psdi-data-conversion 0.0.37__py3-none-any.whl → 0.0.39__py3-none-any.whl

psdi_data_conversion/static/javascript/convert.js

@@ -7,7 +7,9 @@
 
 
 import { getInputFlags, getOutputFlags, getInputArgFlags, getOutputArgFlags } from "./data.js";
-import { commonConvertReady, convertFile, getExtCheck, splitArchiveExt, isArchiveExt } from "./convert_common.js"
+import {
+    SAFE_CHAR_REGEX, commonConvertReady, convertFile, getExtCheck, splitArchiveExt, isArchiveExt
+} from "./convert_common.js"
 
 var token = "",
     in_ext = "",
@@ -51,8 +53,24 @@ function enterArgument(event) {
     }
 }
 
+
+/**
+ * Validate the input for a format option - if invalid, display the error message, if valid, hide it
+ *
+ * @param {*} event 
+ */
+function validateInput(event) {
+    var err_id = this.id.replace('text', 'err')
+    if (this.validity.patternMismatch) {
+        $('#' + err_id).css({ display: "block" })
+    } else {
+        $('#' + err_id).css({ display: "none" })
+    }
+}
+
 // Uploads a user-supplied file
 function submitFile() {
+
     const file = $("#fileToUpload")[0].files[0],
         [fname, ext] = splitArchiveExt(file.name);
 
@@ -78,9 +96,16 @@ function submitFile() {
     const checked_in = $('input[name=in_arg_check]:checked'),
         checked_out = $('input[name=out_arg_check]:checked');
 
+    let security_passed = true;
+
     checked_in.each(function () {
         read_arg_flags += $("#" + this.id).val()[0];
-        const arg = $("#in_arg_text" + this.id.substring(this.id.length - 1, this.id.length)).val();
+        const e = $("#in_arg_text" + this.id.substring(this.id.length - 1, this.id.length));
+        const arg = e.val();
+
+        if (e[0].validity.patternMismatch) {
+            security_passed = false;
+        }
 
         if (/\S/.test(arg)) {
             read_args += arg.trim() + '£';
@@ -92,7 +117,12 @@ function submitFile() {
 
     checked_out.each(function () {
         write_arg_flags += $("#" + this.id).val()[0];
-        const arg = $("#out_arg_text" + this.id.substring(this.id.length - 1, this.id.length)).val();
+        const e = $("#out_arg_text" + this.id.substring(this.id.length - 1, this.id.length));
+        const arg = e.val();
+
+        if (e[0].validity.patternMismatch) {
+            security_passed = false;
+        }
 
         if (/\S/.test(arg)) {
             write_args += arg.trim() + '£';
@@ -102,9 +132,21 @@ function submitFile() {
         }
     })
 
+    let alert_msg = '';
+
+    if (!security_passed) {
+        alert_msg += 'ERROR: One or more ticked options contains invalid characters. They must match the regex /' +
+            SAFE_CHAR_REGEX + '/ .\n';
+    }
+
     if (!all_args_entered) {
-        alert('All ticked option flags need additional information to be entered into the associated text box.');
-        return;
+        alert_msg += 'ERROR: All ticked options need additional information to be entered into the associated ' +
+            'text box.\n';
+    }
+
+    if (alert_msg) {
+        alert(alert_msg);
+        return
     }
 
     const coordinates = $('input[name="coordinates"]:checked').val(),
@@ -216,11 +258,17 @@ function addCheckboxes(argFlags, type) {
                 <tr>
                     <td><input type='checkbox' id="${type}_check${flagCount}" name=${type}_check value="${flag}"></input></td>
                     <td><label for="${type}_check${flagCount}">${flag} [${brief}]: ${description}<label></td>
-                    <td><input type='text' id=${type}_text${flagCount} placeholder='-- type info. here --'></input></td>
+                    <td><input type='text' id="${type}_text${flagCount}" placeholder='-- type info. here --'
+                         pattern='` + SAFE_CHAR_REGEX + `'></input>
+                         <p class="init-hidden" id="${type}_err${flagCount}"><strong>ERROR:</strong> Input contains
+                         invalid characters; it must match the regex 
+                         <code class="secondary">/` + SAFE_CHAR_REGEX + `/</code></p>
+                    </td>
                     <td><span id= ${type}_label${flagCount}>${furtherInfo}</span></td>
                 </tr>`);
 
