ioChem-BD

https://docs.iochem-bd.org/
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ioChem-BD is a modular computational chemistry platform that centralizes, curates, publishes and...
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### Input text example for calculation.setup

Source: https://docs.iochem-bd.org/data/codes/xtb/calculation.setup-d3e54022.html

Example input text showing the calculation setup section from an xtb log file, including program call, coordinate file, and omp threads.

```text
           -------------------------------------------------
          |                Calculation Setup                |
           -------------------------------------------------

          program call               : xtb water.xyz --input water.inp
          coordinate file            : water.xyz
          omp threads                :                     8

```

--------------------------------

### Install libcap-progs and run postinstall.sh

Source: https://docs.iochem-bd.org/doc/guides/installation/installation.html

Install the libcap-progs package using zypper and then run the postinstall script again as root.

```bash
root# zypper install libcap-progs
root# BASEPATH/postinstall.sh
```

--------------------------------

### Run the ioChem-BD installer script

Source: https://docs.iochem-bd.org/doc/guides/installation/installation.html

Execute the visual installer by moving to the BASE_PATH directory and running init.sh as the iochembd user.

```bash
iochembd$ cd *BASEPATH*
iochembd$ ./init.sh
```

--------------------------------

### Example handle input

Source: https://docs.iochem-bd.org/doc/faqs/admin/unpublish-collection.html

Example of providing the handle identifier when prompted by the script.

```bash
Handle (example: 100/300) : 100/1234
```

--------------------------------

### Example collection URL

Source: https://docs.iochem-bd.org/doc/faqs/admin/unpublish-collection.html

Example URL showing the handle identifier as the last part after /handle/.

```text
https://your-domain.com/handle/100/1234
```

--------------------------------

### Start the web service

Source: https://docs.iochem-bd.org/doc/guides/other-operations/replace-https-certificate/with-existing-certificate.html

Starts the Apache Tomcat service using the startup script after a successful certificate replacement.

```bash
iochembd$    BASE_PATH/apache-tomcat/bin/startup.sh
```

--------------------------------

### Start ioChem-BD web service

Source: https://docs.iochem-bd.org/doc/guides/other-operations/replace-https-certificate/validate-domain-owner.html

Starts the ioChem-BD web service again after copying the file and editing the configuration.

```bash
iochembd$  BASE_PATH/apache-tomcat/bin/startup.sh
```

--------------------------------

### Pagination example request

Source: https://docs.iochem-bd.org/api/browse.html

Example GET request using pagination parameters limit and offset to retrieve items from a collection.

```http
GET https://iochem-bd.iciq.es/rest/collections/19/items?limit=5&offset=10
```

--------------------------------

### Update process log output

Source: https://docs.iochem-bd.org/doc/faqs/admin/update-current-distribution.html

Example output from the updater script showing successful update. The server starts automatically after the update completes. If the update fails, copy this output and send it to contact@iochem-bd.org.

```bash
17:01:09.543 [main] INFO  update.UpdatePatch -  Task: Running Ant target : update
17:03:42.600 [main] INFO  utils.SqlRunner -     Running update vxxx.SetCalculationOrdering
17:03:43.073 [main] INFO  update.UpdatePatch -  Task: Updating Browse dspace.cfg file
17:03:43.120 [main] INFO  update.TomcatManager - Starting Apache Tomcat...  <== Server started
17:03:43.128 [main] INFO  utils.Utils - Running command:[/home/iochembd/iochem-bd/apache-tomcat/bin/startup.sh]
17:03:43.128 [main] INFO  update.UpdateProcess - ioChem-BD updated to latest version.
Update process finished.
```

--------------------------------

### Pagination example: GET /rest/collections?limit=5&offset=10

Source: https://docs.iochem-bd.org/api/find.html

Shows how to paginate results from endpoints that return arrays by adding the limit and offset query parameters. The default limit is 100 and the default offset is 0.

```http
GET https://www.iochem-bd.org/rest/collections?limit=5&offset=10
```

