Add OscarDB to experimental

.github/oscardb_dump/oscar/TransitiveSimplicialComplexes.metadata.json

@@ -0,0 +1 @@
+{"indexes":[{"v":{"$numberInt":"2"},"key":{"_id":{"$numberInt":"1"}},"name":"_id_"}],"uuid":"65282c16f2af431aaf80186178a83b40","collectionName":"TransitiveSimplicialComplexes","type":"collection"}

.github/oscardb_dump/oscar/prelude.json

@@ -0,0 +1 @@
+{"ServerVersion":"8.0.11","ToolVersion":"100.12.2"}

.github/workflows/CI.yml

@@ -290,6 +290,63 @@ jobs:
             ${{ steps.julia-cache.outputs.cache-paths }}
           key: ${{ steps.julia-cache.outputs.cache-key }}
 
+  test-mongodb:
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.julia-version == '1.12-nightly' || matrix.julia-version == 'nightly' }}
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version:
+          - '1.10'
+          - '1.11'
+          - '1.12-nightly'
+          - 'nightly'
+        os: ['ubuntu-latest']
+
+            # Service containers to run
+    services:
+      # Label used to access the service container
+      mongodb:
+        # Docker Hub image
+        image: mongo:6.0
+        # Provide the login data
+        env:
+          MONGO_INITDB_ROOT_USERNAME: admin
+          MONGO_INITDB_ROOT_PASSWORD: admin
+        ports:
+          # Maps tcp port 27017 on service container to the host
+          - 27017:27017
+    env:
+      JULIA_PKG_SERVER: ""
+      OSCARDB_TEST_URI: "mongodb://admin:admin@localhost:27017/?authSource=admin"
+      OSCAR_TEST_SUBSET: "oscar_db"
+    steps:
+      - uses: actions/checkout@v4
+      - name: "Set up Julia"
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.julia-version }}
+      - uses: julia-actions/cache@v2
+        with:
+          cache-name: julia-cache;workflow=${{ github.workflow }};julia=${{ matrix.julia-version }};arch=${{ runner.arch }}
+          include-matrix: false
+          cache-scratchspaces: false
+      - name: "Fill OscarDB container"
+        run: |
+          wget -qO - https://www.mongodb.org/static/pgp/server-6.0.asc | sudo apt-key add -
+          echo "deb [ arch=amd64 ] https://repo.mongodb.org/apt/ubuntu jammy/mongodb-org/6.0 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-6.0.list
+          sudo apt-get update
+          sudo apt-get install -y mongodb-database-tools
+          mongorestore --host localhost -u admin -p admin --port 27017 .github/oscardb_dump
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: false
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+
 # adapted from gap-system/gap
   slack-notification:
     name: Send Slack notification on status change

Project.toml

@@ -14,7 +14,9 @@ JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
+Mongoc = "4fe8b98c-fc19-5c23-8ec2-168ff83495f2"
 Nemo = "2edaba10-b0f1-5616-af89-8c11ac63239a"
+NetworkOptions = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Polymake = "d720cf60-89b5-51f5-aff5-213f193123e7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
@@ -39,7 +41,9 @@ JSON = "^0.20, ^0.21"
 JSON3 = "1.13.2"
 LazyArtifacts = "1.6"
 Markdown = "1.6"
+Mongoc = "0.9.2"
 Nemo = "0.52.1"
+NetworkOptions = "1.2.0"
 Pkg = "1.6"
 Polymake = "0.13.1"
 ProgressMeter = "1.10.2"

docs/oscar_references.bib

@@ -843,6 +843,19 @@ @Misc{D-VJL24
   primaryclass  = {math.CO}
 }
 
+@InProceedings{D-VJL24*1,
+  author        = {Della Vecchia, Antony and Joswig, Michael and Lorenz, Benjamin},
+  title         = {A {FAIR} file format for mathematical software},
+  editor        = {Buzzard, Kevin and Dickenstein, Alicia and Eick, Bettina and Leykin, Anton and Ren, Yue},
+  booktitle     = {Mathematical software -- ICMS 2024},
+  series        = {Lecture Notes in Computer Science},
+  volume        = {14749},
+  publisher     = {Springer},
+  pages         = {234--244},
+  year          = {2024},
+  doi           = {10.1007/978-3-031-64529-7_25}
+}
+
 @InCollection{DE02,
   author        = {Decker, Wolfram and Eisenbud, David},
   title         = {Sheaf algorithms using the exterior algebra},
@@ -1581,6 +1594,16 @@ @Article{HM05
   doi           = {10.1016/j.jsc.2004.11.009}
 }
 