             $(`#${type}_text${flagCount}`).hide();
+            $(`#${type}_text${flagCount}`).on('input', validateInput);
             $(`#${type}_label${flagCount}`).hide();
             $(`#${type}_check${flagCount}`).change(enterArgument);
 

psdi_data_conversion/static/javascript/convert_common.js

@@ -18,6 +18,20 @@ const TARGZ_EXT = "tar.gz"
 const TARBZ_EXT = "tar.bz"
 const TARXZ_EXT = "tar.xz"
 
+// Short list of safe allowed characters:
+// \w: All letters and digits
+// \s: All whitespace characters
+// .: Period
+// \-: Hyphen
+// :: Colon
+// +: Plus symbol
+// *: Asterisk
+// =: Equals sign
+// $: Dollar sign
+// /: Forward-slash
+// \\: Backslash
+export const SAFE_CHAR_REGEX = "[\\w\\s.\\-:+*=$\\/\\\\]*"
+
 // Whether or not file extensions will be checked
 let extCheck = true;
 
@@ -271,10 +285,10 @@ function checkFile(event) {
 }
 
 /**
- * Allow the file upload to only accept the expected type of file
+ * Allow the file upload to only accept the expected type of file, plus archives
  */
 function limitFileType() {
-    $("#fileToUpload")[0].accept = "." + in_ext;
+    $("#fileToUpload")[0].accept = "." + in_ext + ", .zip, .tar, .tar.gz, .tar.xz, .tar.bz";
 }
 
 /**

psdi_data_conversion/static/javascript/data.js

@@ -1,7 +1,21 @@
 // data.js
 
 const response = await fetch("/static/data/data.json");
-const data = JSON.parse(await response.text());
+
+let data = null;
+try {
+    data = JSON.parse(await response.text());
+} catch (err) {
+    console.log("ERROR: Database could not be loaded, error: " + err)
+}
+
+/**
+ * Indicates whether or not the database was successfully loaded
+ * @returns {boolean}
+ */
+export function databaseLoaded() {
+    return data !== null;
+}
 
 const collator = new Intl.Collator();
 
@@ -49,6 +63,24 @@ export async function getOutputFormats() {
     return outFormats.sort((a, b) => compare([a.extension, b.extension], [a.note, b.note]))
 }
 
+/**
+ * Gets the ID for a format, given its extension and note
+ * 
+ * @param {string} extension - The extension of the format, e.g. 'pdb'
+ * @param {string} note - The note of the format, e.g. 'Protein Databank'
+ * @returns {(int|null)} - The ID of the format if found, or else null
+ */
+export async function getFormatId(extension, note) {
+
+    var format = (data.formats.filter(format => (format.extension === extension) && (format.note === note)));
+
+    if (format === undefined) {
+        return null;
+    }
+
+    return format[0].id;
+}
+
 export async function getOutputFormatsForInputFormat(inExtension, inNote) {
 
     const inputFormat = (data.formats.filter(format => (format.extension === inExtension) && (format.note === inNote)))[0];
@@ -84,7 +116,7 @@ export async function getConverters(inExtension, inNote, outExtension, outNote)
     const inputFormat = (data.formats.filter(format => (format.extension === inExtension) && (format.note === inNote)))[0];
     const outputFormat = (data.formats.filter(format => (format.extension === outExtension) && (format.note === outNote)))[0];
 
-    if ((inputFormat === undefined) || (outputFormat === undefined))  {
+    if ((inputFormat === undefined) || (outputFormat === undefined)) {
         return [];
     }
 
@@ -96,7 +128,7 @@ export async function getConverters(inExtension, inNote, outExtension, outNote)
         name: convertersById.get(conversion.converters_id).name
     }));
 
