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Updated the requirements to resolve security issues and also install mysqlclient. This resulted in the following changes having to be made
# Django 3.2 -> 4.2 changes ## ./datamad2/models/users.py from django.utils.translation import ugettext_lazy as _ --> from django.utils.translation import gettext_lazy as _ ## ./datamad2/admin.py admin.site.register(User, UserAdmin) etc at eof changed to @admin.register(User) decorator above class definition of the user type. eof registers all deleted Slightly concerned this does not give the same functionality, TODO check ## ./datamad2/utils.py from django.utils.encoding import force_text --> from django.utils.encoding import force_str ## ./datamadsite/settings.py USE_L10N = True --> line deleted crispy_bootstrap4 added to INSTALLED_APPS # ./datamadsite/settings_local.py.tmpl Added the Additional allowed template packs: CRISPY_ALLOWED_TEMPLATE_PACKS = "bootstrap4" CRISPY_TEMPLATE_PACK = "bootstrap4" # bootstrap_datepicker_plus updates ## grants.py and data_products.py from bootstrap_datepicker_plus import DatePickerInput --> from bootstrap_datepicker_plus.widgets import DatePickerInput ## Changed format='' for bootstrap_datepicker_plus.widgets.DatePickerInput from format='%d/%m/%Y' to options={'format':'%d/%m/%Y'} to fix the following error: ./app_datamad_new/Lib/site-packages/bootstrap_datepicker_plus/_base.py:38: FutureWarning: The 'format' parameter is ignored, set 'format' in options instead. see https://github.com/monim67/django-bootstrap-datepicker-plusbootstrap_datepicker_plus.widgets Removed ifequal from pagination.html as it was removed in Django 4.0 and replaced with "if x = condition" instead # djangorestframework updating to 3.15.2 from 3.12.4 # Updating to drf 3.15.2 from 3.12.4, had to specify basename for datacentres/ datacenter in datamad2_api/urls.py due to importing name from "DataCentre" model queryset leading to identical routings for the "datacentre" and "datacenter" base URLs. This is due to a change from drf 3.14 -> 3.15 enforcing the following encode/django-rest-framework#8438 Added new script DataMad_csv_create.py to import data from UKRIs DataBank database into a .csv file Created two example Docker files for local debugging, if the user wanted to. setup.py to Python 3.12 from Python 3.6 Updated the README.md file.
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‎.gitignore

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/static
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# scripts
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.vscode
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Databank.conf
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sql_alchemy_mysql_conn_string.txt
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odbc_conn_scratch.py
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/local_temp
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/import_csvs

