Merge pull request #3 from spectre-team/develop

New release

.bettercodehub.yml

@@ -1,5 +1,3 @@
 component_depth: 2
 languages:
 - csharp
-- cpp
-- typescript

.gitignore

@@ -17,6 +17,7 @@ test_files/single.txt
 octave-workspace
 
 ## Python artifacts
+*.pyc
 
 # Jupyter notebook checkpoints
 .ipynb_checkpoints/

appveyor.yml

@@ -1,4 +1,4 @@
-version: 2.24.7.{build}
+version: 3.0.0.{build}
 # enable patching of AssemblyInfo.* files
 assembly_info:
   patch: true
@@ -17,7 +17,6 @@ environment:
 configuration:
   - Debug
   - Release
-services: iis
 
 # skip branch build if there is an active pull request
 skip_branch_with_pr: true
@@ -39,55 +38,48 @@ nuget:
   project_feed: false
 
 install:
-- cmd: C:\projects\spectre\scripts\restore_nugets.bat
-- ps: C:\projects\spectre\scripts\InstallNode.ps1
+- cmd: C:\projects\DiviK-standalone-client\scripts\restore_nugets.bat
 
 build_script:
-- cmd: msbuild "C:\projects\spectre\src\Spectre.sln" /p:Configuration=%CONFIGURATION% /p:Platform=%PLATFORM% /m /verbosity:quiet /p:DeployOnBuild=true /p:PublishProfile=%CONFIGURATION% /logger:"C:\Program Files\AppVeyor\BuildAgent\Appveyor.MSBuildLogger.dll"
-- cmd: C:\projects\spectre\scripts\build_ng_client.bat %CONFIGURATION%
+- cmd: msbuild "C:\projects\DiviK-standalone-client\src\DiviK-standalone-client.sln" /p:Configuration=%CONFIGURATION% /p:Platform=%PLATFORM% /m /verbosity:quiet /p:DeployOnBuild=true /p:PublishProfile=%CONFIGURATION% /logger:"C:\Program Files\AppVeyor\BuildAgent\Appveyor.MSBuildLogger.dll"
 after_build:
-- ps: C:\projects\spectre\scripts\BindPageToIisAndCreateDataDir.ps1 -AppVeyor
-- cmd: C:\projects\spectre\scripts\package_project.bat DiviK Spectre.DivikWpfClient
-- cmd: C:\projects\spectre\scripts\package_web_project.bat WebAPI Spectre
-- cmd: C:\projects\spectre\scripts\package_angular_client.bat
+- cmd: C:\projects\DiviK-standalone-client\scripts\package_project.bat DiviK Spectre.DivikWpfClient
+- cmd: C:\projects\DiviK-standalone-client\scripts\package_project.bat DataValidatorApp Spectre.DataValidatorApp
+- cmd: C:\projects\DiviK-standalone-client\scripts\package_project.bat DivikResultConverter Spectre.DivikResultConverter
 
 test_script:
-- cmd: C:\projects\spectre\scripts\test_native_code.bat
-- cmd: C:\projects\spectre\scripts\test_dotnet.bat --except Algorithm
-- cmd: C:\projects\spectre\scripts\test_frontend.bat
-- cmd: C:\projects\spectre\scripts\test_frontend_e2e.bat
+- cmd: C:\projects\DiviK-standalone-client\scripts\test_dotnet.bat --except Algorithm
 
 artifacts:
 - path: DiviK-$(configuration).zip
   name: DivikExecutables
-- path: WebClient-$(configuration).zip
-  name: WebClient
-- path: WebAPI-$(configuration).zip
-  name: WebAPI
+- path: DataValidatorApp-$(configuration).zip
+  name: DataValidatorExecutables
+- path: DivikResultConverter-$(configuration).zip
+  name: DivikResultConverterExecutables
 
 deploy:
 - provider: GitHub
-  release: Spectre-v$(appveyor_build_version)
+  release: DiviK-standalone-client-v$(appveyor_build_version)
   auth_token:
     secure: dQadz+smqtuxpigZ/LmrUKyA0uVZ5kgljKntyoHEdobTycbeMywbfmiJtZPNcOQ2
   artifact: DivikExecutables
   draft: true
 - provider: GitHub
-  release: Spectre-v$(appveyor_build_version)
+  release: DiviK-standalone-client-v$(appveyor_build_version)
   auth_token:
     secure: dQadz+smqtuxpigZ/LmrUKyA0uVZ5kgljKntyoHEdobTycbeMywbfmiJtZPNcOQ2
-  artifact: WebClient
+  artifact: DataValidatorExecutables
   draft: true
 - provider: GitHub
-  release: Spectre-v$(appveyor_build_version)
+  release: DiviK-standalone-client-v$(appveyor_build_version)
   auth_token:
     secure: dQadz+smqtuxpigZ/LmrUKyA0uVZ5kgljKntyoHEdobTycbeMywbfmiJtZPNcOQ2
-  artifact: WebAPI
+  artifact: DivikResultConverterExecutables
   draft: true
 
