CAiMIRA merge requestshttps://gitlab.cern.ch/caimira/caimira/-/merge_requests2024-03-08T11:24:27+01:00https://gitlab.cern.ch/caimira/caimira/-/merge_requests/484Draft: Fixed schema custom distributions2024-03-08T11:24:27+01:00Luis AleixoDraft: Fixed schema custom distributions**Using `QA` instance (Data Service)**
- Fixed refs on virus distributions.
- Added a restriction for the conditional plot generation (only available if `covid_overal_vl_data` is selected) - **TODO** for other distributions.
- Fixed min...**Using `QA` instance (Data Service)**
- Fixed refs on virus distributions.
- Added a restriction for the conditional plot generation (only available if `covid_overal_vl_data` is selected) - **TODO** for other distributions.
- Fixed minor display error when probability of infection is higher than `99.9%` (before it was displaying `100%` while it should be `>99.9%`).
- Removed `Linear Space` option from available options on distributions dropdown.
- Added `Constant` as an option for the options on distributions dropdown (which is not anymore only distributions). Schema in **QA** is updated.
Next step is to update the schema to allow single float values for `viral_load_in_sputum`, as well as to work on it to allow other distributions (question with `LogCustom` and `LogCustomKernel` distributions).Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/485tests: run tests2024-02-28T13:33:23+01:00Nicola Taroccotests: run testshttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/471Draft: config: inject data registry instance instead of static config2023-12-12T19:19:26+01:00Nicola TaroccoDraft: config: inject data registry instance instead of static config* closes #365* closes #365https://gitlab.cern.ch/caimira/caimira/-/merge_requests/462Draft: Test Data Service api2023-10-27T11:43:39+02:00Luis AleixoDraft: Test Data Service apiLuis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/468Draft: added open source acknowledgments2023-10-24T11:36:49+02:00Luis AleixoDraft: added open source acknowledgmentshttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/455Draft: Data Service - Data Integration2023-08-08T10:36:03+02:00Luis AleixoDraft: Data Service - Data IntegrationThis MR implements a first procedure to digest the data that comes from the Data Service (WP3).
It uses a test JSON blob containing the descriptors to generate the `viral_load_in_sputum` distribution for the virus class, as well as a fl...This MR implements a first procedure to digest the data that comes from the Data Service (WP3).
It uses a test JSON blob containing the descriptors to generate the `viral_load_in_sputum` distribution for the virus class, as well as a float value for the `evaporation_factor`. These data are injected on the `requested_model_config` data field to be digested by the `from_dict` method on the `model_generator.py` file. Once the `ServiceData` generates the data form the parameters/descriptors, this data can be widely used in the modules via the `ServiceData` object previously created with the corresponding data.
Validation on the input data is needed once the original JSON blob containing the final data is ready.M2.1 - Prioritise model improvementsLuis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/447Draft: Dynamic number of exposed occupants2023-06-30T10:18:26+02:00Luis AleixoDraft: Dynamic number of exposed occupantsThis MR contains the changes for the dynamic number of occupants for the incidence rate.This MR contains the changes for the dynamic number of occupants for the incidence rate.Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/449Removed LFS file and script2023-06-07T11:42:15+02:00Luis AleixoRemoved LFS file and scriptTemporary fix for Git LFS bandwidth - the script will be re-introduced, and the excel file hosted in CERNBox.Temporary fix for Git LFS bandwidth - the script will be re-introduced, and the excel file hosted in CERNBox.Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/377Draft: Terminal warnings control2023-04-17T16:47:35+02:00Luis AleixoDraft: Terminal warnings controlThis MR handles the warnings that were displayed on the terminal.
Steps:
- ExpertApp: removed arguments that didn't exist on some widgets.
- ExpertApp: suppressed deprecation warning related to the `Tool Manager` constructor.
- Added `...This MR handles the warnings that were displayed on the terminal.
Steps:
- ExpertApp: removed arguments that didn't exist on some widgets.
- ExpertApp: suppressed deprecation warning related to the `Tool Manager` constructor.
- Added `dtype=object` for a `ndarray` creation in the `air_exchange` method.
- Restricted the `tornado` version to `6.1` due to deprecation errors.
