feat: Add DoclingParseV4 backend, using high-level docling-parse API (#905)
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* Add DoclingParseV3 backend implementation

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Use docling-core with docling-parse types

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Fixes and test updates

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Fix streams

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Fix streams

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Reset tests

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* update test cases

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* update test units

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Add back DoclingParse v1 backend, pipeline options

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Update locks

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* fix: update docling-core to 2.22.0

Update dependency library docling-core to latest release 2.22.0
Fix regression tests and ground truth files

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* Ground-truth files updated

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Update tests, use TextCell.from_ocr property

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Text fixes, new test data

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Rename docling backend to v4

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Test all backends, fixes

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Reset all tests to use docling-parse v1 for now

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* Fixes for DPv4 backend init, better test coverage

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

* test_input_doc use default backend

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>

---------

Signed-off-by: Christoph Auer <cau@zurich.ibm.com>
Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>
Co-authored-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>
This commit is contained in:
Christoph Auer
2025-03-18 10:38:19 +01:00
committed by GitHub
parent 772487f9c9
commit 3960b199d6
126 changed files with 1138 additions and 709 deletions

View File

@@ -1,10 +1,10 @@
# Carbocation containing cyanine-type dye
## ABSTRACT
### ABSTRACT
To provide a reagent with excellent stability under storage, which can detect a subject compound to be measured with higher specificity and sensitibity. Complexes of a compound represented by the general formula (IV):
## BACKGROUND OF THE INVENTION
### BACKGROUND OF THE INVENTION
1. Field of the Invention
@@ -26,7 +26,7 @@ However, these known cyanine dyes emitting fluorescence via absorption or excita
If the dyes are used as labeling agents and bonded to substances from living organisms such as antibodies for preparing complexes, the complexes are likely to be oxidized easily by environmental factors such as light, heat, moisture, atmospheric oxygen and the like or to be subjected to modification such as generating cross-links. Particularly in water, a modification such as hydrolysis is further accelerated, disadvantageously. Therefore, the practical use of these complexes as detecting reagents in carrying out the microassay of the components of living organisms has encountered difficulties because of their poor stability under storage.
## SUMMARY OF THE INVENTION
### SUMMARY OF THE INVENTION
The present inventors have made various investigations so as to solve the above problems, and have found that a dye of a particular structure, more specifically a particular polymethine dye, and among others, a dye having an azulene skelton, are extremely stable even after the immobilization thereof as a labeling agent onto substances from living organisms. Thus, the inventors have achieved the present invention. It is an object of the present invention to provide a labeled complex with excellent storage stability which can overcome the above problems.
@@ -38,11 +38,11 @@ According to another aspect of the present invention, there is provided a method
According to still another aspect of the present invention, there is provided a method of detecting a subject compound to be analyzed by means of optical means which method comprises using a labeled complex comprised of a substance from a living organism and a labeling agent fixed onto the substance and bonding the complex to the subject compound to be analyzed, wherein the labeling agent comprises a compound represented by the general formula (iv).
## BRIEF DESCRIPTION OF THE DRAWINGS
### BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 depicts one example of fluorescence emitting wave form of a labeling agent.
## DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
### DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
The present invention will now be explained in detail hereinbelow.
@@ -106,7 +106,7 @@ Specific examples of these labeling agents are illustrated in Tables 1, 2 and 3,
The synthetic method of these azulene dyes is described in U.S. Pat. No. 4,738,908.
## CLAIMS
### CLAIMS
1. A labeled complex for detecting a subject compound to be analyzed by means of optical means using near-infrared radiation which complex comprises a substance from a living organism and a labeling agent fixed onto the substance, the substance capable of specifically binding to the subject compound, wherein the labeling agent comprises a compound represented by the general formula (IV): wherein A, B, D and E are independently selected from the group consisting of hydrogen atom, a substituted or an unsubstituted alkyl group having two or more carbon atoms, alkenyl group, aralkyl group, aryl group, styryl group and heterocyclic group, and at least one of A and B is a substituted or unsubstituted aryl group, and at least one of D and E is a substituted or unsubstituted aryl group; r.sub.1 ' and r.sub.2 ' are individually selected from the group consisting of hydrogen atom, a substituted or an unsubstituted alkyl group, cyclic alkyl group, alkenyl group, aralkyl group and aryl group; k is 0 or 1; is 0, 1 or 2; and X.sub.2.sup..crclbar. represents an anion.