 on_finish:
 #- ps: $blockRdp = $true; iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/appveyor/ci/master/scripts/enable-rdp.ps1'))
-- cmd: C:\projects\spectre\scripts\upload-frontend-test-results.bat
 
 notifications:
 # this publishes to Continuous Integration channel in Glip
@@ -99,7 +91,7 @@ notifications:
   body: >-
     {
       "icon": "https://www.appveyor.com/assets/img/appveyor-logo-256.png",
-      "activity": "AppVeyor",
+      "activity": "AppVeyor for DiviK-standalone-client",
       "title": "Build {{buildVersion}} **{{#failed}}failed{{/failed}}{{#passed}}passed{{/passed}}** in {{duration}}",
       "body": "{{#isPullRequest}}Pull request: [#{{pullRequestId}}](https://github.com/spectre-team/spectre/pull/{{pullRequestId}})\n{{/isPullRequest}}Branch: [{{branch}}](https://github.com/spectre-team/spectre/tree/{{branch}})\nCommit: [{{commitId}} {{commitMessage}}](https://github.com/spectre-team/spectre/commit/{{commitId}})\nAuthor: {{commitAuthor}}\n[Build details]({{buildUrl}})"
     }

docs/Spectre.DataValidatorApp.md

@@ -0,0 +1,71 @@
+---
+title: "DataValidator Software Manual"
+date: "24.10.2017"
+author:
+    - Grzegorz Mrukwa [email protected]
+institute: |
+    The Spectre Team, Data Mining Group, Silesian University of Technology
+toc: true
+tags: [divik, maldi, msi, mass spectrometry, compression, clustering]
+abstract: |
+    This tool is intended to verify, whether a text data file is a valid data format to be used with Spectre software.
+colorlinks: true
+---
+
+# Installation
+
+No installation required. Once the files are unpacked from the `.zip ` archive,
+software can be used without further delay.
+
+# Usage
+
+Usage is simplified to minimum. Just drag-and-drop your txt data file on the
+validator application file, and the validation process launches. After
+validation report press *enter* to finish.
+
+# Parameters
+
+Application can be also used from command line.
+
+1. **Input path** - must point to the file with data to validate.
+2. **--nonblocking** - if specified, program will exit without waiting for
+confirmation.
+
+# Final notes
+
+In case of any questions, do not hesitate to contact us by
+[mail](mailto:[email protected]?subject=[Spectre] Help request).
+
+# References
+
+This software is part of contribution made by
+[Data Mining Group of Silesian University of Technology](http://www.zaed.polsl.pl/),
+rest of which is published [here](https://github.com/ZAEDPolSl).
+
++ [Marczyk M, Polanska J, Polanski A: Comparison of Algorithms for Profile-Based
+Alignment of Low Resolution MALDI-ToF Spectra. In Advances in Intelligent
+Systems and Computing, Vol. 242 of Man-Machine Interactions 3, Gruca A,
+Czachorski T, Kozielski S, editors. Springer Berlin Heidelberg 2014, p. 193-201
+(ISBN: 978-3-319-02308-3), ICMMI 2013, 22-25.10.2013 Brenna,
+Poland](http://link.springer.com/chapter/10.1007/978-3-319-02309-0_20)
++ [P. Widlak, G. Mrukwa, M. Kalinowska, M. Pietrowska, M. Chekan, J. Wierzgon, M.
+Gawin, G. Drazek and J. Polanska, "Detection of molecular signatures of oral
+squamous cell carcinoma and normal epithelium - application of a novel
+methodology for unsupervised segmentation of imaging mass spectrometry data,"
+Proteomics, vol. 16, no. 11-12, pp. 1613-21,
+2016](http://onlinelibrary.wiley.com/doi/10.1002/pmic.201500458/pdf)
++ [M. Pietrowska, H. C. Diehl, G. Mrukwa, M. Kalinowska-Herok, M. Gawin, M.
+Chekan, J. Elm, G. Drazek, A. Krawczyk, D. Lange, H. E. Meyer, J. Polanska, C.
+Henkel, P. Widlak, "Molecular profiles of thyroid cancer subtypes:
+Classification based on features of tissue revealed by mass spectrometry
+imaging," Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics,
+2016](http://www.sciencedirect.com/science/article/pii/S1570963916302175)
++ [G. Mrukwa, G. Drazek, M. Pietrowska, P. Widlak and J. Polanska, "A Novel
+Divisive iK-Means Algorithm with Region-Driven Feature Selection as a Tool for
+Automated Detection of Tumour Heterogeneity in MALDI IMS Experiments," in
+International Conference on Bioinformatics and Biomedical Engineering,
+2016](http://link.springer.com/chapter/10.1007/978-3-319-31744-1_11)
++ [A. Polanski, M. Marczyk, M. Pietrowska, P. Widlak and J. Polanska, "Signal
+partitioning algorithm for highly efficient Gaussian mixture modeling in mass
+spectrometry," PloS one, vol. 10, no. 7, p. e0134256,
+2015](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134256)

