Merge pull request #15 from michaelwenk/filter-data-by-ppm

chore: enable stereo information in spectral knowlegde base & filter data by ppm
michaelwenk · Jun 22, 2023 · 812a58b · 812a58b
2 parents c166a3c + c3a10c9
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diff --git a/README.md b/README.md
@@ -61,121 +61,3 @@ If the removal of the network created by docker-compose is desired, then use the
 
     docker-compose -f docker-compose.yml -f docker-compose.publish.yml down
 
-<!---
-## Self Compilation and Dependencies
-
-### Compilation
-CASEkit (https://github.com/michaelwenk/casekit) has to be downloaded and compiled beforehand.
-
-Now add the jar file to the local Maven repository by following command:
-
-(note: replace "PATH/TO/CASEKIT-JAR-WITH-DEPENDENCIES" by the path to previously built CASEkit jar):
-
-    mvn install:install-file -Dfile=PATH/TO/CASEKIT-JAR-WITH-DEPENDENCIES -DgroupId=org.openscience -DartifactId=casekit -Dversion=1.0 -Dpackaging=jar
-
-Clone this repository:
-
-    git clone https://github.com/michaelwenk/sherlock.git
-
-Change the directory and build all the .jar files needed for this project using the build shell script:
-
-    cd sherlock
-    sh buildJars.sh
-
-### Dependencies
-Some services rely on specific software or file dependencies which has to be downloaded and put into certain places.
-#### PyLSD
-For the structure generation part PyLSD (http://eos.univ-reims.fr/LSD/JmnSoft/PyLSD/) is needed.
-PyLSD can be downloaded from http://eos.univ-reims.fr/LSD/JmnSoft/PyLSD/INSTALL.html.
-
-Extract and rename the new PyLSD folder to "PyLSD", if needed.
-
-Now put the PyLSD folder into 
-
-    backend/sherlock-pylsd/data/lsd/
-
-In case custom filters are desired to use one can create a folder "filters" in
-
-    backend/sherlock-pylsd/data/lsd/
-
-and put the custom filters there. The system will use them automatically.
-
-For more details about LSD and defining substructures and filters see http://eos.univ-reims.fr/LSD/MANUAL_ENG.html#SSTR .
-
-#### NMRShiftDB
-For the dereplication, automatic hybridization detection und chemical shift prediction via HOSE codes the NMRShiftDB (https://nmrshiftdb.nmr.uni-koeln.de) is required.
-
-Download the "nmrshiftdb2withsignals.sd" from https://sourceforge.net/projects/nmrshiftdb2/files/data/ and copy it into 
-
-    backend/sherlock-db-service-dataset/data/nmrshiftdb/
-
-and rename the file to "nmrshiftdb.sdf". 
-
-### Docker and Application Start/Stop
-This project uses Docker containers (https://www.docker.com) and starts them via docker-compose. Make sure that docker-compose is installed.
-
-#### Build
-To build the container images use the following command:
-
-    docker-compose -f docker-compose.yml -f docker-compose.production.yml build
-
-#### Start 
-To start this application (in detached mode) use
-
-    docker-compose -f docker-compose.yml -f docker-compose.production.yml up -d
-
-Note: It can take a few minutes until all services are available and registered.
-
-#### Stop
-To stop this application use
-
-    docker-compose -f docker-compose.yml -f docker-compose.production.yml down
-
-### Docker Container and Data Preparation/Persistence
-The databases for datasets and hybridizations have to be filled when starting the application the first time.
-
-After that procedure, the container database contents are stored in the "data/db" subdirectory of each "db-instance" service.
-That enables the persistence of database content to access the data whenever the database services are restarting.
-
-#### Dataset
-For dataset creation and insertion use:
-
-    curl -X POST -i 'http://localhost:8081/sherlock-db-service-dataset/replaceAll?nuclei=13C'
-
-This will fill-in datasets with 13C spectra only. If multiple nuclei are desired, 
-then this could be done by adding them separated by comma, e.g. 13C, 15N: 
-
-    curl -X POST -i 'http://localhost:8081/sherlock-db-service-dataset/replaceAll?nuclei=13C,15N'
-
-One can then check the number of datasets:
-
-    curl -X GET -i 'http://localhost:8081/sherlock-db-service-dataset/count' 
-
-#### Statistics
-As for datasets we need to build the hybridization and connectivity statistics and can decide which nuclei to consider:
-
-    curl -X POST -i 'http://localhost:8081/sherlock-db-service-statistics/hybridization/replaceAll?nuclei=13C'
-    curl -X POST -i 'http://localhost:8081/sherlock-db-service-statistics/connectivity/replaceAll?nuclei=13C'
-
-
-To check the number of hybridization/connectivity entries:
-
-    curl -X GET -i 'http://localhost:8081/sherlock-db-service-statistics/hybridization/count'
-    curl -X GET -i 'http://localhost:8081/sherlock-db-service-statistics/connectivity/count'
-
-#### HOSE Codes
-One needs to insert the HOSE code information as well:
-
-    curl -X POST -i 'http://localhost:8081/sherlock-db-service-hosecode/replaceAll?nuclei=13C&maxSphere=6'
-
-To check the number of HOSE code entries:
-
-    curl -X GET -i 'http://localhost:8081/sherlock-db-service-hosecode/count'
-
-For spectra prediction a map of HOSE code and assigned statistics is needed. 
-Due to this one now needs to execute following command to store such map in a shared volume:
-
-    curl -X GET -i 'http://localhost:8081/sherlock-db-service-hosecode/saveAllAsMap'
-
--->
-