[Feature] Minimal IUCLID export (#338)

This is an initial implementation that creates a working minimal .i6z document.
It passes schema validation and can be imported into IUCLID.

Caveat:
IUCLID files target individual compounds.
Pathway is not actually covered by the format.

It can be added in either soil or water and soil OECD endpoints.
**I currently only implemented the soil endpoint for all data.**

This sort of works, and I can report all degradation products in a pathway (not a nice view, but we can report many transformation products and add a diagram attachment in the future).

Adding additional information is an absolute pain, as we need to explicitly map each type of information to the relevant OECD field.
I use the XSD scheme for validation, but unfortunately the IUCLID parser is not fully compliant and requires a specific order, etc.

The workflow is: finding the AI structure from the XSD scheme -> make the scheme validation pass -> upload to IUCLID to get obscure error messages -> guess what could be wrong -> repeat 💣

New specifications get released once per year, so we will have to update accordingly.
I believe that this should be a more expensive feature, as it requires significant effort to uphold.

Currently implemented for root compound only in SOIL:

- Soil Texture 2
- Soil Texture 1
- pH value
- Half-life per soil sample / scenario (mapped to disappearance; not sure about that).
- CEC
- Organic Matter (only Carbon)
- Moisture content
- Humidity

<img width="2123" alt="image.png" src="attachments/d29830e1-65ef-4136-8939-1825e0959c62">
<img width="2124" alt="image.png" src="attachments/ac9de2ac-bf68-4ba4-b40b-82f810a9de93">
<img width="2139" alt="image.png" src="attachments/5674c7e6-865e-420e-974a-6b825b331e6c">

Reviewed-on: enviPath/enviPy#338
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>

epiuclid/serializers/manifest.py

@@ -0,0 +1,120 @@
+import xml.etree.ElementTree as ET
+from datetime import datetime, timezone
+
+from epiuclid.builders.base import document_key
+
+NS_MANIFEST = "http://iuclid6.echa.europa.eu/namespaces/manifest/v1"
+NS_XLINK = "http://www.w3.org/1999/xlink"
+
+ET.register_namespace("", NS_MANIFEST)
+ET.register_namespace("xlink", NS_XLINK)
+
+
+def _i6d_filename(uuid) -> str:
+    """Convert UUID to i6d filename (uuid_0.i6d for raw data)."""
+    return f"{uuid}_0.i6d"
+
+
+def _tag(local: str) -> str:
+    return f"{{{NS_MANIFEST}}}{local}"
+
+
+def _add_link(links_elem: ET.Element, ref_uuid: str, ref_type: str) -> None:
+    """Add a <link> element with ref-uuid and ref-type."""
+    link = ET.SubElement(links_elem, _tag("link"))
+    ref_uuid_elem = ET.SubElement(link, _tag("ref-uuid"))
+    ref_uuid_elem.text = ref_uuid
+    ref_type_elem = ET.SubElement(link, _tag("ref-type"))
+    ref_type_elem.text = ref_type
+
+
+class ManifestBuilder:
+    def build(
+        self,
+        documents: list[tuple[str, str, str, str | None]],
+        base_document_uuid: str,
+        links: dict[str, list[tuple[str, str]]] | None = None,
+    ) -> str:
+        """Build manifest.xml.
+
+        Args:
+            documents: List of (filename, doc_type, uuid, subtype) tuples.
+            base_document_uuid: UUID of the base document (the substance export started from).
+            links: Optional dict mapping document UUID to list of (target_doc_key, ref_type) tuples.
+                   ref_type is one of: PARENT, CHILD, REFERENCE.
+        """
+        if links is None:
+            links = {}
+
+        root = ET.Element(_tag("manifest"))
+
+        # general-information
+        gi = ET.SubElement(root, _tag("general-information"))
+        title = ET.SubElement(gi, _tag("title"))
+        title.text = "IUCLID 6 container manifest file"
+
+        created = ET.SubElement(gi, _tag("created"))
+        created.text = datetime.now(timezone.utc).strftime("%a %b %d %H:%M:%S %Z %Y")
+
+        author = ET.SubElement(gi, _tag("author"))
+        author.text = "enviPath"
+
+        application = ET.SubElement(gi, _tag("application"))
+        application.text = "enviPath IUCLID Export"
+
+        submission_type = ET.SubElement(gi, _tag("submission-type"))
+        submission_type.text = "R_INT_ONSITE"
+
+        archive_type = ET.SubElement(gi, _tag("archive-type"))
+        archive_type.text = "RAW_DATA"
+
+        legislations = ET.SubElement(gi, _tag("legislations-info"))
+        leg = ET.SubElement(legislations, _tag("legislation"))
+        leg_id = ET.SubElement(leg, _tag("id"))
+        leg_id.text = "core"
+        leg_ver = ET.SubElement(leg, _tag("version"))
+        leg_ver.text = "10.0"
+
+        # base-document-uuid
+        base_doc = ET.SubElement(root, _tag("base-document-uuid"))
+        base_doc.text = document_key(base_document_uuid)
+
+        # contained-documents
+        contained = ET.SubElement(root, _tag("contained-documents"))
+
+        now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
+
+        for filename, doc_type, uuid, subtype in documents:
+            doc_key = document_key(uuid)
+            doc_elem = ET.SubElement(contained, _tag("document"))
+            doc_elem.set("id", doc_key)
+
+            type_elem = ET.SubElement(doc_elem, _tag("type"))
+            type_elem.text = doc_type
+
+            if subtype:
+                subtype_elem = ET.SubElement(doc_elem, _tag("subtype"))
+                subtype_elem.text = subtype
+
+            name_elem = ET.SubElement(doc_elem, _tag("name"))
+            name_elem.set(f"{{{NS_XLINK}}}type", "simple")
+            name_elem.set(f"{{{NS_XLINK}}}href", filename)
+            name_elem.text = filename
+
+            first_mod = ET.SubElement(doc_elem, _tag("first-modification-date"))
+            first_mod.text = now
+
+            last_mod = ET.SubElement(doc_elem, _tag("last-modification-date"))
+            last_mod.text = now
+
+            uuid_elem = ET.SubElement(doc_elem, _tag("uuid"))
+            uuid_elem.text = doc_key
+
+            # Add links for this document if any
+            doc_links = links.get(uuid, [])
+            if doc_links:
+                links_elem = ET.SubElement(doc_elem, _tag("links"))
+                for target_key, ref_type in doc_links:
+                    _add_link(links_elem, target_key, ref_type)
+
+        return ET.tostring(root, encoding="unicode", xml_declaration=True)