diff --git a/_sources/misc/debugging.rst.txt b/_sources/misc/debugging.rst.txt index 92c20cf..ade84e5 100644 --- a/_sources/misc/debugging.rst.txt +++ b/_sources/misc/debugging.rst.txt @@ -74,6 +74,6 @@ Then rebuild/restart:: Examine container ------------------------------------------- -To examine containers at a shell prompt:: +To examine flask container at a shell prompt:: sudo docker exec -it sp_network-nginx-1 /bin/sh diff --git a/_sources/misc/deploy.rst.txt b/_sources/misc/deploy.rst.txt index 3e1ee70..ec13f88 100644 --- a/_sources/misc/deploy.rst.txt +++ b/_sources/misc/deploy.rst.txt @@ -340,3 +340,106 @@ Solution ............... Stop apache2 on the host machine + + +Problem: Permission denied for downloading/accessing S3 data +--------------------------------------- + +For now, we are using a local configuration file in the home directory with +aws_access_key_id and aws_secret_access_key. + +Configuration Solution (fail) +...................... + +Create an .aws directory in the user directory, and create the files +credentials and config. In the credentials file, put the +permitted user's access key and secret access key:: + + [default] + aws_access_key_id = + aws_secret_access_key = + +The config file should contain:: + + [default] + region = us-east-1 + output = json + +This works for the host EC2 instance, but still getting ClientError Forbidden in +analyst code on container. + +IAM Role Solution (fail) +..................... + +Create an IAM role for S3 access, attach it to the EC2 instance, then verify: +https://repost.aws/knowledge-center/ec2-instance-access-s3-bucket + +This works for the host EC2 instance, but still getting ClientError Forbidden in +analyst code on container. + +Bind-mount solution (success!) +..................... + +Using the aws cli and the command:: + + aws s3 cp s3://specnet-us-east-1/summary/speciesxdataset_matrix_2024_02_01.zip /tmp/ + +The EC2 instance successfully used the Configuration Solution (~/.aws/credentials) +above to download files from S3. + +However, when using only the IAM Role Solution, with the EC2 instance having a role +full access to the specnet-us-east-1 bucket, the EC2 instance got:: + + "fatal error: An error occurred (403) when calling the HeadObject operation: Forbidden" + + +Chose to download the data to the EC2 instance, and bind-mount that directory to the +container. + +TODO: In the future, this should be done as soon as new data from GBIF has +been processed at the first of the month. The API will query for the data named with +the date as the first of the current month (aka, on July 2, 2024, search for +_2024-07-01.) + +General debug messages for the flask container +---------------------------------------------- + +* Print logs:: + + sudo docker logs sp_network-nginx-1 --tail 100 + +Problem: Only broker endpoints are active +-------------------------------------------- + +Specify network uses 2 flask apps, broker and analyst, each with their own subdomain. +The Docker file and docker-compose files must be configured for the correct flask app +to send API requests from a subdomain to the appropriate docker container. + +Solution: +.................. + +Make sure that the following 3 files have the correct FQDN values in them: + + * .env.analyst.conf: contains the analyst FQDN (i.e. FQDN=analyst(-dev).) + * .env.broker.conf: contains the broker FQDN (i.e. FQDN=broker(-dev).) + * config/nginx.conf: contains the server_name and proxy_pass (to container) for each + flask app.:: + + # Broker + server { + listen 443 ssl; + index index.html; + server_name broker-dev.; + location / { + ... + # pass queries to the broker container + proxy_pass http://broker:5000; + ... + # Analyst + server { + listen 443 ssl; + index index.html; + server_name analyst-dev.; + location / { + # pass queries to the analyst container + proxy_pass http://analyst:5000; diff --git a/misc/debugging.html b/misc/debugging.html index 9ccb231..a124133 100644 --- a/misc/debugging.html +++ b/misc/debugging.html @@ -171,7 +171,7 @@

Rebuild/restart

Examine container

-

To examine containers at a shell prompt:

+

To examine flask container at a shell prompt:

sudo docker exec -it sp_network-nginx-1 /bin/sh
diff --git a/misc/deploy.html b/misc/deploy.html index af09333..c2af006 100644 --- a/misc/deploy.html +++ b/misc/deploy.html @@ -84,6 +84,17 @@
  • Solution
    • +
  • Problem: Permission denied for downloading/accessing S3 data +
    • +
  • General debug messages for the flask container
    • +
  • Problem: Only broker endpoints are active +
    • @@ -449,6 +460,112 @@

    SolutionStop apache2 on the host machine

    +
    +

    Problem: Permission denied for downloading/accessing S3 data

    +

    For now, we are using a local configuration file in the home directory with +aws_access_key_id and aws_secret_access_key.

    +
    +

    Configuration Solution (fail)

    +

    Create an .aws directory in the user directory, and create the files +credentials and config. In the credentials file, put the +permitted user’s access key and secret access key:

    +
    [default]
+aws_access_key_id = <access_key>
+aws_secret_access_key = <secret key>
+
    +
    +

    The config file should contain:

    +
    [default]
+region = us-east-1
+output = json
+
    +
    +

    This works for the host EC2 instance, but still getting ClientError Forbidden in +analyst code on container.