--------------------------------

### Connect to repository with start-rep-shell

Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html

Use 'source start-rep-shell' or '. start-rep-shell' to connect to the repository. Must be preceded by 'source' or '.' to work.

```console
$ source start-rep-shell   #Connect to repository using long format
$ . start-rep-shell        #Connect to repository using short format
```

--------------------------------

### Private key file example (.key)

Source: https://docs.iochem-bd.org/doc/guides/other-operations/replace-https-certificate/with-existing-certificate.html

Example of a private key file in unencrypted PKCS#8 PEM format with .key extension. The content is truncated with '...' in the source.

```console
-----BEGIN PRIVATE KEY-----
MHcCAQEEIBdVHnnzZmJm+Z1HAYYOZlvnB8Dj8kVx9XBH+6UCWlGUoAoGCCqGSM49
AwEHoUQDQgAEThPp/xgEov0mKg2s0GII76VkZAcCc//3quAqzg+PuFKXgruaF7K
...
-----END PRIVATE KEY-----
```

--------------------------------

### Start server manually

Source: https://docs.iochem-bd.org/doc/faqs/admin/update-current-distribution.html

Starts the Apache Tomcat server manually if the update process did not start it automatically. Use this only if the update did not end successfully.

```bash
iochembd$   cd BASE_PATH/apache-tomcat/bin
iochembd$   ./startup.sh
```

--------------------------------

### Initialize PostgreSQL database (initdb)

Source: https://docs.iochem-bd.org/doc/guides/installation/installation.html

Run as root to initialize the PostgreSQL database after installing the server and postgresql-contrib package.

```bash
root# /sbin/service postgresql initdb
```

--------------------------------

### start-rep-shell

Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html

Connects to the repository. Must be preceded by 'source' or '.' to work.

```APIDOC
## start-rep-shell

### Description
Connects to the repository. Must be preceded by `source` or `.` (dot) to work.

### Usage
```
$ source start-rep-shell   #Connect to repository using long format
$ . start-rep-shell        #Connect to repository using short format
```

```

--------------------------------

### Start and stop the web service with Tomcat scripts

Source: https://docs.iochem-bd.org/doc/guides/installation/installation.html

Use these commands to start and stop the ioChem-BD web service. Replace BASE_PATH with the actual path. After starting, check BASE_PATH/apache-tomcat/logs/catalina.out for startup errors.

```console
iochembd$  BASE_PATH/apache-tomcat/bin/startup.sh    # to start service
iochembd$  BASE_PATH/apache-tomcat/bin/shutdown.sh -force  # to stop service
```

--------------------------------

### Start ioChem-BD web service

Source: https://docs.iochem-bd.org/doc/guides/installation/migration-guide.html

Run as the iochembd user to start the Apache Tomcat service.

```bash
iochembd$ BASE_PATH/apache-tomcat/bin/startup.sh
```

--------------------------------

### Example news.html for Create module welcome page

Source: https://docs.iochem-bd.org/doc/guides/other-operations/customizing-system-interface.html

HTML file loaded as an independent file in the Create module welcome panel. Must be valid and well-formed. Contains commented maintenance alert that can be uncommented to notify users.

```html
<html>
   <body>
      <center>
         <h4>Current version 1.1.0</h4>
         View <a href="http://www.iochem-bd.org/changelog.html" target="_blank">changelog</a>
         <!--
            <h2>System maintenance alert</h2>
            <p>ioChem-BD will be under maintenance from XXXXX to XXXXX</p>
         -->
      </center>
   </body>
</html>
```

--------------------------------

### source start-rep-shell

Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html

Connects to the repository.

```APIDOC
## source start-rep-shell

### Description
Connects to the repository.

### Command
`source start-rep-shell`

### Parameters
- `-h` (flag) - Optional - Displays help message with wider description of usage.