With these changes there are no warnings being triggered.Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/418Draft: Internationalization: EN-FR2023-04-14T17:18:10+02:00Luis AleixoDraft: Internationalization: EN-FR**How to extract new strings to be translated:**
Make sure that `pybabel` is installed:
```
pip install pybabel
```
In the `caimira/apps` directory run the following command:
```
pybabel extract -F babel-mapping.ini -o locale/base.po...**How to extract new strings to be translated:**
Make sure that `pybabel` is installed:
```
pip install pybabel
```
In the `caimira/apps` directory run the following command:
```
pybabel extract -F babel-mapping.ini -o locale/base.pot ./
```
**How to update the .po file:**
In the `caimira/apps` directory run the following command:
```
msgmerge --no-wrap --sort-by-file --output-file=locale/fr/LC_MESSAGES/messages.po locale/fr/LC_MESSAGES/messages.po locale/base.pot
```
At this stage the translations can be done in the `.po` file.
**How to compile and genera the .mo file:**
```
msgfmt locale/fr/LC_MESSAGES/messages.po --output-file=locale/fr/LC_MESSAGES/messages.mo
```
Reference: https://st4lk.github.io/en/blog/2015/01/31/tornado-internationalization-and-localization.htmlLuis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/429Method to generate P(I|vl) uncertainties graphs2023-03-03T17:32:43+01:00Luis AleixoMethod to generate P(I|vl) uncertainties graphsCreate and save matplotlib figure for the probability of Iifection given a certain value of viral load, with a confidence interval of 90%.Create and save matplotlib figure for the probability of Iifection given a certain value of viral load, with a confidence interval of 90%.Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/356Revert "Merge branch 'model/humidity_function' into 'master'"2022-05-11T16:12:16+02:00James DevineRevert "Merge branch 'model/humidity_function' into 'master'"This reverts merge request !351, will be re-merged after a rebase with !354This reverts merge request !351, will be re-merged after a rebase with !354Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/330Draft: Moved leftovers from expiration types to the tests2022-05-11T12:04:27+02:00Luis AleixoDraft: Moved leftovers from expiration types to the testsCloses https://gitlab.cern.ch/cara/cara/-/issues/241
Since the values used in `_ExpirationBase.types` are leftovers from the previous model, this MR moves its declaration to the tests (`conftest.py`).Closes https://gitlab.cern.ch/cara/cara/-/issues/241
Since the values used in `_ExpirationBase.types` are leftovers from the previous model, this MR moves its declaration to the tests (`conftest.py`).Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/297Ventilation scheme block - Window height, width and opening distance2022-04-14T14:25:12+02:00Luis AleixoVentilation scheme block - Window height, width and opening distanceThis MR solve issues of https://gitlab.cern.ch/cara/cara/-/issues/112:
**Ventilation scheme block:**
* [X] Add the window_type, window_height and window_width as an input
Added the two different window types: ```Sliding/Side-Hung``` a...This MR solve issues of https://gitlab.cern.ch/cara/cara/-/issues/112:
**Ventilation scheme block:**
* [X] Add the window_type, window_height and window_width as an input
Added the two different window types: ```Sliding/Side-Hung``` and ```Top-or Bottom-Hung```. The former does not contain a widget for the ```Width of window (m)```, while the later does. For both window types, ```window_height``` and ```opening_length``` are asked.Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/296Expert App Ventilation and Resizable window2022-04-14T12:25:24+02:00Luis AleixoExpert App Ventilation and Resizable windowThis MR is the first of some that are going to solve issues of https://gitlab.cern.ch/cara/cara/-/issues/112.
The main implementations on this are:
- Resizable size for **desktop** screens (previously it was hard to view the entire App...This MR is the first of some that are going to solve issues of https://gitlab.cern.ch/cara/cara/-/issues/112.
The main implementations on this are:
- Resizable size for **desktop** screens (previously it was hard to view the entire App on a ```13.3”``` diagonal display, for example).
- Ventilation has now the ```No ventilation``` option.
- Added ```RadioButtons``` for ```Air supply flow rate``` or ```Air changes per hour``` on ```Mechanical Ventilation```.
- Changed header (text and image).
- ```ToggleButtons``` style.