‎DataMad_csv_create.py

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import pandas as pd
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import sqlalchemy as sa
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import numpy as np
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# TODO, try and get both parent and child grants in the SQL query,
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# for now only parent grants are present (i.e. lead PI grants)
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# Load connection string for SQLAlchemy
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conn_str = []
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with open('./local_temp/sql_alchemy_mysql_conn_string.txt', 'r') as fn:
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for line in fn:
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conn_str.append(str(line))
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# Setup SQLAlchemy to use mysqlclient as MySQL driver
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# (need to use SQLAlchemy as pandas now only accepts SQLAlchemey engine + SQL query input, not pyodbc or similar)
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engine = sa.create_engine(conn_str[0]) # mysqlclient connection for Docker
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# engine = sa.create_engine('mysql+pyodbc://DataBank?charset=utf8mb4') # pyodbc connection (used for Windows testing)
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saconn = engine.connect()
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# SQL query to pull information needed by DataMAD, also renames to DataMad names.
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sql_datamad_renamed = "SELECT \
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fact_application.ApplicationID AS GRANTREFERENCE, \
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fact_application.ApplicationTitle AS PROJECT_TITLE, \
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dim_scheme.SchemeName AS SCHEME, \
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dim_opportunity.OpportunityName AS 'CALL', \
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dim_scheme.SchemeType AS GRANT_TYPE, \
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dim_person.FullName AS GRANT_HOLDER, \
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dim_person.Email AS EMAIL, \
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dim_organisation.OrganisationName AS RESEARCH_ORG, \
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dim_department.DepartmentName AS DEPARTMENT, \
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dim_application_date.ActualStartDate AS ACTUAL_START_DATE, \
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dim_application_date.ActualEndDate AS ACTUAL_END_DATE, \
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fact_application.AdministratingCouncil AS NEW_ADMINISTRATING_COUNCIL, \
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dim_application_date.ProposedStartDate AS PROPOSED_ST_DT, \
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dim_application_date.ProposedEndDate AS PROPOSED_END_DT, \
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fact_application.ApplicationStatus AS GRANT_STATUS, \
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dim_organisation.AddressLine1 AS ADDRESS1, \
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dim_organisation.TownOrCity AS CITY, \
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dim_organisation.PostCode AS POSTCODE, \
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fact_application.AwardedAmount AS 'AMOUNT', \
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dim_application_ext.RoutingClassification AS ROUTING_CLASSIFICATION, \
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dim_classification_area.SubjectArea AS SCIENCE_AREA, \
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dim_organisation.region AS GEOGRAPHIC_AREA, \
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dim_classification_area.ResearchTopic AS SECONDARY_CLASSIFICATION, \
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dim_application_ext.ApplicationSummary AS ABSTRACT \
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FROM fact_application \
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LEFT OUTER JOIN dim_scheme \
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ON fact_application.SchemeSKey = dim_scheme.SchemeSKey \
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LEFT OUTER JOIN dim_opportunity \
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ON fact_application.OpportunitySKey = dim_opportunity.OpportunitySKey \
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LEFT OUTER JOIN dim_person \
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ON fact_application.ApplicantPersonSKey = dim_person.PersonSKey \
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LEFT OUTER JOIN dim_department \
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ON fact_application.OrganisationDepartmentSKey = dim_department.OrganisationDepartmentSKey \
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LEFT OUTER JOIN dim_application_date \
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ON fact_application.ApplicationSKey = dim_application_date.ApplicationSKey \
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LEFT OUTER JOIN dim_organisation\
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ON fact_application.LeadOrganisationSKey = dim_organisation.OrganisationSKey \
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LEFT OUTER JOIN dim_application_ext\
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ON fact_application.ApplicationSKey = dim_application_ext.ApplicationSKey \
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LEFT OUTER JOIN dim_classification_area \
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ON fact_application.PrimaryClassificationAreaSKey = dim_classification_area.ClassificationAreaSKey \
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WHERE fact_application.AdministratingCouncil = 'NERC' AND fact_application.ApplicationStatus = 'ACCEPTED' \
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GROUP BY fact_application.ApplicationID \
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LIMIT 200"
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# TODO May potentially need to add this back in (trying to join on fact_application_team.LeadApplicantPersonSKey instead)
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"""
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LEFT OUTER JOIN dim_person \
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ON fact_application.ApplicantPersonSKey = dim_person.PersonSKey \
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"""
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# Query data from Databank
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data_renamed = pd.read_sql(sql_datamad_renamed, engine)
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# Add in blank columns to cover fields missing in Databank that were in Siebel
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# TODO, should delete some of these once app_datamad is updated to remove these fields from the models
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# Definitely don't need WORK_NUMBER, NCAS, NCEO, ADDRESS2, OVERALL_SCORE, PROPOSED_ST_DT_ORG or PROPOSED_END_DT_ORG
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# Try to find (or extract from another field): FACILITY, LEAD_GRANT, PARENT_GRANT and OBJECTIVES
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no_longer_needed_cols = ['WORK_NUMBER', 'NCAS', 'NCEO', 'ADDRESS2', 'OVERALL_SCORE',
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'PROPOSED_ST_DT_ORG', 'PROPOSED_END_DT_ORG']
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data_renamed = data_renamed.reindex(columns=[*data_renamed.columns.tolist(), *no_longer_needed_cols], fill_value=np.nan)
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needed_cols = ['FACILITY', 'LEAD_GRANT', 'PARENT_GRANT', 'OBJECTIVES']
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data_renamed = data_renamed.reindex(columns=[*data_renamed.columns.tolist(), *needed_cols], fill_value=np.nan)
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# Reorder columns to Siebel order (easier to read for user, not needed for import via Django)
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col_order = ['GRANTREFERENCE', 'PROJECT_TITLE', 'SCHEME', 'CALL', 'GRANT_TYPE',
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'GRANT_HOLDER', 'WORK_NUMBER', 'EMAIL', 'RESEARCH_ORG',
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'DEPARTMENT', 'ACTUAL_START_DATE', 'ACTUAL_END_DATE',
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'NCAS', 'NCEO', 'PROPOSED_ST_DT', 'PROPOSED_END_DT',
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'GRANT_STATUS', 'ADDRESS1', 'ADDRESS2', 'CITY',
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'POSTCODE', 'LEAD_GRANT', 'PARENT_GRANT', 'AMOUNT',
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'ROUTING_CLASSIFICATION', 'SCIENCE_AREA',
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'GEOGRAPHIC_AREA', 'SECONDARY_CLASSIFICATION',
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'ABSTRACT', 'OBJECTIVES', 'FACILITY', 'OVERALL_SCORE',
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'PROPOSED_ST_DT_ORG', 'PROPOSED_END_DT_ORG']
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data_renamed = data_renamed[col_order]
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# Save .csv file
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data_renamed.to_csv("./import_csvs/datamad_databank_debug.csv")
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pause = 1