-    return convertersWithDegreeOfSuccess.sort((a, b) => compare(a.name, b.name ));
+    return convertersWithDegreeOfSuccess.sort((a, b) => compare(a.name, b.name));
 }
 
 export async function getConverterByName(name) {
@@ -170,7 +202,7 @@ export async function getOutputArgFlags(extension, note) {
 export async function getLevelChemInfo(inExtension, inNote, outExtension, outNote) {
 
     const inputFormat = (data.formats.filter(format => (format.extension === inExtension) && (format.note === inNote)))[0],
-          outputFormat = (data.formats.filter(format => (format.extension === outExtension) && (format.note === outNote)))[0];
+        outputFormat = (data.formats.filter(format => (format.extension === outExtension) && (format.note === outNote)))[0];
 
     return [inputFormat, outputFormat];
 }

psdi_data_conversion/static/javascript/format.js

@@ -7,7 +7,7 @@
 
 import { disableDirtyForms, cleanDirtyForms, initDirtyForms, loadServiceMode, loadProductionMode } from "./common.js";
 import {
-    getInputFormats, getOutputFormats, getOutputFormatsForInputFormat,
+    databaseLoaded, getInputFormats, getOutputFormats, getOutputFormatsForInputFormat,
     getInputFormatsForOutputFormat, getConverters, getConverterByName, getLevelChemInfo
 } from "./data.js";
 
@@ -18,15 +18,20 @@ var fromList = new Array(),
 
 $(document).ready(function () {
 
-    // Populates the "Convert from" selection list
-    getInputFormats().then((formats) => {
-        populateList(formats, "from");
-    });
+    // Populate the available formats if the database successfully loaded, otherwise display an error message
+    if (databaseLoaded()) {
+        // Populates the "Convert from" selection list
+        getInputFormats().then((formats) => {
+            populateList(formats, "from");
+        });
 
-    // Populates the "Convert to" selection list
-    getOutputFormats().then((formats) => {
-        populateList(formats, "to");
-    });
+        // Populates the "Convert to" selection list
+        getOutputFormats().then((formats) => {
+            populateList(formats, "to");
+        });
+    } else {
+        displayDatabaseLoadError();;
+    }
 
     sessionStorage.setItem("token", token);
     sessionStorage.setItem("max_file_size", max_file_size);
@@ -52,6 +57,14 @@ $(document).ready(function () {
     initDirtyForms();
 });
 
+/**
+ * Hides the format and converter selection and displays an error message that the database could not be loaded.
+ */
+function displayDatabaseLoadError() {
+    $("#format-selection").css({ display: "none" });
+    $("#database-error").css({ display: "block" });
+}
+
 /**
  * Gets the input and output extensions and their notes from what's currently selected in the search boxes.
  * @returns {Array<str>} Input extension, Input note, Output extension, Output note

psdi_data_conversion/static/styles/format.css

@@ -44,6 +44,13 @@ form {
   }
 }
 
+/* Invalid input fields switch to alternate background */
+
+input:invalid {
+  background-color: var(--ifm-color-primary);
+  color           : var(--ifm-hero-text-color);
+}
+
 /* Converter details, user input and file conversion initially not displayed. */
 .init-hidden {
   display: none