docs/Spectre.DivikResultConverter.md

@@ -0,0 +1,83 @@
+---
+title: "DivikResultConverter Software Manual"
+date: "08.11.2017"
+author:
+    - Grzegorz Mrukwa [email protected]
+institute: |
+    The Spectre Team, Data Mining Group, Silesian University of Technology
+toc: true
+tags: [divik, maldi, msi, mass spectrometry, compression, clustering]
+abstract: |
+    This tool is intended to convert MATLAB DiviK algorithm result file into a data format to be used with Spectre software.
+colorlinks: true
+---
+
+# Installation
+
+## MATLAB MCR
+
+In order to make DiviK software fully operational, a MCR (MATLAB Compiler
+Runtime) has to be installed.
+
+However, due to the [licensing by MathWorks](https://www.mathworks.com/matlabcentral/answers/25863-mcr-installer-is-there-a-license-file-whic#comment_57242),
+it is not available through project website. Nevertheless, we are still eligible
+to share it with you personally, so feel free to contact us by
+[mail](mailto:[email protected]?subject=[Spectre] MCR installer).
+
+Please note, that it can be also downloaded through
+[MathWorks website](https://www.mathworks.com/products/compiler/mcr.html) for
+free, but this way has not been tested yet.
+
+## Conversion software
+No installation required. Once the files are unpacked from the `.zip ` archive,
+software can be used without further delay.
+
+# Usage
+
+Usage is simplified to minimum. Just drag-and-drop your `mat` result file on the
+converter application file, and the conversion process launches. Result will be named exactly the same, but with `json` extension.
+
+# Parameters
+
+Application can be also used from command line.
+
+1. **Input path** - must point to the file with data to validate.
+
+# Final notes
+
+In case of any questions, do not hesitate to contact us by
+[mail](mailto:[email protected]?subject=[Spectre] Help request).
+
+# References
+
+This software is part of contribution made by
+[Data Mining Group of Silesian University of Technology](http://www.zaed.polsl.pl/),
+rest of which is published [here](https://github.com/ZAEDPolSl).
+
++ [Marczyk M, Polanska J, Polanski A: Comparison of Algorithms for Profile-Based
+Alignment of Low Resolution MALDI-ToF Spectra. In Advances in Intelligent
+Systems and Computing, Vol. 242 of Man-Machine Interactions 3, Gruca A,
+Czachorski T, Kozielski S, editors. Springer Berlin Heidelberg 2014, p. 193-201
+(ISBN: 978-3-319-02308-3), ICMMI 2013, 22-25.10.2013 Brenna,
+Poland](http://link.springer.com/chapter/10.1007/978-3-319-02309-0_20)
++ [P. Widlak, G. Mrukwa, M. Kalinowska, M. Pietrowska, M. Chekan, J. Wierzgon, M.
+Gawin, G. Drazek and J. Polanska, "Detection of molecular signatures of oral
+squamous cell carcinoma and normal epithelium - application of a novel
+methodology for unsupervised segmentation of imaging mass spectrometry data,"
+Proteomics, vol. 16, no. 11-12, pp. 1613-21,
+2016](http://onlinelibrary.wiley.com/doi/10.1002/pmic.201500458/pdf)
++ [M. Pietrowska, H. C. Diehl, G. Mrukwa, M. Kalinowska-Herok, M. Gawin, M.
+Chekan, J. Elm, G. Drazek, A. Krawczyk, D. Lange, H. E. Meyer, J. Polanska, C.
+Henkel, P. Widlak, "Molecular profiles of thyroid cancer subtypes:
+Classification based on features of tissue revealed by mass spectrometry
+imaging," Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics,
+2016](http://www.sciencedirect.com/science/article/pii/S1570963916302175)
++ [G. Mrukwa, G. Drazek, M. Pietrowska, P. Widlak and J. Polanska, "A Novel
+Divisive iK-Means Algorithm with Region-Driven Feature Selection as a Tool for
+Automated Detection of Tumour Heterogeneity in MALDI IMS Experiments," in
+International Conference on Bioinformatics and Biomedical Engineering,
+2016](http://link.springer.com/chapter/10.1007/978-3-319-31744-1_11)
++ [A. Polanski, M. Marczyk, M. Pietrowska, P. Widlak and J. Polanska, "Signal
+partitioning algorithm for highly efficient Gaussian mixture modeling in mass
+spectrometry," PloS one, vol. 10, no. 7, p. e0134256,
+2015](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134256)

docs/render.bat

@@ -0,0 +1 @@
+pandoc -t latex -o %1.pdf %1.md