Task Manager¶

Microservices system mode
Download
Software requirements
Installation
Licenses
Logging
Configuration
- Retry mechanism
Running the server
API documentation
Demo site
Usage
- Basic endpoints
- All available endpoints
- JWSDB tasks
- JWS-CALCULATIONS tasks
- JWS-CHECKER-FIXER tasks

Task Manager provides the possibility of scheduling special long lasting tasks for the following web services.

1
DB Web Services

1
Calculations Web Services

1
Structure Checker Web Services

This documentation describes installation, administration and usage of Task Manager.

Task Manager application is available as part of a microservices system.

Microservices system mode¶

In microservices system mode the Task Manager runs together with Config service, Discovery service, Gateway service. These three services are mandatory and optionally other services can also be part of the system. All configuration must be done in the Config module.

DB Web Service and/or Calculations Web Services and/or Structure Checker Web Services must also run according to the tasks planned to be created, executed.

The default configuration applies to the microservices system mode.

The web application runs on host and listens on port .

Download¶

See here.

Software requirements¶

See here

Installation¶

See here.

Module is installed into folder: jws/jws-taskmanager

Licenses¶

See here.

" JChem Microservices DB " and/or " JChem Microservices Structure Checker " and/or " JChem Microservices Calculations " licenses are needed.

Logging¶

See here.

Configuration¶

**Default configuration: **

application.properties
server.port=8068
logging.file.name=../logs/jws-taskmanager.log
eureka.client.enabled=true

bootstrap.properties
spring.cloud.config.failFast=true spring.cloud.config.uri=${CONFIG_SERVER_URI:http://localhost:8888/} spring.cloud.config.retry.initialInterval=3000 spring.cloud.config.retry.multiplier=1.2 spring.cloud.config.retry.maxInterval=60000 spring.cloud.config.retry.maxAttempts=100

For more settings possibilities see spring documentation page.

Retry mechanism¶

Task manager and the services it communicates with have a retry mechanism implemented in them when they call out to each other. This is adjustable with these two properties in all of these services, in their application.properties file

1 2	`com.chemaxon.retrytemplate.backOffPeriod=10000 com.chemaxon.retrytemplate.maxAttempts=20`

BackOffPeriod is the time in milliseconds the service waits between two attempts to send the request to the other service again if no response was given.

MaxAttempts is the maximum number of attempts. Note, that it also contains the very first call.

With the above written default values the service tries to get a response for about 3 minutes.

Running the server¶

Prerequisites in case of microservices system mode:

Config service is running
Discovery service is running
Gateway service is running

Run the service in command line in folder jws/jws-taskmanager:

jws-taskmanager-service start (on Windows)

jws-taskmanager-service start (on Linux)

or

run-jws-taskmanager.exe (on Windows)

run-jws-tarkmanager (on Linux)

API documentation¶

Find and try out the API on the Swagger UI.

Mode	URL of Swagger UI	Default URL of Swagger UI
microservices system	<serverhost>:<gateway-port>/jws-taskmanager/API/	localhost:8080/jws-taskmanager/API/
standalone web application mode	<serverhost>:<server-port>/API/	localhost:8068/API/

Demo site¶

For detailed description check out the JWS Task Manager demo site:

https://jchem-microservices.chemaxon.com/jws-taskmanager/api/index.html

Usage¶

The guidelines, examples on the Demo site or on the Swagger UI API documentation of your installed module display the methods and syntax implemented for reaching the functionalities of the Task Manager toolkit.

Basic endpoints¶

create task (see taskId in the response)

add/upload molecules to the task referenced by taskId

manage (Start) the task referenced by taskId

get the results of task referenced by taskId

All available endpoints¶

create task

delete task referenced by taskId

list all tasks

add structures to task referenced by taskId

upload structures from file to task referenced by taskId

modify structures referenced by structureID of a task referenced by taskId

remove structures referenced by structureID from task referenced by taskId

get structure referenced by structureID from a task referenced by taskId

delete structure referenced by structureID from a task referenced by taskId

get all structures of a task referenced by taskId

manage task (Start) referenced by taskId

get the state of a task referenced by taskId

get the results of a task referenced by taskId

JWSDB tasks¶

Task manager can be applied for importing structures into an already existing table. The table must be created at the endpoint /rest-v1/db/additional/createTable/{tableName} of DB Web Services.