+@Article{HM16,
+  author        = {Höhn, Gerald and Mason, Geoffrey},
+  title         = {The 290 fixed-point sublattices of the Leech lattice},
+  journal       = {J. Algebra},
+  volume        = {448},
+  pages         = {618--637},
+  year          = {2016},
+  doi           = {10.1016/j.algebra.2015.08.028}
+}
+
 @Article{HM73,
   author        = {Horrocks, G. and Mumford, D.},
   title         = {A rank 2 vector bundle on $\text{P}^4$ with 15,000 symmetries},
@@ -2294,6 +2317,17 @@ @InCollection{Los18
   doi           = {10.1007/978-3-030-01588-6\_1}
 }
 
+@Article{Lut08,
+  author        = {Lutz, Frank H.},
+  title         = {Combinatorial 3-manifolds with 10 vertices},
+  mrnumber      = {2410566},
+  journal       = {Beiträge Algebra Geom.},
+  volume        = {49},
+  number        = {1},
+  pages         = {97--106},
+  year          = {2008}
+}
+
 @Misc{MNP24,
   author        = {Merkwitz, Thomas and Naughton, Liam and Pfeiffer, Götz},
   title         = {TomLib, The GAP Library of Tables of Marks, Version 1.2.11},

docs/src/DeveloperDocumentation/serialization.md

@@ -11,8 +11,8 @@ is the process of reading and writing data. There are many reasons for this
 feature in OSCAR, but the main reason is communication on mathematics by
 mathematicians.
 
-We implement our serialization in accordance with the [MaRDI](https://www.mardi4nfdi.de/about/mission) file format specification described [here](https://arxiv.org/abs/2309.00465).
-Which means we use a JSON extension to serialize data.
+We implement our serialization in accordance with the [MaRDI](https://www.mardi4nfdi.de/about/mission) file format specification developed by Della Vecchia, Joswig and Lorenz [D-VJL24*1](@cite).
+In particular, we use a JSON extension to serialize data.
 
 
 ## How it works
@@ -25,7 +25,7 @@ julia> load("/tmp/fourtitwo.mrdi")
 42
 
 ```
-The filename hints to the [MaRDI file format](https://arxiv.org/abs/2309.00465), which employs JSON.  The file looks as follows:
+The filename hints to the MaRDI file format [D-VJL24*1](@cite), which employs JSON.  The file looks as follows:
 ```json
 {
   "_ns": {

experimental/OscarDB/docs/doc.main

@@ -0,0 +1,5 @@
+[
+   "OscarDB" => [
+      "introduction.md"
+   ],
+]

experimental/OscarDB/docs/src/introduction.md

@@ -0,0 +1,64 @@
+```@meta
+CurrentModule = Oscar
+CollapsedDocStrings = true
+DocTestSetup = Oscar.doctestsetup()
+```
+
+# OscarDB
+
+This module provides a general database framework which, conceptually, works for all OSCAR types.
+
+There are two main ingredients:
+- the database backend is [MongoDB](https://www.mongodb.com);
+- communication with the database relies on OSCAR's serialization, via the mrdi file format [D-VJL24*1](@cite).
+
+The overall design is inspired by polymake's [PolyDB](https://polydb.org/).
+
+## Collections
+
+The database is organized into collections.
+Within each collection the datasets are uniform.
+
+### Vertex-transitive combinatorial manifolds [TransitiveSimplicialComplexes]
+The OSCAR DB provides access to [Frank Lutz' collection of vertex transitive triangulations](https://www3.math.tu-berlin.de/IfM/Nachrufe/Frank_Lutz/stellar/vertex-transitive-triangulations.html).
+It comprises all vertex-transitive combinatorial manifolds with up to 15 vertices in dimensions $d=2,3,9,10,11,12$.
+In the remaining dimensions below 12, the enumeration is complete up to 13 vertices.
+
+See also [Lut08](@cite).
+
+### Leech pairs [LeechPairs]
+The OSCAR DB provides access to the [fixed-point sublattices of the Leech lattice](http://monstrous-moonshine.de/~gerald/),
+computed by Gerald Höhn and Geoffrey Mason.
+Each entry of the collection is a pair consisting of a copy of the Leech lattice
+and of the largest subgroup of the Conway group fixing pointwise the associated
+fixed-point sublattice.
+
+See also [HM16](@cite), Table 1, and [the supplementary non-published tables](https://arxiv.org/src/1505.06420v3/anc).
+
+## Status
+
+This part of OSCAR is in an experimental state; please see [Adding new projects to experimental](@ref) for what this means.
+
+## Contact
+
+Please direct questions about this part of OSCAR to the following people:
+* [Antony Della Vecchia](https://antonydellavecchia.github.io/)
+* Benjamin Lorenz
+
+You can ask questions in the [OSCAR Slack](https://www.oscar-system.org/community/#slack).
+
+Alternatively, you can [raise an issue on github](https://www.oscar-system.org/community/#how-to-report-issues).
+
+```@meta
+CurrentModule = Oscar.OscarDB
+```
+
+```@docs
+get_db
+find_one
+find
+length(c::Collection, d::Dict=Dict())
+getindex(db::Database, name::AbstractString)
+get_collection_names
+```
+