‎Dockerfile_debug

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FROM rockylinux:9.3
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WORKDIR /app
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# Installing Python in the image
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RUN dnf install python3 -y
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# RUN wget https://www.python.org/ftp/python/3.10.0/Python-3.10.0.tar.xz
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# RUN tar -xf Python-3.10.0.tar.xz
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# WORKDIR /Python-3.10.0
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# RUN ls
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# RUN ./configure --enable-optimizations
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# RUN make -j 2
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# RUN nproc
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# RUN make altinstall
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# Ensure pip is installed
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RUN python3 -m ensurepip --upgrade
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# Install MySQL and required drivers for Django to use MySQL
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# RUN dnf config-manager --set-enabled crb
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RUN dnf install epel-release -y
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RUN crb enable
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RUN dnf install python3-devel -y
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RUN dnf install mysql-server -y
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RUN dnf install pkgconf pkgconf-pkg-config -y
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RUN dnf install mysql-devel -y
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RUN dnf install gcc -y
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RUN pip3 install mysqlclient
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# Install git to clone ceda-elasticsearch-tools into image (cloned in requirements.txt)
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RUN dnf -y install git
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COPY requirements.txt requirements.txt
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RUN pip install --no-cache-dir -r requirements.txt
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# Add sqllite support for existing DataMad data (imported from Siebel via UKCEH)
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RUN dnf install sqlite -y
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# TODO needed for debug only
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RUN pip install debugpy
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# Copy the project code into the container
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COPY ./ /app/
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# ENV DJANGO_SUPERUSER_PASSWORD = Password
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# RUN python3 manage.py createsuperuser [email protected] --first_name=Test --last_name=Person --noinput
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# RUN python3 manage.py import_database --file ./import_csvs/datamad_databank_debug.csv
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# RUN yes | python3 manage.py rebuild_index
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# EXPOSE 8000
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# CMD [ "python3", "manage.py"]

