+from datetime import datetime
+import time
+from nameparser import HumanName
+import dateutil.parser as date_parser
+
+from regolith.builders.basebuilder import LatexBuilderBase
+from regolith.dates import (month_to_int,
+                            get_dates,
+                            get_due_date,
+                            is_current,
+                            is_after,
+                            is_before)
+from regolith.fsclient import _id_key
+from regolith.sorters import position_key
+from regolith.tools import (
+    all_docs_from_collection,
+    filter_grants,
+    filter_presentations,
+    fuzzy_retrieval,
+    filter_publications
+)
+
+
+def subparser(subpi):
+    subpi.add_argument("start_date", help="start date of the reporting period, formatted as YYYY-MM-DD",
+                       default=None)
+    subpi.add_argument("end_date", help="end date of the reporting period, formatted as YYYY-MM-DD")
+    return subpi
+
+
+class GrantReportBuilder(LatexBuilderBase):
+    """Build a proposal review from database entries"""
+    btype = "grantreport"
+    needed_dbs = ['presentations', 'projecta', 'people', 'grants', 'institutions', 'expenses', 'citations']
+
+    def construct_global_ctx(self):
+        """Constructs the global context"""
+        super().construct_global_ctx()
+        gtx = self.gtx
+        rc = self.rc
+        for dbs in rc.needed_dbs:
+            gtx[dbs] = sorted(
+                all_docs_from_collection(rc.client, dbs), key=_id_key
+            )
+        gtx["all_docs_from_collection"] = all_docs_from_collection
+        gtx["float"] = float
+        gtx["str"] = str
+        gtx["zip"] = zip
+
+    def latex(self):
+        """Render latex template"""
+        rc = self.rc
+
+        # Convert Date Strings to Datetime Objects
+        rp_start_date = date_parser.parse(rc.start_date)
+        rp_end_date = date_parser.parse(rc.end_date)
+
+        # NSF Grant _id
+        grant_name = "dmref"
+
+        # Get prum associated to grant and active during reporting period
+        grant_prums = []
+        for prum in self.gtx['projecta']:
+            if grant_name in prum['grants']:
+                begin_date = get_dates(prum).get('begin_date')
+                due_date = get_due_date(prum['deliverable'])
+                # if projectum was finished during reporting period or is still current
+                # some projectum don't have an "end date", but all projecta have a deliverable
+                # due_date
+                if (rp_start_date <= due_date <= rp_end_date and prum['status'] is "finished") or is_current(prum):
+                    grant_prums.append(prum)
+        # Get people associated with grant
+        grant_people = list(set([prum['lead'] for prum in grant_prums]))
+
+        # Accomplishments
+        major_activities = []
+        significant_results = []
+        for prum in grant_prums:
+            if prum['status'] is "finished":
+                significant_results.append(prum)
+            else:
+                major_activities.append(prum)
+
+        # Opportunities for Training and Professional Development
+        training_and_professional_development = []
+        # presentations
+        for id in grant_people:
+            training_and_professional_development.extend(
+                filter_presentations(self.gtx["people"], self.gtx["presentations"], self.gtx["institutions"], id,
+                                     types=["all"], since=rp_start_date, before=rp_end_date, statuses=["accepted"]))
+        # thesis defendings
+        # how do i access people.yml in rg-db-public vs the people.yml file in rg-db-group?
+        defended_theses = []
+        for id in grant_people:
+            person = self.gtx['people'][id]
+            for education in person['education']:
+                if 'phd' in education['degree'].lower() and 'columbia' in education['institution'].lower() and \
+                        rp_start_date.year <= education['end_year'] <= rp_end_date.year:
+                    defended_theses.append(id)
+
+        # Products
+        # need rg-db-public's citation.yml... how to access that instead of the rg-db-group's citation.yml file
+        publications = filter_publications(self.gtx["citations"], grant_people, since=rp_start_date, before=rp_end_date)
+
+        # Participants/Organizations
+        participants = {}
+        for person in grant_people:
+            p = self.gtx["people"].get(person)
+            months = 0
+            if p['active']:
+                difference = datetime.today() - rp_start_date
+                if difference.day > 15:
+                    months = months + 1
+                months = difference.year * 12 + difference.month
+            else:
+
+                end_date = datetime.date(p['year'])
+            info = [p.get('position'), months]
+        self.render(
+            "grantreport.txt",
+            "billinge_grant_report.txt",
+            beginYear=rp_start_date.year,
+            endYear=rp_end_date.year,
+            majorActivities=major_activities,
+            significantResults=significant_results,
+            trainingAndProfessionalDevelopment=training_and_professional_development,
+            defendedTheses=defended_theses,
+            products=publications,
+            grantPeople=grant_people
+        )

regolith/templates/grantreport.txt

@@ -0,0 +1,134 @@
+NSF {{beginYear}}-{{endYear}} Annual Report
+
+Accomplishments
+------------------------------------------------------------------------------
+* What are the major goals of the project?