psdi_data_conversion/templates/index.htm

@@ -60,55 +60,64 @@
       <p>Your one-stop shop for file format conversion, PSDI's Data Conversion Service enables users to seamlessly
         convert between different file formats and assess the quality of proposed conversions. This is the web version
         of our service. To find out more about Data Conversion and our other tools, click
-        <a href="https://resources.psdi.ac.uk/resource-themes/7bcc430a-fdc9-413e-bf32-bf163236430b"
-          id="more" target="_blank">here.</a></p>
-      <p>Select 'from' and 'to' file formats in the 'Convert from/to' boxes, in either order. Typing where indicated
-        filters the options (case insensitive); for example, typing 'can' or 'NON' reduces the number of options to one:
-        'can: Canonical SMILES.' If you change your mind about a conversion, it is advisable to click on the 'Reset'
-        button. When both formats have been selected, converters able to carry out this conversion appear in the
-        'Conversion options' box along with an indication of conversion quality (many conversions have not yet been
-        tested) and whether or not the converter is supported on this site.</p>
-      <p>
-        <label for="searchFrom" id="fromLabel">Convert from:</label><br>
-        <input type="text" placeholder="-- type here to filter options --" size="12" id="searchFrom"
-          class="large-width"><br>
-        <select size="4" id="fromList" class="large-width"></select>
+        <a href="https://resources.psdi.ac.uk/resource-themes/7bcc430a-fdc9-413e-bf32-bf163236430b" id="more"
+          target="_blank">here.</a>
       </p>
-      <div class="smallGap"></div>
-      <p>
-        <label for="searchTo" id="toLabel">Convert to:</label><br>
-        <input type="text" placeholder="-- type here to filter options --" size="12" id="searchTo"
-          class="large-width"><br>
-        <select size="4" id="toList" class="large-width"></select>
-      </p>
-      <input type="button" class="button" value=" Reset " name="resetButton" id="resetButton">
-      <br><br>
-      <p>Selecting a converter displays information
-        about it, along with a link to a relevant website. Selecting a supported converter affords the opportunity to
-        carry out a conversion on this site. Clicking on the 'Yes' button takes us to the 'Conversion' page. If a
-        file format has not been found, or if there are no converters capable of carrying out a required conversion
-        please click on 'Report Missing Format/Conversion' in the navigation bar.</p>
-      <p>
-        <label for="success">Select from available conversion
-          options:</label><br>
-        <select size="4" id="success" class="large-width"></select>
-      </p>
-      <span class="normalText">Show how the conversion quality was determined for the selected converter.</span>
-      <input type="button" class="button" value=" Show " name="showButton" id="showButton">
-      <br>
-      <h6>Converter details:</h6>
-      <p id="converter" , class="init-hidden">
-        <span id="name"></span>
-        <br><span id="description"></span>
-        <br><span id="url"></span>
-        <br><span id="info"></span>
-        <a id="visit" target="_blank">this website.</a>
-      <div id="formatWarning" class="init-hidden"></div>
-      <div id="offer" class="init-hidden">
-        <span id="question"></span>
-        <input type="button" class="button" value=" Yes " name="yesButton" id="yesButton">
+      <div id="format-selection">
+        <p>Select 'from' and 'to' file formats in the 'Convert from/to' boxes, in either order. Typing where indicated
+          filters the options (case insensitive); for example, typing 'can' or 'NON' reduces the number of options to
+          one:
+          'can: Canonical SMILES.' If you change your mind about a conversion, it is advisable to click on the 'Reset'
+          button. When both formats have been selected, converters able to carry out this conversion appear in the
+          'Conversion options' box along with an indication of conversion quality (many conversions have not yet been
+          tested) and whether or not the converter is supported on this site.</p>
+        <p>
+          <label for="searchFrom" id="fromLabel">Convert from:</label><br>
+          <input type="text" placeholder="-- type here to filter options --" size="12" id="searchFrom"
+            class="large-width"><br>
+          <select size="4" id="fromList" class="large-width"></select>
+        </p>
+        <div class="smallGap"></div>
+        <p>
+          <label for="searchTo" id="toLabel">Convert to:</label><br>
+          <input type="text" placeholder="-- type here to filter options --" size="12" id="searchTo"
+            class="large-width"><br>
+          <select size="4" id="toList" class="large-width"></select>
+        </p>
+        <input type="button" class="button" value=" Reset " name="resetButton" id="resetButton">
+        <br><br>
+        <p>Selecting a converter displays information
+          about it, along with a link to a relevant website. Selecting a supported converter affords the opportunity to
+          carry out a conversion on this site. Clicking on the 'Yes' button takes us to the 'Conversion' page. If a
+          file format has not been found, or if there are no converters capable of carrying out a required conversion
+          please click on 'Report Missing Format/Conversion' in the navigation bar.</p>
+        <p>
+          <label for="success">Select from available conversion
+            options:</label><br>
+          <select size="4" id="success" class="large-width"></select>
+        </p>
+        <span class="normalText">Show how the conversion quality was determined for the selected converter.</span>
+        <input type="button" class="button" value=" Show " name="showButton" id="showButton">
+        <br>
+        <h6>Converter details:</h6>
+        <p id="converter" , class="init-hidden">
+          <span id="name"></span>
+          <br><span id="description"></span>
+          <br><span id="url"></span>
+          <br><span id="info"></span>
+          <a id="visit" target="_blank">this website.</a>
+        <div id="formatWarning" class="init-hidden"></div>
+        <div id="offer" class="init-hidden">
+          <span id="question"></span>
+          <input type="button" class="button" value=" Yes " name="yesButton" id="yesButton">
+        </div>
+        </p>
+      </div>
+      <div id="database-error" class="init-hidden">
+        <p><strong>ERROR:</strong> Connection to the conversion database failed. Please try refreshing this page. If
+          this issue persists, please report it to us using the "Contact" link in the header. You can also download
+          a version of this service for local use using the "Download" link in the header if you'd prefer.</p>
       </div>
-      </p>
       <div class="medGap"></div>
     </div>
   </form>
@@ -123,4 +132,4 @@
 