![Screenshot_2021-11-24_at_10.10.13](/uploads/4ee2221b65668ca13155d92c4a54073d/Screenshot_2021-11-24_at_10.10.13.png)Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/173WIP: Simplify the base theme2021-12-14T11:20:37+01:00Philip ElsonWIP: Simplify the base themeSimplify the base theme, removing items that don't exist such as the Expert app, as well as CERN specific information on COVID.
This is a zero change for the CERN theme. For the base theme the following changed:
* No longer a link to ...Simplify the base theme, removing items that don't exist such as the Expert app, as well as CERN specific information on COVID.
This is a zero change for the CERN theme. For the base theme the following changed:
* No longer a link to the Expert app (it won't work unless you have set it up appropriately anyway, which we do for the CERN managed instance)
* Remove the covid information link from the base theme (it is CERN specific, and remains on the CERN theme)
* Remove the COVID@CERN context form the base theme. It remains on the CARA homepage (which is running the CERN theme)
@gaazzopa - from a theming perspective, this begins the process of not separating "cara.apps" from "cara.apps.calculator". I don't propose needing a theme for both ``cara.apps`` *and* a theme for ``cara.apps.calculator``, and as a result we need to bring the layout/index/etc. into the calculator templates directory (gradually). This is really a reflection of the fact that when you start cara, you are starting ``cara.apps.calculator``, not ``cara.apps``. If we need to do something different in the futrue, we can figure it out then (but I still expect there to be a single theme most likely).Gabriella AzzopardiGabriella Azzopardihttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/292'No ventilation' option on expert app2021-11-24T10:17:56+01:00Luis Aleixo'No ventilation' option on expert appThis MR accomplishes the first suggestion on https://gitlab.cern.ch/cara/cara/-/issues/112 , regarding the **Ventilation scheme block**.
The ```No ventilation``` option was added to the expert app.This MR accomplishes the first suggestion on https://gitlab.cern.ch/cara/cara/-/issues/112 , regarding the **Ventilation scheme block**.
The ```No ventilation``` option was added to the expert app.Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/294Nearest weather station for all the ventilation types2021-11-19T17:25:31+01:00Luis AleixoNearest weather station for all the ventilation typesThe ```Nearest weather station``` field in the report was missing when the ```Ventilation``` was other than ```Natural```.
I decided to keep it in the report even when there is no ventilation, since the ```Geographic Location``` is alwa...The ```Nearest weather station``` field in the report was missing when the ```Ventilation``` was other than ```Natural```.
I decided to keep it in the report even when there is no ventilation, since the ```Geographic Location``` is always present there (in my opinion it makes sense to keep them together).
![Screenshot_2021-11-19_at_17.11.18](/uploads/dad1a6b437fe590ffe125b14b272712d/Screenshot_2021-11-19_at_17.11.18.png)Luis AleixoLuis Aleixohttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/264Correct doc string in the concentration method2021-10-05T18:06:03+02:00Andre HenriquesCorrect doc string in the concentration methodThe `integrated_concentration` methods return the `exposure` which is the number of viruses per m3 of room volume (`virions/m3`) and not the `dose` which is in `infectious virions`.
when integrated C(t) dt you get `exposure * t` which ...The `integrated_concentration` methods return the `exposure` which is the number of viruses per m3 of room volume (`virions/m3`) and not the `dose` which is in `infectious virions`.
when integrated C(t) dt you get `exposure * t` which is in `virions * h / m3` then, when multiplied by the breathing rate (m3/h) you get the dose in `virions`.
The math is correct (I assume?), just the docstring caused confusion when performing the plots for the paper.Nicolas MounetLuis AleixoNicolas Mounethttps://gitlab.cern.ch/caimira/caimira/-/merge_requests/252WIP: Collection of recent model updates2021-09-17T15:01:11+02:00Luis AleixoWIP: Collection of recent model updatesThis merge request is to guarantee a staged review of all of the model updates with MR coming from the ```development``` folder.
To be merged only when all the updates are reviewed - sub merge requests approved:This merge request is to guarantee a staged review of all of the model updates with MR coming from the ```development``` folder.
To be merged only when all the updates are reviewed - sub merge requests approved: