rxome-generator 1.0.3 → 1.0.4-beta.2

package/README.md

@@ -1,6 +1,14 @@
+<!--
 # TODO:
 * how to connect to docker container (shell)
 
+```
+docker run -it -rm node /bin/bash
+cd root/
+npm install rxome-generator
+node_modules/.bin/rxcode id key
+```
+-->
 # FindMe2care (RxOME) QR-code generator
 Generates QR codes containing medical information for use with the FindMe2care platform
 (formerly called RxOME).
@@ -63,7 +71,7 @@ For detailed descriptions see
 
 #### Library Functions
 Import the library with
-> `const Coder = require( 'rxome-generator' );`
+> `import * as Coder from './lib/rxome-generator.js';`
 
 The following two async library functions generate QR codes:
 > `Coder.writeQR( filename, data, api = RXAPI )`
@@ -226,7 +234,7 @@ rxcode U my_qr_code.png my_key_id my_private_key
 ```
 
 ## 2.  QR-code generator service
-The packages *rxome-server* generates QR codes containing medical information for use with the FindMe2Care database
+The package *rxome-server* generates QR codes containing medical information for use with the FindMe2Care database
 (formerly called RxOME). The command line tool `rxsrv` starts the QR generator as local service listening on localhost:*port* (default: port 1607).
 A client can send POST requests to this port and retrieves the generated QR code by HTTP protocol.
 
@@ -286,10 +294,10 @@ export RXPORT=4242
 rxsrv -e
 ```
 
-Where `RXID` is the username of the laboratory on the FindMe2Care platform, `RXKEY` is the 
-private API access key matching the public key stored on the lab's profile on the 
-FindMe2Care platform. See the README of the rxome-qrcode-generator for generating the
-API keys.
+Where `RXID` is the API username (not to be confused with the login name) 
+of the laboratory on the FindMe2Care platform, `RXKEY` is the 
+private API access key matching the public key stored in the user's/lab's profile on the 
+FindMe2Care platform.
 
 Note that storing secret information in environment variables may pose a security risk; therefore, this option is not recommended and should only be used if the software runs in an isolated environment.
 
@@ -332,13 +340,28 @@ Note that the Windows service is configured with a config file given by `%RXCFG%
 the default file `%APPDATA\npm\node_modules\rxome-server-win\demo.cfg` is used.
 
 ### 2.3 Using Docker
-Instead of installing node.js and starting the server manually, you can use a docker image to run the server, e.g. by
+Instead of installing node.js and starting the server manually, you can use a docker image to run the service, e.g., with
+
+```
+docker run -d -p 1607:1607 tomkamphans/rxsrv:current -i "your_key_id" -s "your_private_key"
+```
+
+Also, you can specify key ID and key using environment variables, which may be useful in a docker compose or kubernetes setting: 
 
 ```
-docker run -d -p 1607:1607 -e RXID="rxome" -e RXKEY="...private_key..." tomkamphans/rxsrv 
+docker run -d -p 1607:1607 -e RXID=" your_key_id" -e RXKEY="your_private_key" tomkamphans/rxsrv:current
 ```
 
-Where `RXID` is the lab's user name and `RXKEY` the private API key as described above.
+Where `your_key_id` is the lab's API user name and your_key is the private API key as described above.
+
+When starting the first time (or when a new key pair should be used), you can start the service with
+
+```
+docker run -d -p 1607:1607 tomkamphans/rxsrv:current -i "your_key_id" -K
+```
+
+to generate a new key pair. Before starting the service, the script outputs the new keys. You should copy the public key into your FM2C profile, the private key 
+is immediately used to run the service.
 
 Note that the first port number in `-p 1607:1607` denotes the port on *localhost* to which the docker internal port (denoted the second port number, in this case 1607 also) is mapped. So if you need to run the service on another port, say 8081, use 
 `docker run -p 8081:1607 ...`.
@@ -395,19 +418,25 @@ This yields a JSON response containing
 ### 2.5 Server Command-Line Tool
 
 ```
-RxOME QR Code generation server
+FindMe2care QR-Code generation server
+
+Usage: rxsrv -e | -c <cfg_file> | -i <id> (-k <key_file> | -s <key> | -K) [-p <port>]
+
+Starts the QR-code tool as service listening on localhost:<port>.
+Before first use, please use the -K option to generate an API access key and deposit the public key 
+on the FindMe2care server.
 
-Usage: rxsrv usage: rxsrv -i <id> (-e | -c <cfg_file> | -k <key_file> | -s <key>) [-p <port>]
+Given multiple key options, -K has highest priority.
 
-Start the QR-code tool as service listening on localhost:<port>.
-Before first use, please generate an API access key with rxcode and deposit the public key on the
-RxOME server.
+The command-line parameters -k, -s, -p precede the environment variables (if -e specified), which, 
+in turn, precede the config file (if -c is also specified).
+A key string (-s) has precedence over a key from a key file (-k).
+
+If no parameter is given, -e is assumed.
 
-The command-line parameters -k, -s, -p precede the environment variables (if -e specified), which, in
-turn, precede the config file (if -c is also specified). A key string (-s) has precedence over a key
-from a key file (-k).
 
 Options:
+  -V, --version             output the version number
   -c, --config <filename>   JSON file with config, entries id, key, [port]; -c-- to read from stdin
   -e, --environment         use environment variables RXID, RXKEY, RXPORT to configure rxsrv (useful
                             for working with docker)
@@ -415,8 +444,10 @@ Options:
   -k, --keyFile <filename>  Filename with API access key (default: use -s)
   -s, --key <key string>    API access key
   -p, --port <port>         Set port for server, default: 1607
-  -V, --version             output the version number
-  -h, --help                display help
+  -K, --newkey              Generate new key pair, print both keys and start the server with the keys
+  -h, --help                display help for command
+
+Author: Tom Kamphans, GeneTalk GmbH, 2023
 ```
 
 

package/demos/demo_overfull.json

@@ -0,0 +1,144 @@
+{
+  "id": "QR-Code ID",
+  "comment": "Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod mazim placerat facer possim assum. Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, At accusam aliquyam diam diam dolore dolores duo eirmod eos erat, et nonumy sed tempor et et invidunt justo labore Stet clita ea et gubergren, kasd magna no rebum. sanctus sea sed takimata ut vero voluptua. est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat. Consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod mazim placerat facer possim assum. Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in",
+  "subject": {
+    "id": "proband A",
+    "dateOfBirth": "1994-01-01T00:00:00Z",
+    "sex": "FEMALE"
+  },
+  "phenotypicFeatures": [
+    {
+      "type": {
+        "id": "HP:0030084"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000555"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000486"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000541"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0084369"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0112358"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000145"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:1234567"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:9876543"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:5678912"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0031360"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001234"
+      },
+      "excluded": true
+    }
+  ],
+  "interpretations": [
+    {
+      "id": "interpretation.id",
+      "progressStatus": "SOLVED",
+      "diagnosis": {
+        "disease": {
+          "id": "OMIM:263750"
+        },
+        "genomicInterpretations": [
+          {
+            "variantInterpretation": {
+              "acmgPathogenicityClassification": "PATHOGENIC",
+              "variationDescriptor": {
+                "geneContext": {
+                  "valueId": "HGNC:9884",
+                  "symbol": "RB1"
+                },
+                "expressions": [
+                  {
+                    "syntax": "hgvs.c",
+                    "value": "NM_000321.2:c.958C>T"
+                  }
+                ],
+                "allelicState": {
+                  "id": "GENO:0000135"
+                },
+                "extensions": [
+                  {
+                    "name": "test-type",
+                    "value": "Exome, short read"
+                  }
+                ]
+              }
+            }
+          },
+          {
+            "variantInterpretation": {
+              "acmgPathogenicityClassification": "LIKELY_PATHOGENIC",
+              "variationDescriptor": {
+                "geneContext": {
+                  "valueId": "HGNC:9884",
+                  "symbol": "RB1"
+                },
+                "expressions": [
+                  {
+                    "syntax": "hgvs.c",
+                    "value": "NM_000321.2:c.1234A>G"
+                  }
+                ],
+                "allelicState": {
+                  "label": "heterozygous"
+                },
+                "extensions": [
+                  {
+                    "name": "test-type",
+                    "value": "Exome, short read"
+                  }
+                ]
+              }
+            }
+          }
+        ]
+      }
+    }
+  ],
+  "metaData": {
+    "created": "2021-05-14T10:35:00Z",
+    "createdBy": "mgz",
+    "submittedBy": "a_clinician@mgz-muenchen.de",
+    "phenopacketSchemaVersion": "2.0"
+  }
+}

package/index.js

@@ -1,3 +1,3 @@
-export * from './lib/rxome-api.cjs';
-export * from './lib/rxome-api-demo.cjs';
-export * from './lib/rxome-generator.cjs';
+export * from './lib/rxome-api';
+export * from './lib/rxome-api-demo';
+export * from './lib/rxome-generator';

package/lib/package-info.js

@@ -0,0 +1,4 @@
+// Auto-generated package info for browser compatibility
+export const version = "1.0.4-beta.1";
+export const name = "rxome-generator";
+export const description = "Generates QR codes containing medical information for use with the FindMe2Care platform.";