The structures can be added or can be uploaded from file.

The structures will have ID data in the table. If the structures to be imported have their own IDproperty, this IDproperty can be set as ID in the table.

** Example1 **

/rest-v1/work-queue/task

{
  "params": {
    "tableName": "mytable"
  },
  "service": "jwsdb",
  "task": "import"
}

/rest-v1/work-queue/task/{taskId}

{
  "inputFormat": "smiles",
  "structures": [
   "CCO"
  ]
}

/rest-v1/work-queue/task/{taskId}/manage

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2
3

{
  "action": "START"
}

/rest-v1/work-queue/task/{taskId}/results

The results of the given task can be found in the file shown by the Download file link in the response.

** Example2 **

/rest-v1/work-queue/task

{
  "params": {
    "tableName": "mytable",
    "idProperty": "myID"
  },
  "service": "jwsdb",
  "task": "index"
}

/rest-v1/work-queue/task/{taskId}

{
  "inputFormat": "mrv",
  "structures": [
    "<?xml version=\"1.0\" encoding=\"windows-1252\"?>\r\n<cml xmlns=\"http:\/\/www.chemaxon.com\" xmlns:xsi=\"http:\/\/www.w3.org\/2001\/XMLSchema-instance\" xsi:schemaLocation=\"http:\/\/www.chemaxon.com\/marvin\/schema\/mrvSchema_18_11_0.xsd\" version=\"ChemAxon file format v18.11.0, generated by v19.9.0\">\r\n<MDocument>\r\n  <MChemicalStruct>\r\n    <molecule molID=\"m1\">\r\n      <propertyList>\r\n        <property dictRef=\"myID\" title=\"myID\">\r\n          <scalar>5<\/scalar>\r\n        <\/property>\r\n      <\/propertyList>\r\n      <atomArray atomID=\"a1 a2 a3 a4 a5\" elementType=\"C C C C C\" x2=\"-12.625 -13.870866329017026 -13.395003911629807 -11.854996088370193 -11.379133670982972\" y2=\"4.184992254777558 3.279775656265557 1.8152282163456634 1.8152282163456634 3.279775656265557\"\/>\r\n      <bondArray>\r\n        <bond id=\"b1\" atomRefs2=\"a1 a2\" order=\"1\"\/>\r\n        <bond id=\"b2\" atomRefs2=\"a2 a3\" order=\"1\"\/>\r\n        <bond id=\"b3\" atomRefs2=\"a3 a4\" order=\"1\"\/>\r\n        <bond id=\"b4\" atomRefs2=\"a4 a5\" order=\"1\"\/>\r\n        <bond id=\"b5\" atomRefs2=\"a1 a5\" order=\"1\"\/>\r\n      <\/bondArray>\r\n    <\/molecule>\r\n  <\/MChemicalStruct>\r\n<\/MDocument>\r\n<\/cml>"
  ]
}

/rest-v1/work-queue/task/{taskId}/manage

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2
3

{
  "action": "START"
}

/rest-v1/work-queue/task/{taskId}/results

The results of the given task can be found in the file shown by the Download file link in the response.

** Example3 **

/rest-v1/work-queue/task

{
  "params": {
    "tableName": "mytable",
    "idProperty": "myID"
  },
  "service": "jwsdb",
  "task": "index"
}

/rest-v1/work-queue/task/{taskId}/upload

Upload the the structures from file.

/rest-v1/work-queue/task/{taskId}/manage

1
2
3

{
  "action": "START"
}

/rest-v1/work-queue/task/{taskId}/results

The results of the given task can be found in the file shown by the Download file link in the response.

JWS-CALCULATIONS tasks¶

Use similar syntax like at /rest-v1/calculator/calculate endpoint of Calculations Web Services with the exception of "structure" and "inputFormat".

Do not add the structures to be calculated in the 'Create task' step. The structures must be added in the 'Add structures' step.

** Example1 **

/rest-v1/work-queue/task

{
  "params": {
    "calculations": {
      "charge": {
        "ph": 7.4
      }
    }
  },
  "service": "jws-calculations",
  "task": "charge"
}

/rest-v1/work-queue/task/{taskId}

{
  "inputFormat": "smiles",
  "structures": [
   "CC([O-])=O"
  ]
}

/rest-v1/work-queue/task/{taskId}/manage

1
2
3

{
  "action": "START"
}

/rest-v1/work-queue/task/{taskId}/results

The results of the given task can be found in the file shown by the Download file link in the response.

** Example2 **

/rest-v1/work-queue/task

{
  "params": {
    "calculations": {
      "topology-analyser": {        
          "aliphaticRingSize": 0,
          "aromaticRingSize": 0,
         "aromatizationMethod": "GENERAL",
          "carboRingSize": 0,
          "fusedAliphaticRingSize": 0,
          "fusedAromaticRingSize": 0,
          "heteroAliphaticRingSize": 0,
          "heteroAromaticRingSize": 0,
          "heteroRingSize": 0,
          "operations": "aromaticRingCount, aromaticRings",
          "ringSize": 0,
          "ringSystemSize": 0
      },
         "charge": {
        "ph": 7.4
      }
    }
  },
  "service": "jws-calculations",
  "task": "topology-and-charge"
}

/rest-v1/work-queue/task/{taskId}

{
  "inputFormat": "smiles",
  "structures": [
    "NC(CC1=CC=CC=C1)C(O)=O",
    "CCO"
  ]
}

/rest-v1/work-queue/task/{taskId}/manage

1
2
3

{
  "action": "START"
}

/rest-v1/work-queue/task/{taskId}/results

The results of the given task can be found in the file shown by the Download file link in the response.

JWS-CHECKER-FIXER tasks¶

Use similar syntax like at /rest-v1/checker-fixer/ endpoint of Structure Checker Web Services with the exception of "structure".

Do not add the structures to be checked/fixed in the 'Create task' step. The structures must be added in the 'Add structures' step.

** Example1 **

/rest-v1/work-queue/task

{
  "params": {
      "exportFormat": "mrv",
      "filter": {
        "fixed": false,
        "untriggered": false
      },
      "settings": [
        {
              "checkerSettings": {
                "checkerClass": "IncorrectTetrahedralStereoChecker",
                "displayName": "MyStructureChecker"
              }
        }
  ]
},
  "service": "jws-checker-fixer",
  "task": "incorrecttetrahedral"
}

/rest-v1/work-queue/task/{taskId}

{
  "inputFormat": "mrv",
  "structures": [
    "<?xml version=\"1.0\" encoding=\"windows-1252\"?>\r\n<cml xmlns=\"http:\/\/www.chemaxon.com\" xmlns:xsi=\"http:\/\/www.w3.org\/2001\/XMLSchema-instance\" xsi:schemaLocation=\"http:\/\/www.chemaxon.com\/marvin\/schema\/mrvSchema_18_11_0.xsd\" version=\"ChemAxon file format v18.11.0, generated by v19.9.0\">\r\n<MDocument>\r\n  <MChemicalStruct>\r\n    <molecule molID=\"m1\">\r\n      <atomArray atomID=\"a1 a2 a3 a4 a5 a6\" elementType=\"N C C O C C\" x2=\"-8.125 -6.752849952749914 -6.672252580135781 -5.461297278113961 -8.044402627385868 -5.300102532885694\" y2=\"3.0833332538604736 2.3841878842615714 0.8462984007395276 3.222931998184713 1.54544377033843 0.14715303114062528\"\/>\r\n      <bondArray>\r\n        <bond id=\"b1\" atomRefs2=\"a2 a1\" order=\"1\">\r\n          <bondStereo>W<\/bondStereo>\r\n        <\/bond>\r\n        <bond id=\"b2\" atomRefs2=\"a2 a3\" order=\"1\"\/>\r\n        <bond id=\"b3\" atomRefs2=\"a2 a4\" order=\"1\">\r\n          <bondStereo>W<\/bondStereo>\r\n        <\/bond>\r\n        <bond id=\"b4\" atomRefs2=\"a2 a5\" order=\"1\"\/>\r\n        <bond id=\"b5\" atomRefs2=\"a3 a6\" order=\"1\"\/>\r\n      <\/bondArray>\r\n    <\/molecule>\r\n  <\/MChemicalStruct>\r\n<\/MDocument>\r\n<\/cml>"
  ]
}