 </body>
 
-</html>
+</html>

psdi_data_conversion/testing/constants.py

@@ -13,3 +13,6 @@ TEST_DATA_LOC_IN_PROJECT = "./test_data"
 
 INPUT_TEST_DATA_LOC_IN_PROJECT = TEST_DATA_LOC_IN_PROJECT
 OUTPUT_TEST_DATA_LOC_IN_PROJECT = os.path.join(TEST_DATA_LOC_IN_PROJECT, "output")
+
+DEFAULT_ORIGIN = "http://127.0.0.1:5000"
+"""The default location of the server for running GUI unit tests"""

psdi_data_conversion/testing/conversion_callbacks.py

@@ -6,10 +6,10 @@ conversion test, run with the functions and classes defined in the `utils.py` mo
 """
 
 import abc
-from collections.abc import Callable, Iterable
-from dataclasses import dataclass, field
 import os
 import re
+from collections.abc import Callable, Iterable
+from dataclasses import dataclass, field
 from tempfile import TemporaryDirectory
 
 from psdi_data_conversion.constants import DATETIME_RE_RAW
@@ -352,7 +352,8 @@ class CheckException:
 
         # Check the exception type
         if self.ex_type and not issubclass(exc_info.type, self.ex_type):
-            l_errors.append(f"ERROR: Raised exception is of type '{exc_info.type}', but expected '{self.ex_type}'")
+            l_errors.append(f"ERROR: Raised exception is of type '{exc_info.type}', but expected '{self.ex_type}'. "
+                            f"Raised exception's message was: {str(exc_info)}")
 
         exc = exc_info.value
 

psdi_data_conversion/testing/conversion_test_specs.py

@@ -8,17 +8,18 @@ application, and GUI.
 
 from psdi_data_conversion import constants as const
 from psdi_data_conversion.converters.atomsk import CONVERTER_ATO
-from psdi_data_conversion.converters.base import (FileConverterAbortException, FileConverterHelpException,
-                                                  FileConverterInputException, FileConverterSizeException)
+from psdi_data_conversion.converters.base import (FileConverterAbortException, FileConverterInputException,
+                                                  FileConverterSizeException)
 from psdi_data_conversion.converters.c2x import CONVERTER_C2X
 from psdi_data_conversion.converters.openbabel import CONVERTER_OB, COORD_GEN_KEY, COORD_GEN_QUAL_KEY
-from psdi_data_conversion.testing.conversion_callbacks import (CheckArchiveContents, CheckException, CheckLogContents,
-                                                               CheckLogContentsSuccess, CheckFileStatus,
+from psdi_data_conversion.database import FileConverterDatabaseException
+from psdi_data_conversion.testing.conversion_callbacks import (CheckArchiveContents, CheckException, CheckFileStatus,
+                                                               CheckLogContents, CheckLogContentsSuccess,
                                                                CheckStderrContents, CheckStdoutContents,
-                                                               MatchOutputFile, MultiCallback as MCB)
+                                                               MatchOutputFile)
+from psdi_data_conversion.testing.conversion_callbacks import MultiCallback as MCB
 from psdi_data_conversion.testing.utils import ConversionTestSpec as Spec
 
-
 l_all_test_specs: list[Spec] = []
 """All test specs defined in this file"""
 
