Merge pull request #136 from spectre-team/develop

Release 2.0

.bettercodehub.yml

@@ -0,0 +1,5 @@
+component_depth: 2
+languages:
+- csharp
+- cpp
+- typescript

.gitignore

@@ -1,3 +1,6 @@
+## Large test files
+test_files/single.txt
+
 ## Ignore MATLAB artifacts
 *.asv
 
@@ -13,6 +16,11 @@
 # Session info
 octave-workspace
 
+## Python artifacts
+
+# Jupyter notebook checkpoints
+.ipynb_checkpoints/
+
 ## Ignore Visual Studio temporary files, build results, and
 ## files generated by popular Visual Studio add-ons.
 

README.md

@@ -1,9 +1,11 @@
 # Spectre
 
+![Spectre](https://user-images.githubusercontent.com/1897842/31115297-0fe2c3aa-a822-11e7-90e6-92ceccf76137.jpg)
+
 Spectre is a versatile tool used for analysis of MALDI-MSI data sets.
 
 For the sake of simplicity, the toolset provided is available to be used
-through interfacing with web application, which is currently a work-in-progress.
+through web application interface, which is currently a work-in-progress.
 
 In order to build and run the application, please refer to the
 [installation](#install) section.
@@ -13,54 +15,86 @@ In order to build and run the application, please refer to the
 The project is currently in its early stage. However, it comprises the
 implementation of our own spectra modelling based on Gaussian Mixture Models,
 and Divisive IK-means algorithm for unsupervised segmentation, which can be
-used for efficient dataset compression as well as for knowledge discovery.
-Aformentioned algorithms have already been published and links refering
+used for efficient dataset compression, as well as for knowledge discovery.
+Aformentioned algorithms have already been published and refering links
 have been enclosed under [references](#references) section.
 
 Also, several classification and clusterization methods will be provided soon,
 along with supporting statistics.
 
 ## Install
 
-Please refer to [docs](docs/Spectre.DivikWpfClient.pdf).
+### DiviK local client
+
+Please refer to [this manual](docs/Spectre.DivikWpfClient.pdf), as MATLAB
+Common Runtime has to be installed.
+
+### Spectre service & web application
+
+The Web service is all the time available [here](http://vaei-bit01.aei.polsl.pl/).
+If you still would like to host it yourself, please contact us by
+[e-mail](mailto:[email protected]). We will provide you with exhaustive
+explanation.
 
 ## Exemplary usage
 
+### DiviK local client
+
 Please refer to [docs](docs/Spectre.DivikWpfClient.pdf).
 
+### Spectre service & web application
+
+The application is available online [here](http://vaei-bit01.aei.polsl.pl/).
+
+Right now, our web application allows only for an interactive visualization
+of some of the data we were using in the research, along with Divisive
+Intelligent K-means algorithm results. More features will get documented
+when they appear.
+
 ## How to contribute?
 
-Please contact us by an [e-mail](mailto:[email protected]). We will
-answer you in details.
+Please contact us by [e-mail](mailto:[email protected]). We will answer
+you in details.
+
+Short contribution guide is actively constructed on
+[the project's wiki](https://github.com/spectre-team/spectre/wiki)
+as the development progresses.
 
 ## Environment
 
-Please refer to [docs](docs/Spectre.DivikWpfClient.pdf).
+Please refer to [the docs](docs/Spectre.DivikWpfClient.pdf).
 
 ## 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).
+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)
+(ISBN: 978-3-319-02308-3), ICMMI 2013, 22-25.10.2013 Brenna, Poland][1]
 + [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)
+Proteomics, vol. 16, no. 11-12, pp. 1613-21, 2016][2]
 + [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)
+imaging," Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 2016][3]
 + [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)
+International Conference on Bioinformatics and Biomedical Engineering, 2016][4]
 + [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)
+spectrometry," PloS one, vol. 10, no. 7, p. e0134256, 2015][5]
+
+[1]: http://link.springer.com/chapter/10.1007/978-3-319-02309-0_20
+[2]: http://onlinelibrary.wiley.com/doi/10.1002/pmic.201500458/pdf
+[3]: http://www.sciencedirect.com/science/article/pii/S1570963916302175
+[4]: http://link.springer.com/chapter/10.1007/978-3-319-31744-1_11
+[5]: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134256