+In real-world applications, materials are rarely perfect crystals and their properties
+depend sensitively on defects, nanoscale structures, interfaces, surfaces and multi-scale
+heterogeneities. A major challenge is to gain a greater understanding of how such
+"imperfect" materials operate, including on different length and time-scales. In situations
+as complicated as this it is essential to validate theories against experiment, and vice versa.
+A more tightly coupled partnership between experiment and theory is needed, having its roots
+in information theory: the models need to capture all the physics of the problem become more
+complicated, while at the same time the information content of experimental data is reduced,
+due to lower resolution from finite size effects, defects, the presence of multiple components
+with overlapping problems, which yield unreliable and non-unique solutions, a bottleneck to
+predictive materials discovery. We will develop novel mathematical approaches to address this
+problem. We will study as a test case the nanostructure inverse problem (NIP), a well defined
+but generally ill-posed materials inverse problem; however, the methods that we develop will
+have much broader applicability in the world of materials discovery.
+
+Goal 1: Develop databases of nanostructure data from model systems
+Goal 2: Develop data analytic and stochastic optimization methodologies for robust
+nanostructure solutions
+Goal 3: Develop software infrastructure for nanostructure modeling that use the databases
+and the new methodologies for nanostructure solution
+Goal 4: Apply this to real scientific problems
+
+* What was accomplished under these goals (you must provide information for
+at least one of the 4 categories below)?
+------------------------------------------------------------------------------
+- Major Activities (currently worked on projecta):
+PDF in the cloud (PDFitc): Development of a web-based service for determining
+structures from measured PDFs given known structures in structural databases
+xpdTools, xpdAcq, xpdAn, xpdView: Software tools for streaming data analysis
+and visualization of diffraction data from the XPD diffractometer at NSLS-II
+synchrotron. The tools can also be used to analyze data from other diffraction
+beamlines.
+{%- for prum in majorActivities %}
+    {{ prum.get('name') }}: {{ prum.get('description') }}
+{% endfor -%}
+
+- Specific Objectives:
+PDF in the cloud (PDFitc): Development of a web-based service for determining
+structures from measured PDFs given known structures in structural databases
+
+- Significant Results (finished projecta):
+{%- for prum in significantResults %}
+    {{ prum.get('name') }}: {{ prum.get('description') }}
+{% endfor -%}
+
+Key outcomes or Other achievements:
+* What opportunities for training and professional development has the project provided?
+{%- for opportunity in trainingAndProfessionalDevelopment %}
+    - Authors: {{ opportunity.get('authors') }}
+    - Title: {{ opportunity.get('title') }}
+    - Location: {{ opportunity.get('meeting_name') }}
+{% endfor -%}}
+{%- for thesis in defendedTheses %}
+    {{thesis}} wrote and successfully defended their thesis.
+{% endfor -%}}
+
+* How have the results been disseminated to communities of interest?
+1. Publications
+2. Software releases and deployment of software packages on conda-forge and pypi for ease of installation
+3. Presentations at conferences and seminars
+
+* What do you plan to do during the next reporting period to accomplish the goals?
+#############################################################
+##                                                         ##
+##                                                         ##
+##      FILL THIS PART IN !!! FILL THIS PART IN !!!        ##
+##                                                         ##
+##                                                         ##
+#############################################################
+
+Products
+------------------------------
+{%- for doi in products %}
+    - {{doi.get('doi')}}
+{% endfor -%}}
+
+Participants/Organizations
+------------------------------
+What individuals have worked on the project?
+
+Name, Most Senior Project Role, Nearest Person Month Worked
+{%- for person in grantPeople %}
+    - {{person.get('_id')}}, {{person.get(''}}
+{% endfor -%}}
+Full details of individuals who have worked on the project:
+
+Name:
+Email:
+Most Senior Project Role:
+Nearest Person Month Worked:
+Contribution to the Project:
+Funding Support:
+International Collaboration:
+International Travel:
+
+What other organizations have been involved as partners?
+What other collaborators or contacts have been involved?
+
+Impacts
+------------------------------
+What is the impact on the development of the principal discipline(s) of the project?
+
+What is the impact on other disciplines?
+
+What is the impact on the development of human resources?
+
+What is the impact on physical resources that form infrastructure?
+
+What is the impact on institutional resources that form infrastructure?
+
+What is the impact on information resources that form infrastructure?
+
+What is the impact on technology transfer?
+
+What is the impact on society beyond science and technology?
+
+Changes/Problems
+------------------------------
+Changes in approach and reason for change
+
+Actual or Anticipated problems or delays and actions or plans to resolve them
+
+Changes that have a significant impact on expenditures
+
+Significant changes in use or care of human subjects
+
+Significant changes in use or care of vertebrate animals
+
+Significant changes in use or care of biohazards