/rest-v1/work-queue/task/{taskId}/manage

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2
3

{
  "action": "START"
}

/rest-v1/work-queue/task/{taskId}/results

The results of the given task can be found in the file shown by the Download file link in the response.

** Example2 **

/rest-v1/work-queue/task

{
"params": {
  "exportFormat": "mrv",
  "filter": {
    "fixed": false,
    "untriggered": false
  },
  "settings": [
    {
      "checkerSettings": {
        "checkerClass": "MissingAtomMapChecker"
      },
      "fixerSettings": {
        "exportFormat": "mrv",
        "fixerClass": "MapMoleculeFixer"
      }
    }
  ]
},
  "service": "jws-checker-fixer",
  "task": "checker-fixer"
}

/rest-v1/work-queue/task/{taskId}

{
  "inputFormat": "mrv",
  "structures": [
    "<?xml version=\"1.0\" encoding=\"windows-1252\"?>\r\n<cml xmlns=\"http:\/\/www.chemaxon.com\" xmlns:xsi=\"http:\/\/www.w3.org\/2001\/XMLSchema-instance\" xsi:schemaLocation=\"http:\/\/www.chemaxon.com\/marvin\/schema\/mrvSchema_18_11_0.xsd\" version=\"ChemAxon file format v18.11.0, generated by v19.9.0\">\r\n<MDocument>\r\n  <MChemicalStruct>\r\n    <molecule molID=\"m1\">\r\n      <atomArray atomID=\"a1 a2 a3 a4 a5 a6\" elementType=\"C C C C C C\" mrvMap=\"1 2 0 0 0 3\" x2=\"-8.666666984558105 -10.000336325606362 -10.000336325606362 -8.666666984558105 -7.332997643509847 -7.332997643509847\" y2=\"3.9983671349785546 3.228350194419514 1.6883163133014332 0.9182993727423927 1.6883163133014332 3.228350194419514\"\/>\r\n      <bondArray>\r\n        <bond id=\"b1\" atomRefs2=\"a1 a2\" order=\"1\"\/>\r\n        <bond id=\"b2\" atomRefs2=\"a2 a3\" order=\"1\"\/>\r\n        <bond id=\"b3\" atomRefs2=\"a3 a4\" order=\"1\"\/>\r\n        <bond id=\"b4\" atomRefs2=\"a4 a5\" order=\"1\"\/>\r\n        <bond id=\"b5\" atomRefs2=\"a5 a6\" order=\"1\"\/>\r\n        <bond id=\"b6\" atomRefs2=\"a1 a6\" order=\"1\"\/>\r\n      <\/bondArray>\r\n    <\/molecule>\r\n  <\/MChemicalStruct>\r\n<\/MDocument>\r\n<\/cml>"
  ]
}

/rest-v1/work-queue/task/{taskId}/manage

1
2
3

{
  "action": "START"
}

/rest-v1/work-queue/task/{taskId}/results

The results of the given task can be found in the file shown by the Download file link in the response.