```

--------------------------------

### loadamber with name and description

Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/using-shell-client/shell-automated-scripts.html

Uploads all matching files in the directory, setting the calculation name to "Au-CoO-H2O" and description to "Sample upload".

```bash
$ loadamber -n Au-CoO-H2O -d "Sample upload"
```

--------------------------------

### Initialize and configure PostgreSQL

Source: https://docs.iochem-bd.org/doc/guides/installation/migration-guide.html

Initialize PostgreSQL databases (only necessary on CentOS/Fedora/Rocky/RHEL), enable the service to start on boot, and edit pg_hba.conf to allow password authentication. The file path may vary by version and OS; create the file if it doesn't exist.

```bash
# Initialize PostgreSQL databases (if not already done), only necessary on CentOS/Fedora/Rocky/RHEL
root# postgresql-setup initdb

# Configure PostgreSQL to start on boot
root# systemctl enable postgresql

# Edit pg_hba.conf to allow password authentication, folder names can vary depending on your version and OS
# If file doesn't exist, just create it.
root# vi /var/lib/postgresql/16/main/pg_hba.conf
```

--------------------------------

### getxyz examples

Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html

Examples of the getxyz command to retrieve the geometry of a calculation by ID, either to stdout or to a file.

```console
$ getxyz -n 14837                   # Retrieve geometry of calculation with ID 14837 and display on stdout
$ getxyz -n 14837 -o geom.xyz       # Retrieve geometry of calculation with ID 14837 and store it in geom.xyz file
```

--------------------------------

### GET /create/rest/project/descendant

Source: https://docs.iochem-bd.org/api/create.html

Gets children of a project based on type and depth parameters. Requires bearer authentication.

```APIDOC
## GET /create/rest/project/descendant

### Description
Gets children of a project. Handles hierarchy based on type and depth parameters.

### Method
GET

### Endpoint
/create/rest/project/descendant

### Parameters
#### Query Parameters
- **id** (integer) - Required - id
- **type** (string) - Optional - type of search ( calculation, project )
- **depth** (string) - Optional - depth of search ( 1, 2 ... or all )

### Response
#### Success Response (200)
Successful operation

#### Error Responses
- **400** - Invalid ID supplied
- **404** - Project not found

### Security
- bearerAuth
```

--------------------------------

### loadxtb with name and description

Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/using-shell-client/shell-automated-scripts.html

Uploads matching files and sets calculation name to 'water' and description to 'Water geometry optimization'.

```bash
$ loadxtb -n water -d "Water geometry optimization"
```

--------------------------------

### Output XML for calculation.setup

Source: https://docs.iochem-bd.org/data/codes/xtb/calculation.setup-d3e54022.html

Example output XML generated by the template, showing the extracted parameters as scalar elements with dictRef attributes.

```xml
<comment class="example.output" id="calculation.setup">
        <module cmlx:templateRef="calculation.setup">
                <list cmlx:templateRef="parameter">
                        <list>
                                <scalar dataType="xsd:string" dictRef="xtb:name">program call</scalar>
                                <scalar dataType="xsd:string" dictRef="xtb:value">xtb water.xyz --opt</scalar>
                        </list>
                        <list>
                                <scalar dataType="xsd:string" dictRef="xtb:name">hostname</scalar>
                                <scalar dataType="xsd:string" dictRef="xtb:value">p038</scalar>
                        </list>
                        <list>
                                <scalar dataType="xsd:string" dictRef="xtb:name">coordinate file</scalar>
                                <scalar dataType="xsd:string" dictRef="xtb:value">water.xyz</scalar>
                        </list>
                        <list>
                                <scalar dataType="xsd:string" dictRef="xtb:name">omp threads</scalar>
                                <scalar dataType="xsd:string" dictRef="xtb:value">24</scalar>
                        </list>
                </list>
        </module>
    </comment>

```

--------------------------------

### sharepro command example with output

Source: https://docs.iochem-bd.org/doc/guides/usage/uploading-content-to-create/shell-commands.html

Shows the sharepro command and its output listing shared projects with project ID, path, group, and permission.

```console
$ sharepro 

Shared Projects:
================
Project_id Path                               Group           Permission   

------------------------------------------------------------------------
449        /db/kpotts/turbomole               fock_group      WRITE        
584        /db/slester/adf                    fock_group      WRITE        
628        /db/slester/turbomole/fetz         fock_group      FULLACCESS   
635        /db/slester/turbomole/fluorophenol fock_group      WRITE
```
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