‎README.md

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## Editing docs
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The documentation is written using Jekyll. A usefull getting started guide
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The documentation is written using Jekyll. A useful getting started guide
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can be found [here](https://jekyllrb.com/docs/step-by-step/01-setup/)
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Once you have the pre-requisites installed, navigate to the docs directory and run:
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This will serve the docs locally and will update as you change the source.
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## Set up Guide
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## Setup guide Python environment
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- Clone the datamad2 repository to your local machine in a directory of your choosing `git clone https://github.com/cedadev/datamad2.git`
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- Install Python if you haven't already (see datamad2 requirements.txt for Python version)
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Process to set up Datamad2
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### Docker
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If you have Docker installed (for example via Rancher Desktop) then the simplest install method is to run either Windows:
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```
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docker build -f .\Dockerfile_debug -t datamad-debug .
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```
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- Install the datamad2 repository `git clone https://github.com/cedadev/datamad2.git`
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or Linux (rocky9 tested):
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```
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docker build -f ./Dockerfile_debug -t datamad-debug .
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```
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- Install the required packages found in the requirements.txt file within the datamad repository in a virtual
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environment `pip install -r requirements.txt`
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This will install a Rocky9 image with everything needed for Python mysqlclient, the Databank download script and the Django web application to run.
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Note one, Rancher Desktop needs to be running for the docker command to work (at least in Windows).
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Note two, this does not use any CEDA specific Docker images and should not be used in deployment
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### Windows
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These instructions may not be extensive
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- Download and Install MySQL server (mysql.exe is required for mysqlclient to run)
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- Create a Python virtual environment
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```
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python virtualenv app_datamad
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```
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- Install the required packages found in the requirements.txt file within the datamad repository into the virtual
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environment you created `pip install -r requirements.txt`
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If there are errors such as mysql.exe not found then you might need to add MySQL Server\bin to your user path environment variable. For example for MySQL 8.0 add:
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```
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C:\Program Files\MySQL\MySQL Server 8.0\bin
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```
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Note, you might need to check where mysql.exe has been installed on your system as the above might not be the install path for later (or earlier) versions of MySQL server.
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Alternatively you could try and use MariaDB instead, but this is untested or Microsoft SQL server, setup an ODBC connection in windows and then change the connection settings in "DataMad_csv_create.py".
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### Linux (Rocky9 example)
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The install order ensures all dependencies are installed in the correct order.
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- Install python
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```
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dnf install python3 -y
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```
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Install all dependencies needed for mysqlclient to get access to DataBank through the "DataMad_csv_create.py" script
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```
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dnf install epel-release -y
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crb enable
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dnf install python3-devel -y
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dnf install mysql-server -y
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dnf install pkgconf pkgconf-pkg-config -y
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dnf install mysql-devel -y
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dnf install gcc -y
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pip3 install mysqlclient
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```
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- Install sqllite support for local database
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dnf install sqlite -y
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- If somehow not already installed (if you downloaded the datamad repo from a .zip file on the web) then install git to clone ceda-elasticsearch-tools (and others) in in requirements.txt
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```
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dnf -y install git
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```
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- Create Python virtual environment in the directory of your choice, then activate it (depending on how Pyton installed you may need to replace "python3" with "python")
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```
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python3 virtualenv app_datamad
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/bin/activate
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```
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- Then install DataMad requirements into the virtual environment
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```
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pip install --no-cache-dir -r requirements.txt
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pip install debugpy
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```
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## Setup guide DataBank Access
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DataBank is a UKRI service containing grant information which is pulled from "The Funding Service" grant application system. The Django application DataMad used a Python script "DataMad_csv_create.py" to generate a .csv file, which Django then uses to import data from DataBank and save it into a local SQLLite file for debugging, or a PostGres database in production.
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To use it:
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- a local_temp directory must be created
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- Within it create a .txt file with the name "sql_alchemy_mysql_conn_string.txt" and place the following into it:
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```
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mysql+mysqldb://<User>:<Password>@<host>/databank
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<User>, <Password> and <host> should be replaced with the DataBank login details.
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```
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## Setup Guide Django application
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Process to set up Datamad2 web application
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- In the datamadsite folder you should see a settings_local.py.tmpl file, copy said file and past in the same
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location but remove the `.tmpl` extension.
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...
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```
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- Within the terminal, run `python manage.py migrate`.
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In the instructions below you might, depending on your setup, need to replace the string "python" with the string "python3".
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If using Docker, then start an interactive Docker shell using `docker run -it -p 8000:8000 datamad-debug` before running the instructions below.
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- Within the terminal, run `python manage.py migrate`.
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- With the .csv containing the database, save the file in the same folder as manage.py and run
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`python manage.py import_database --f datamad_csv.csv`
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`python manage.py import_database --file datamad.csv`
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- You will want to create a superuser to log in to the site, to do this run `python manage.py createsuperuser`, enter
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in a username and password, this will be local, so you can keep it simple.
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- Within the terminal run `python manage.py rebuild_index`, this process may take some time.
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- Lastly, if all was successful, run `python manage.py runserver` and a local server of the site should be running. The
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address to which should be given in the terminal. Open the address in your browser to visit the site.
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‎datamad2/admin.py

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# #
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################################################################################
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@admin.register(User)
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class UserAdmin(BaseUserAdmin):
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list_display = ( 'first_name', 'last_name', 'email','data_centre', 'is_admin')
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search_fields = ('email',)
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)
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@admin.register(ImportedGrant)
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class ImportedGrantAdmin(admin.ModelAdmin):
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search_fields = ['grant_ref', 'title']
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list_display = ('grant_ref', 'title', 'creation_date')
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@admin.register(Grant)
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class GrantAdmin(admin.ModelAdmin):
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readonly_fields = ['updated_imported_grant', 'science_area']
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search_fields = ['grant_ref', 'importedgrant__title']
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@admin.register(DataProduct)
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class DataProductAdmin(admin.ModelAdmin):
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pass
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@admin.register(Document)
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class DocumentAdmin(admin.ModelAdmin):
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list_display = ('title', 'grant')
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search_fields = ['title', 'grant__grant_ref']
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autocomplete_fields = ['grant']
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@admin.register(DataCentre)
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class DataCentreAdmin(admin.ModelAdmin):
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inlines = [
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JIRAIssueTypeInline,
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DataFormatInline,
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PreservationPlanInline,
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# Register the Admin classes
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admin.site.register(User, UserAdmin)
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admin.site.register(ImportedGrant, ImportedGrantAdmin)
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admin.site.register(Grant, GrantAdmin)
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admin.site.register(DataProduct, DataProductAdmin)
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admin.site.register(Document, DocumentAdmin)
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admin.site.register(DataCentre, DataCentreAdmin)

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