    +
    +
    +

    IAM Role Solution (fail)

    +

    Create an IAM role for S3 access, attach it to the EC2 instance, then verify: +https://repost.aws/knowledge-center/ec2-instance-access-s3-bucket

    +

    This works for the host EC2 instance, but still getting ClientError Forbidden in +analyst code on container.

    +
    +
    +

    Bind-mount solution (success!)

    +

    Using the aws cli and the command:

    +
    aws s3 cp s3://specnet-us-east-1/summary/speciesxdataset_matrix_2024_02_01.zip /tmp/
+
    +
    +

    The EC2 instance successfully used the Configuration Solution (~/.aws/credentials) +above to download files from S3.

    +

    However, when using only the IAM Role Solution, with the EC2 instance having a role +full access to the specnet-us-east-1 bucket, the EC2 instance got:

    +
    "fatal error: An error occurred (403) when calling the HeadObject operation: Forbidden"
+
    +
    +

    Chose to download the data to the EC2 instance, and bind-mount that directory to the +container.

    +

    TODO: In the future, this should be done as soon as new data from GBIF has +been processed at the first of the month. The API will query for the data named with +the date as the first of the current month (aka, on July 2, 2024, search for +<datatype>_2024-07-01.<ext>)

    +
    +
    +
    +

    General debug messages for the flask container

    +
      +

    • Print logs:

      +

      sudo docker logs sp_network-nginx-1 –tail 100

      +
      • +
    +
    +
    +

    Problem: Only broker endpoints are active

    +

    Specify network uses 2 flask apps, broker and analyst, each with their own subdomain. +The Docker file and docker-compose files must be configured for the correct flask app +to send API requests from a subdomain to the appropriate docker container.

    +
    +

    Solution:

    +

    Make sure that the following 3 files have the correct FQDN values in them:

    +
    +
      +

    • .env.analyst.conf: contains the analyst FQDN (i.e. FQDN=analyst(-dev).<domain>)

      • +

    • .env.broker.conf: contains the broker FQDN (i.e. FQDN=broker(-dev).<domain>)

      • +

    • config/nginx.conf: contains the server_name and proxy_pass (to container) for each +flask app.:

      +
      # Broker
+
      +
      +
      +
      server {

      listen 443 ssl; +index index.html; +server_name broker-dev.<domain>; +location / {

      +
      +

      … +# pass queries to the broker container +proxy_pass http://broker:5000;

      +
      +

      …

      +
      +
      +

      # Analyst +server {

      +
      +

      listen 443 ssl; +index index.html; +server_name analyst-dev.<domain>; +location / {