appveyor.yml

@@ -1,36 +1,69 @@
-version: 1.0.{build}
+version: 2.24.7.{build}
 # enable patching of AssemblyInfo.* files
 assembly_info:
   patch: true
   file: AssemblyInfo.*
-  assembly_version: "1.0.{build}"
+  assembly_version: "{version}"
   assembly_file_version: "{version}"
   assembly_informational_version: "{version}"
 platform: x64
+environment:
+  nuget_user:
+    secure: kWtlS49bKmP0IFXmdvDHmxGI8mS0xQGrwiJoco9nYtA=
+  nuget_password:
+    secure: Pzvx2CQjxp8eCBP+nFI2eg==
+  appveyor_rdp_password:
+    secure: Pzvx2CQjxp8eCBP+nFI2eg==
 configuration:
   - Debug
   - Release
 services: iis
 
+# skip branch build if there is an active pull request
+skip_branch_with_pr: true
+
+init:
+- cmd: echo Project - %APPVEYOR_PROJECT_NAME%
+- cmd: echo Worker image - %APPVEYOR_BUILD_WORKER_IMAGE%
+- cmd: echo Branch - %APPVEYOR_REPO_BRANCH%
+- cmd: echo Author - %APPVEYOR_REPO_COMMIT_AUTHOR%
+- cmd: echo Commit - %APPVEYOR_REPO_COMMIT%
+#- cmd: echo (%APPVEYOR_REPO_COMMIT_MESSAGE%)
+#- cmd: echo (%APPVEYOR_REPO_COMMIT_MESSAGE_EXTENDED%)
+- cmd: echo Platform - %PLATFORM%
+- cmd: echo Configuration - %CONFIGURATION%
+#- ps: iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/appveyor/ci/master/scripts/enable-rdp.ps1'))
+
+nuget:
+  account_feed: false
+  project_feed: false
+
 install:
+- cmd: C:\projects\spectre\scripts\restore_nugets.bat
 - ps: C:\projects\spectre\scripts\InstallNode.ps1
 
-before_build:
-- cmd: C:\projects\spectre\scripts\restore_nugets.bat
 build_script:
-- cmd: msbuild "C:\projects\spectre\src\Spectre.sln" /m /verbosity:quiet /logger:"C:\Program Files\AppVeyor\BuildAgent\Appveyor.MSBuildLogger.dll"
-- cmd: C:\projects\spectre\scripts\build_ng2_client.bat
+- 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%
 after_build:
-- cmd: C:\projects\spectre\scripts\package_project.bat "DiviK.zip" Spectre.DivikWpfClient
+- 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
 
 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
 
 artifacts:
-- path: DiviK.zip
+- path: DiviK-$(configuration).zip
   name: DivikExecutables
+- path: WebClient-$(configuration).zip
+  name: WebClient
+- path: WebAPI-$(configuration).zip
+  name: WebAPI
 
 deploy:
 - provider: GitHub
@@ -39,5 +72,37 @@ deploy:
     secure: dQadz+smqtuxpigZ/LmrUKyA0uVZ5kgljKntyoHEdobTycbeMywbfmiJtZPNcOQ2
   artifact: DivikExecutables
   draft: true
-  on:
-    CONFIGURATION: Release
+- provider: GitHub
+  release: Spectre-v$(appveyor_build_version)
+  auth_token:
+    secure: dQadz+smqtuxpigZ/LmrUKyA0uVZ5kgljKntyoHEdobTycbeMywbfmiJtZPNcOQ2
+  artifact: WebClient
+  draft: true
+- provider: GitHub
+  release: Spectre-v$(appveyor_build_version)
+  auth_token:
+    secure: dQadz+smqtuxpigZ/LmrUKyA0uVZ5kgljKntyoHEdobTycbeMywbfmiJtZPNcOQ2
+  artifact: WebAPI
+  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
+- provider: Webhook
+  url:
+    secure: V16hjhyXfcLNyhNUih9v1Lb4wDly5r6CNNufciMrvllwt0m0rkguf6o4DY7pbdKia/vJGmErvQLdEW0MkzqsAhLWiPY7+Z6qvzFjweP8xNg=
+  method: POST
+  content_type: application/json
+  body: >-
+    {
+      "icon": "https://www.appveyor.com/assets/img/appveyor-logo-256.png",
+      "activity": "AppVeyor",
+      "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}})"
+    }
+  on_build_success: true
+  on_build_failure: true
+  on_build_status_changed: true