@@ -36,11 +37,16 @@ l_all_test_specs.append(Spec(name="Standard Multiple Tests",
                                        "hemoglobin.pdb", "hemoglobin.pdb", "nacl.cif",
                                        "hemoglobin.pdb", "hemoglobin.pdb", "nacl.cif",
                                        "ethanol.xyz"],
-                             to_format=["pdb",
+                             to_format=["pdb-0",
                                         "cif", "mol2", "xyz",
                                         "cif", "xyz", "xyz",
-                                        "cif", "xyz", "xyz",
+                                        "cif", "xyz-0", "xyz-0",
                                         "cml"],
+                             from_format=[None,
+                                          None, None, None,
+                                          None, None, None,
+                                          "pdb-0", "pdb-0", None,
+                                          None],
                              converter_name=[CONVERTER_OB,
                                              CONVERTER_OB, CONVERTER_OB, CONVERTER_OB,
                                              CONVERTER_ATO, CONVERTER_ATO, CONVERTER_ATO,
@@ -52,6 +58,17 @@ l_all_test_specs.append(Spec(name="Standard Multiple Tests",
 """A basic set of test conversions which we expect to succeed without issue, running conversions with each of the
 Open Babel, Atomsk, and c2x converters"""
 
+l_all_test_specs.append(Spec(name="c2x Formats Tests",
+                             to_format=["res", "abi", "POSCAR", "cml"],
+                             converter_name=CONVERTER_C2X,
+                             callback=MCB(CheckFileStatus(),
+                                          CheckLogContentsSuccess()),
+                             compatible_with_gui=False,
+                             ))
+"""Test converting with c2x to a few different formats which require special input. This test isn't run in the GUI
+solely to save on resources, since there are unlikely to be an GUI-specific issues raised by this test that aren't
+caught in others."""
+
 archive_callback = MCB(CheckFileStatus(),
                        CheckArchiveContents(l_filename_bases=["caffeine-no-flags",
                                                               "caffeine-ia",
@@ -65,7 +82,7 @@ l_all_test_specs.append(Spec(name="Archive",
                              filename=["caffeine-smi.zip",
                                        "caffeine-smi.tar",
                                        "caffeine-smi.tar.gz"],
-                             conversion_kwargs={"from_format": "smi"},
+                             from_format="smi",
                              to_format="inchi",
                              callback=archive_callback,
                              ))
@@ -74,8 +91,8 @@ l_all_test_specs.append(Spec(name="Archive",
 l_all_test_specs.append(Spec(name="Archive (wrong format) - Library and CLA",
                              filename="caffeine-smi.zip",
                              to_format="inchi",
-                             conversion_kwargs=[{"from_format": "pdb"},
-                                                {"from_format": "pdb", "strict": True}],
+                             from_format=["pdb-0", "pdb-0"],
+                             conversion_kwargs=[{}, {"strict": True}],
                              expect_success=[True, False],
                              callback=[CheckStderrContents(const.ERR_WRONG_EXTENSIONS),
                                        CheckException(ex_type=FileConverterInputException,
@@ -88,8 +105,8 @@ l_all_test_specs.append(Spec(name="Archive (wrong format) - Library and CLA",
 l_all_test_specs.append(Spec(name="Archive (wrong format) - GUI",
                              filename="caffeine-smi.zip",
                              to_format="inchi",
-                             conversion_kwargs=[{"from_format": "pdb"},
-                                                {"from_format": "pdb", "strict": True}],
+                             from_format=["pdb-0", "pdb-0"],
+                             conversion_kwargs=[{}, {"strict": True}],
                              expect_success=[False, False],
                              callback=CheckException(ex_type=FileConverterInputException,
                                                      ex_message=const.ERR_WRONG_EXTENSIONS),
@@ -150,7 +167,7 @@ Not compatible with GUI tests, since the GUI doesn't support quiet mode
 
 l_all_test_specs.append(Spec(name="Open Babel Warning",
                              filename="1NE6.mmcif",
-                             to_format="pdb",
+                             to_format="pdb-0",
                              callback=CheckLogContentsSuccess(["Open Babel Warning",
                                                                "Failed to kekulize aromatic bonds",])
                              ))
@@ -204,7 +221,8 @@ Not compatible with the GUI, since the GUI can't forcibly delete files uploaded
 