      +
      +

      # pass queries to the analyst container +proxy_pass http://analyst:5000;

      +
      +
      +
      • +
    +
    +
    +
    diff --git a/objects.inv b/objects.inv index 914389e..bc83894 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/searchindex.js b/searchindex.js index dc3e349..f174a3f 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1. Subset GBIF for Specify Network processing": [[6, "subset-gbif-for-specify-network-processing"]], "1.5 TODO": [[6, "todo"]], "2. Summarize species and occurrence counts": [[6, "summarize-species-and-occurrence-counts"]], "3. Query counts for quantification and comparison": [[6, "query-counts-for-quantification-and-comparison"]], "AWS Client tools": [[4, "aws-client-tools"]], "AWS Config": [[0, "aws-config"]], "AWS Setup": [[4, "aws-setup"]], "AWS Workflow": [[6, "aws-workflow"]], "AWS strategy": [[5, "aws-strategy"]], "AWS:": [[8, null]], "Add the Specify Network software via Github": [[4, "add-the-specify-network-software-via-github"]], "Baseline": [[4, "baseline"]], "Build/deploy Specify Network": [[10, "build-deploy-specify-network"]], "Citing Data": [[2, "citing-data"]], "Code resources": [[1, "code-resources"]], "Configuration": [[4, "configuration"]], "Configure Debugger": [[0, "configure-debugger"]], "Configure S3/Redshift for data acquisition and analyses": [[4, "configure-s3-redshift-for-data-acquisition-and-analyses"]], "Configure programmatic access to S3": [[4, "configure-programmatic-access-to-s3"]], "Connect and set EC2 SSH service timeout": [[4, "connect-and-set-ec2-ssh-service-timeout"]], "Connect to new namespace in Query Editor": [[4, "connect-to-new-namespace-in-query-editor"]], "Contains": [[0, "contains"]], "Create SSL certificates": [[10, "create-ssl-certificates"]], "Create a Security Group for the region": [[4, "create-a-security-group-for-the-region"]], "Create a new workgroup (and namespace)": [[4, "create-a-new-workgroup-and-namespace"]], "Create an IAM role for the EC2/Redshift/S3 interaction (specnet_ec2_role)": [[4, "create-an-iam-role-for-the-ec2-redshift-s3-interaction-specnet-ec2-role"]], "DNS": [[0, "dns"]], "Data Cleaning": [[3, "data-cleaning"]], "Data Use Agreements": [[2, "data-use-agreements"]], "Debugging Flask and Docker instances": [[9, "debugging-flask-and-docker-instances"]], "Definitions": [[2, "definitions"]], "Dependencies:": [[0, "dependencies"]], "Deploy Specify Network": [[10, "deploy-specify-network"]], "Deployment": [[0, "deployment"]], "Dev Environment": [[0, "dev-environment"]], "Docker": [[0, "docker"], [4, "docker"]], "EC2": [[4, "ec2"]], "EC2 instance creation": [[4, "ec2-instance-creation"]], "Edit the docker environment files": [[10, "edit-the-docker-environment-files"]], "Elastic IP": [[4, "elastic-ip"]], "Enable S3 access from local machine (and EC2?)": [[4, "enable-s3-access-from-local-machine-and-ec2"]], "Environment status checks:": [[10, "environment-status-checks"]], "Error: SSL": [[4, "error-ssl"]], "Examine container": [[9, "examine-container"], [10, "examine-container"]], "For webserver errors": [[0, "for-webserver-errors"]], "GBIF Backbone Taxonomy": [[12, "gbif-backbone-taxonomy"]], "IDE debugging of functions": [[9, "ide-debugging-of-functions"]], "Import error from werkzeug.urls": [[0, "import-error-from-werkzeug-urls"]], "Indices and tables": [[8, "indices-and-tables"]], "Install": [[0, "install"]], "Install Docker": [[0, "install-docker"]], "Install Specify Network code": [[10, "install-specify-network-code"]], "Install certificates into config directory": [[11, "install-certificates-into-config-directory"]], "Install dependencies": [[0, "install-dependencies"]], "Install software on EC2": [[4, "install-software-on-ec2"]], "Install/Run Notes": [[0, "install-run-notes"]], "Install/Update repo from Github": [[0, "install-update-repo-from-github"]], "Local Flask testing": [[0, "local-flask-testing"]], "Local client": [[4, "local-client"]], "Local debugging of Docker": [[9, "local-debugging-of-docker"]], "Local debugging of flask app": [[9, "local-debugging-of-flask-app"]], "Local self-signed certificates": [[11, "local-self-signed-certificates"]], "Misc:": [[8, null]], "Obsolete: solr": [[13, "obsolete-solr"]], "Out of Space Problem": [[10, "out-of-space-problem"]], "Overview": [[1, "overview"], [4, "overview"]], "Overview:": [[8, null]], "Problem: Failed programming external connectivity": [[10, "problem-failed-programming-external-connectivity"]], "Pycharm": [[0, "pycharm"]], "Rebuild/restart": [[9, "rebuild-restart"], [10, "rebuild-restart"]], "Redshift": [[4, "redshift"]], "Reference": [[6, "reference"]], "Renew Certbot SSL certificates": [[11, "renew-certbot-ssl-certificates"]], "Resolver Interaction": [[3, "resolver-interaction"]], "Run Docker containers (development)": [[9, "run-docker-containers-development"]], "Run Docker on OSX": [[10, "run-docker-on-osx"]], "Run the containers (development)": [[10, "run-the-containers-development"]], "Run the containers (production)": [[10, "run-the-containers-production"]], "SSL": [[0, "ssl"]], "Security": [[4, "security"]], "Setup": [[5, "setup"]], "Solution": [[10, "id1"]], "Solution:": [[10, "solution"]], "Specify Export Storage": [[3, "specify-export-storage"]], "Specify Network Analyst services": [[1, "specify-network-analyst-services"]], "Specify Network Broker services": [[1, "specify-network-broker-services"]], "Specify Network SSL certificates": [[11, "specify-network-ssl-certificates"]], "Standard manipulation": [[10, "standard-manipulation"]], "Steps": [[6, "steps"]], "Structure": [[7, "structure"]], "Syft new data": [[3, "syft-new-data"]], "Syft-ed Data Retrieval": [[3, "syft-ed-data-retrieval"]], "Syfting": [[3, "syfting"]], "TLS/SSL using Certificate Authority (CA)": [[11, "tls-ssl-using-certificate-authority-ca"]], "TODO:": [[0, "todo"]], "TODO: Autorenew SSL with Certbot/LetsEncrypt": [[11, "todo-autorenew-ssl-with-certbot-letsencrypt"]], "TODO: SSL through Amazon": [[11, "todo-ssl-through-amazon"]], "Terms of Service": [[2, "terms-of-service"]], "Test": [[0, "test"]], "Testing Specify Network elements": [[13, "testing-specify-network-elements"]], "Troubleshooting": [[0, "troubleshooting"], [4, "troubleshooting"], [10, "troubleshooting"], [13, "troubleshooting"]], "Use Cases": [[3, "use-cases"]], "Welcome to Specify Network\u2019s documentation!": [[8, "welcome-to-specify-network-s-documentation"]], "Workflow": [[5, "workflow"]], "Workflow for Specify Network Analyst pre-computations": [[4, 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