 l_all_test_specs.append(Spec(name="Failed conversion - bad input file",
                              filename=["quartz_err.xyz", "cyclopropane_err.mol"],
-                             to_format=["inchi", "xyz"],
+                             to_format=["inchi", "xyz-0"],
+                             from_format=[None, "mol-0"],
                              expect_success=False,
                              converter_name=[CONVERTER_OB, CONVERTER_C2X],
                              callback=[MCB(CheckFileStatus(expect_output_exists=False,
@@ -246,12 +264,13 @@ l_all_test_specs.append(Spec(name="Errors in logs - GUI",
 
 l_all_test_specs.append(Spec(name="Failed conversion - invalid conversion",
                              filename=["Fapatite.ins", "nacl.mol"],
+                             from_format=["ins", "mol-0"],
                              to_format=["cml", "xyz"],
                              expect_success=False,
-                             converter_name=[CONVERTER_OB, CONVERTER_ATO],
+                             converter_name=[CONVERTER_C2X, CONVERTER_ATO],
                              callback=MCB(CheckFileStatus(expect_output_exists=False,
                                                           expect_log_exists=None),
-                                          CheckException(ex_type=FileConverterHelpException,
+                                          CheckException(ex_type=FileConverterDatabaseException,
                                                          ex_message="is not supported")),
                              compatible_with_gui=False,
                              ))
@@ -263,7 +282,8 @@ Not compatible with the GUI, since the GUI only offers valid conversions.
 l_all_test_specs.append(Spec(name="Blocked conversion - wrong input type",
                              filename="1NE6.mmcif",
                              to_format="cif",
-                             conversion_kwargs={"from_format": "pdb", "strict": True},
+                             from_format="pdb-0",
+                             conversion_kwargs={"strict": True},
                              expect_success=False,
                              callback=MCB(CheckFileStatus(expect_output_exists=False,
                                                           expect_log_exists=None),
@@ -278,7 +298,8 @@ l_all_test_specs.append(Spec(name="Blocked conversion - wrong input type",
 l_all_test_specs.append(Spec(name="Failed conversion - wrong input type",
                              filename="1NE6.mmcif",
                              to_format="cif",
-                             conversion_kwargs={"from_format": "pdb", "strict": False},
+                             from_format="pdb-0",
+                             conversion_kwargs={"strict": False},
                              expect_success=False,
                              callback=MCB(CheckFileStatus(expect_output_exists=False,
                                                           expect_log_exists=None),
@@ -291,6 +312,8 @@ l_all_test_specs.append(Spec(name="Large files - Library and CLA",
                              filename=["ch3cl-esp.cub", "benzyne.molden", "periodic_dmol3.outmol",
                                        "fullRhinovirus.pdb"],
                              to_format=["cdjson", "dmol", "mol", "cif"],
+                             from_format=[None, None, None, "pdb-0"],
+                             conversion_kwargs=[{}, {}, {}, {"strict": False}],
                              converter_name=[CONVERTER_OB, CONVERTER_OB, CONVERTER_OB, CONVERTER_C2X],
                              callback=CheckFileStatus(),
                              compatible_with_gui=False,
@@ -301,6 +324,7 @@ l_all_test_specs.append(Spec(name="Large files - GUI",
                              filename=["ch3cl-esp.cub", "benzyne.molden",
                                        "periodic_dmol3.outmol", "fullRhinovirus.pdb"],
                              to_format=["cdjson", "dmol", "mol", "cif"],
+                             from_format=[None, None, None, "pdb-0"],
                              converter_name=[CONVERTER_OB, CONVERTER_OB, CONVERTER_OB, CONVERTER_C2X],
                              expect_success=[False, False, False, True],
                              callback=[CheckException(ex_type=FileConverterInputException),
@@ -319,7 +343,7 @@ max_size_callback = MCB(CheckFileStatus(expect_output_exists=False),
                                        ex_status_code=const.STATUS_CODE_SIZE))
 l_all_test_specs.append(Spec(name="Max size exceeded",
                              filename=["1NE6.mmcif", "caffeine-smi.tar.gz"],
-                             to_format="pdb",
+                             to_format="pdb-0",
                              conversion_kwargs=[{"max_file_size": 0.0001}, {"max_file_size": 0.0005}],
                              expect_success=False,
                              callback=max_size_callback,